Starting phenix.real_space_refine on Sun Mar 17 05:57:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jam_3047/03_2024/3jam_3047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jam_3047/03_2024/3jam_3047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jam_3047/03_2024/3jam_3047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jam_3047/03_2024/3jam_3047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jam_3047/03_2024/3jam_3047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jam_3047/03_2024/3jam_3047.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1780 5.49 5 Mg 80 5.21 5 S 87 5.16 5 C 42128 2.51 5 N 14136 2.21 5 O 19636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E GLU 118": "OE1" <-> "OE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 220": "OE1" <-> "OE2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 118": "OE1" <-> "OE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G GLU 207": "OE1" <-> "OE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G GLU 225": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "I ARG 74": "NH1" <-> "NH2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "J ARG 6": "NH1" <-> "NH2" Residue "J TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "J ARG 171": "NH1" <-> "NH2" Residue "J ARG 176": "NH1" <-> "NH2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K GLU 33": "OE1" <-> "OE2" Residue "K GLU 84": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "L GLU 101": "OE1" <-> "OE2" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "M GLU 125": "OE1" <-> "OE2" Residue "M GLU 129": "OE1" <-> "OE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N GLU 142": "OE1" <-> "OE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P GLU 69": "OE1" <-> "OE2" Residue "P GLU 71": "OE1" <-> "OE2" Residue "P GLU 88": "OE1" <-> "OE2" Residue "Q GLU 99": "OE1" <-> "OE2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q GLU 125": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 108": "OE1" <-> "OE2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 106": "OE1" <-> "OE2" Residue "S GLU 114": "OE1" <-> "OE2" Residue "T GLU 109": "OE1" <-> "OE2" Residue "T GLU 115": "OE1" <-> "OE2" Residue "T GLU 144": "OE1" <-> "OE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "U GLU 94": "OE1" <-> "OE2" Residue "V GLU 2": "OE1" <-> "OE2" Residue "V GLU 10": "OE1" <-> "OE2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V GLU 42": "OE1" <-> "OE2" Residue "V GLU 49": "OE1" <-> "OE2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W GLU 51": "OE1" <-> "OE2" Residue "W GLU 87": "OE1" <-> "OE2" Residue "W ARG 97": "NH1" <-> "NH2" Residue "W TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 98": "OE1" <-> "OE2" Residue "X GLU 138": "OE1" <-> "OE2" Residue "Y ARG 8": "NH1" <-> "NH2" Residue "Y GLU 39": "OE1" <-> "OE2" Residue "Y GLU 46": "OE1" <-> "OE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Y TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 98": "OE1" <-> "OE2" Residue "Y ARG 131": "NH1" <-> "NH2" Residue "a ARG 51": "NH1" <-> "NH2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "c GLU 34": "OE1" <-> "OE2" Residue "c ARG 61": "NH1" <-> "NH2" Residue "c GLU 62": "OE1" <-> "OE2" Residue "d GLU 4": "OE1" <-> "OE2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d GLU 45": "OE1" <-> "OE2" Residue "e GLU 22": "OE1" <-> "OE2" Residue "f PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 15": "OE1" <-> "OE2" Residue "g GLU 50": "OE1" <-> "OE2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 246": "OE1" <-> "OE2" Residue "g GLU 275": "OE1" <-> "OE2" Residue "g GLU 280": "OE1" <-> "OE2" Residue "g GLU 284": "OE1" <-> "OE2" Residue "i ARG 24": "NH1" <-> "NH2" Residue "i GLU 25": "OE1" <-> "OE2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i GLU 99": "OE1" <-> "OE2" Residue "i GLU 111": "OE1" <-> "OE2" Residue "j ARG 29": "NH1" <-> "NH2" Residue "j TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 76": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 77850 Number of models: 1 Model: "" Number of chains: 42 Chain: "2" Number of atoms: 37797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1780, 37797 Classifications: {'RNA': 1780} Modifications used: {'rna2p_pur': 146, 'rna2p_pyr': 144, 'rna3p_pur': 791, 'rna3p_pyr': 699} Link IDs: {'rna2p': 290, 'rna3p': 1489} Chain breaks: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {' G%rna3p_pur:plan2': 5, ' C%rna3p_pyr:plan': 4, ' A%rna3p_pur:plan2': 4, ' U%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 4, ' G%rna3p_pur:plan': 5, ' A%rna3p_pur:plan': 4} Unresolved non-hydrogen planarities: 161 Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1626 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 191} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1774 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1629 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "D" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1744 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain: "E" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2078 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 13, 'TRANS': 246} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "G" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1812 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 9, 'TRANS': 216} Chain: "H" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1483 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain: "I" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1471 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "K" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 809 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1248 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "M" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 922 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain: "N" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1187 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "O" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 942 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "P" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 114} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "R" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 991 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1193 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "T" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1110 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "U" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 845 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "V" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 687 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "W" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "X" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1119 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "Y" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1061 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "Z" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 558 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "a" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 779 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 609 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "c" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 494 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "d" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "e" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 428 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 5, 'TRANS': 47} Chain: "f" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 549 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 65} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2466 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 8, 'TRANS': 309} Chain breaks: 2 Chain: "h" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 233 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "i" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 778 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "j" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 695 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "2" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Unusual residues: {' MG': 78} Classifications: {'undetermined': 78} Link IDs: {None: 77} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 70462 SG CYS a 23 118.073 80.437 143.859 1.00 46.47 S ATOM 70483 SG CYS a 26 119.644 78.848 140.114 1.00 46.93 S ATOM 70865 SG CYS a 74 118.320 82.718 140.518 1.00 51.54 S ATOM 70885 SG CYS a 77 116.191 79.667 140.379 1.00 49.43 S Time building chain proxies: 30.30, per 1000 atoms: 0.39 Number of scatterers: 77850 At special positions: 0 Unit cell: (251.92, 223.78, 213.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 87 16.00 P 1780 15.00 Mg 80 11.99 O 19636 8.00 N 14136 7.00 C 42128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.50 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 500 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 23 " pdb="ZN ZN a 500 " - pdb=" SG CYS a 74 " Number of angles added : 6 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9402 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 60 sheets defined 34.0% alpha, 18.7% beta 506 base pairs and 885 stacking pairs defined. Time for finding SS restraints: 24.91 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 49 through 67 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 79 through 93 removed outlier: 3.571A pdb=" N GLN A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ALA A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 138 removed outlier: 3.611A pdb=" N TYR A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 removed outlier: 4.332A pdb=" N GLY A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 25 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.544A pdb=" N HIS B 79 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 80 " --> pdb=" O GLU B 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 80' Processing helix chain 'B' and resid 106 through 114 removed outlier: 4.019A pdb=" N SER B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.605A pdb=" N LYS B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'C' and resid 44 through 53 Processing helix chain 'C' and resid 57 through 64 removed outlier: 4.192A pdb=" N ILE C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 removed outlier: 4.365A pdb=" N ILE C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 141 Processing helix chain 'C' and resid 186 through 197 Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.526A pdb=" N THR C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.663A pdb=" N TRP C 235 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.518A pdb=" N TYR C 248 " --> pdb=" O PRO C 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 29 Processing helix chain 'D' and resid 54 through 60 Processing helix chain 'D' and resid 64 through 78 removed outlier: 3.757A pdb=" N GLU D 68 " --> pdb=" O ARG D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 112 Processing helix chain 'D' and resid 114 through 130 Processing helix chain 'D' and resid 162 through 167 removed outlier: 3.550A pdb=" N ASP D 166 " --> pdb=" O GLN D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.519A pdb=" N SER E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 51 removed outlier: 3.563A pdb=" N ARG E 51 " --> pdb=" O PHE E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'F' and resid 32 through 38 Processing helix chain 'F' and resid 90 through 100 Processing helix chain 'F' and resid 108 through 126 removed outlier: 3.659A pdb=" N ALA F 112 " --> pdb=" O LYS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 141 Processing helix chain 'F' and resid 165 through 186 Processing helix chain 'F' and resid 191 through 205 removed outlier: 3.598A pdb=" N THR F 195 " --> pdb=" O THR F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 227 Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.575A pdb=" N VAL G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 28 No H-bonds generated for 'chain 'G' and resid 26 through 28' Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 153 through 157 removed outlier: 3.572A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 223 removed outlier: 3.515A pdb=" N LEU G 184 " --> pdb=" O THR G 180 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU G 218 " --> pdb=" O LYS G 214 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 222 " --> pdb=" O GLU G 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 27 Processing helix chain 'H' and resid 28 through 35 removed outlier: 3.522A pdb=" N SER H 31 " --> pdb=" O GLU H 28 " (cutoff:3.500A) Proline residue: H 32 - end of helix removed outlier: 4.077A pdb=" N LYS H 35 " --> pdb=" O PRO H 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 35' Processing helix chain 'H' and resid 66 through 74 Processing helix chain 'H' and resid 74 through 85 Processing helix chain 'H' and resid 117 through 130 removed outlier: 3.520A pdb=" N VAL H 130 " --> pdb=" O LEU H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 158 through 163 removed outlier: 4.003A pdb=" N ILE H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 177 Processing helix chain 'I' and resid 87 through 94 removed outlier: 3.807A pdb=" N VAL I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 137 through 147 removed outlier: 3.541A pdb=" N GLU I 141 " --> pdb=" O SER I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 164 Processing helix chain 'I' and resid 173 through 178 Processing helix chain 'I' and resid 186 through 201 Processing helix chain 'J' and resid 20 through 35 Processing helix chain 'J' and resid 38 through 62 removed outlier: 4.178A pdb=" N ILE J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 84 removed outlier: 3.580A pdb=" N ASN J 74 " --> pdb=" O LEU J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 4.190A pdb=" N LYS J 91 " --> pdb=" O GLU J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.680A pdb=" N LEU J 97 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU J 99 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS J 100 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 106 Processing helix chain 'J' and resid 108 through 116 Processing helix chain 'J' and resid 121 through 131 Processing helix chain 'J' and resid 171 through 182 removed outlier: 3.904A pdb=" N GLY J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 19 Processing helix chain 'K' and resid 38 through 52 removed outlier: 3.761A pdb=" N LYS K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 81 Processing helix chain 'L' and resid 45 through 51 removed outlier: 3.533A pdb=" N ILE L 49 " --> pdb=" O PRO L 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 32 removed outlier: 3.919A pdb=" N LYS M 22 " --> pdb=" O GLU M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 47 removed outlier: 3.521A pdb=" N SER M 41 " --> pdb=" O GLY M 37 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG M 47 " --> pdb=" O LYS M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 75 removed outlier: 3.749A pdb=" N ASN M 75 " --> pdb=" O LEU M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 removed outlier: 3.678A pdb=" N GLY M 93 " --> pdb=" O GLY M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 133 Processing helix chain 'N' and resid 29 through 44 Processing helix chain 'N' and resid 46 through 58 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 Processing helix chain 'N' and resid 108 through 133 Processing helix chain 'N' and resid 143 through 151 Processing helix chain 'O' and resid 43 through 48 removed outlier: 3.812A pdb=" N LYS O 47 " --> pdb=" O THR O 43 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL O 48 " --> pdb=" O GLY O 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 43 through 48' Processing helix chain 'O' and resid 51 through 55 removed outlier: 3.927A pdb=" N GLU O 54 " --> pdb=" O ASP O 51 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER O 55 " --> pdb=" O ARG O 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 51 through 55' Processing helix chain 'O' and resid 56 through 75 Processing helix chain 'O' and resid 98 through 107 Processing helix chain 'P' and resid 21 through 26 removed outlier: 3.841A pdb=" N LEU P 26 " --> pdb=" O LEU P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 37 removed outlier: 4.470A pdb=" N ASP P 32 " --> pdb=" O MET P 28 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE P 33 " --> pdb=" O PRO P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 47 Processing helix chain 'P' and resid 53 through 66 removed outlier: 3.832A pdb=" N LYS P 58 " --> pdb=" O ALA P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 121 removed outlier: 3.619A pdb=" N ILE P 121 " --> pdb=" O GLY P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 54 removed outlier: 3.905A pdb=" N VAL Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Proline residue: Q 51 - end of helix removed outlier: 3.545A pdb=" N LEU Q 54 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 60 removed outlier: 3.788A pdb=" N LYS Q 59 " --> pdb=" O GLY Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 97 removed outlier: 3.644A pdb=" N LEU Q 89 " --> pdb=" O ILE Q 85 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL Q 90 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 112 removed outlier: 3.619A pdb=" N TYR Q 112 " --> pdb=" O ALA Q 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 21 removed outlier: 4.507A pdb=" N ALA R 12 " --> pdb=" O THR R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 39 Processing helix chain 'R' and resid 43 through 62 removed outlier: 3.659A pdb=" N ARG R 47 " --> pdb=" O SER R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 83 removed outlier: 3.578A pdb=" N GLU R 75 " --> pdb=" O PHE R 71 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU R 76 " --> pdb=" O LYS R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 114 Processing helix chain 'S' and resid 31 through 35 Processing helix chain 'S' and resid 40 through 51 Processing helix chain 'S' and resid 62 through 75 removed outlier: 3.546A pdb=" N ASN S 75 " --> pdb=" O GLN S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 120 Processing helix chain 'S' and resid 121 through 130 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 10 through 26 Processing helix chain 'T' and resid 53 through 68 Processing helix chain 'T' and resid 72 through 81 removed outlier: 3.572A pdb=" N LEU T 76 " --> pdb=" O GLY T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 112 removed outlier: 3.504A pdb=" N ASN T 101 " --> pdb=" O SER T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 144 Processing helix chain 'U' and resid 30 through 49 removed outlier: 3.536A pdb=" N LEU U 34 " --> pdb=" O LYS U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 106 removed outlier: 3.765A pdb=" N ILE U 106 " --> pdb=" O ARG U 102 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 63 removed outlier: 3.747A pdb=" N ARG V 60 " --> pdb=" O SER V 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 74 removed outlier: 3.848A pdb=" N SER V 68 " --> pdb=" O GLU V 64 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.741A pdb=" N ASP W 9 " --> pdb=" O SER W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 45 Processing helix chain 'W' and resid 82 through 84 No H-bonds generated for 'chain 'W' and resid 82 through 84' Processing helix chain 'W' and resid 85 through 94 Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 12 through 24 removed outlier: 3.872A pdb=" N TRP X 24 " --> pdb=" O ARG X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 35 Processing helix chain 'X' and resid 35 through 40 Processing helix chain 'X' and resid 92 through 96 Processing helix chain 'X' and resid 132 through 137 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 95 Processing helix chain 'Y' and resid 104 through 117 Processing helix chain 'Y' and resid 122 through 135 Processing helix chain 'Z' and resid 44 through 52 Processing helix chain 'Z' and resid 61 through 68 removed outlier: 3.516A pdb=" N ARG Z 68 " --> pdb=" O VAL Z 64 " (cutoff:3.500A) Processing helix chain 'Z' and resid 75 through 85 Processing helix chain 'a' and resid 49 through 57 Processing helix chain 'a' and resid 74 through 81 Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'd' and resid 32 through 36 removed outlier: 3.513A pdb=" N GLY d 35 " --> pdb=" O ARG d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 46 Processing helix chain 'd' and resid 46 through 51 removed outlier: 3.578A pdb=" N ILE d 50 " --> pdb=" O LYS d 46 " (cutoff:3.500A) Processing helix chain 'e' and resid 12 through 18 removed outlier: 3.548A pdb=" N SER e 16 " --> pdb=" O GLY e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 44 Processing helix chain 'h' and resid 2 through 25 Processing helix chain 'i' and resid 63 through 66 Processing helix chain 'i' and resid 97 through 107 Processing helix chain 'j' and resid 50 through 63 Processing helix chain 'j' and resid 85 through 95 Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 4.092A pdb=" N VAL A 47 " --> pdb=" O TYR A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 6.410A pdb=" N VAL A 73 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ILE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA A 75 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 121 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 42 through 49 removed outlier: 4.275A pdb=" N GLY B 44 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 13.540A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 12.685A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N HIS B 101 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 65 through 69 removed outlier: 5.562A pdb=" N ARG B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE B 100 " --> pdb=" O ARG B 87 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ASP B 89 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR B 98 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 91 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 96 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 13.540A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 12.685A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N HIS B 101 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL B 134 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE B 142 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN B 209 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 82 through 94 removed outlier: 7.049A pdb=" N VAL C 106 " --> pdb=" O MET C 86 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE C 88 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS C 104 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG C 102 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN C 92 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG C 100 " --> pdb=" O GLN C 92 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 146 through 147 Processing sheet with id= G, first strand: chain 'C' and resid 163 through 167 removed outlier: 3.631A pdb=" N ARG C 173 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 34 through 41 removed outlier: 6.804A pdb=" N ARG D 51 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE D 49 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL D 39 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU D 47 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 150 through 155 Processing sheet with id= J, first strand: chain 'D' and resid 223 through 224 removed outlier: 5.490A pdb=" N ILE g 195 " --> pdb=" O SER g 187 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER g 187 " --> pdb=" O ILE g 195 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA g 197 " --> pdb=" O SER g 185 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL g 183 " --> pdb=" O PHE g 199 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE g 182 " --> pdb=" O GLY g 178 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY g 178 " --> pdb=" O ILE g 182 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL g 175 " --> pdb=" O ARG g 156 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG g 156 " --> pdb=" O VAL g 175 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS g 154 " --> pdb=" O ALA g 177 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 70 through 72 removed outlier: 3.850A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.521A pdb=" N VAL E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.829A pdb=" N THR E 159 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE E 172 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS E 161 " --> pdb=" O THR E 170 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 192 through 193 removed outlier: 6.613A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 197 through 198 removed outlier: 3.565A pdb=" N HIS E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 146 through 149 removed outlier: 8.106A pdb=" N ALA F 161 " --> pdb=" O ASN c 43 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LYS c 45 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP F 163 " --> pdb=" O LYS c 45 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL c 25 " --> pdb=" O ARG c 18 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ARG c 18 " --> pdb=" O VAL c 25 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN c 27 " --> pdb=" O LEU c 16 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU c 31 " --> pdb=" O VAL c 12 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL c 12 " --> pdb=" O GLU c 31 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR c 8 " --> pdb=" O LEU c 56 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU c 56 " --> pdb=" O THR c 8 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.490A pdb=" N LEU G 106 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP G 57 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA G 110 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL G 49 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN G 34 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 73 through 77 Processing sheet with id= S, first strand: chain 'G' and resid 160 through 163 Processing sheet with id= T, first strand: chain 'H' and resid 46 through 50 Processing sheet with id= U, first strand: chain 'H' and resid 180 through 184 removed outlier: 4.456A pdb=" N GLN H 180 " --> pdb=" O LYS H 148 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY H 137 " --> pdb=" O LEU H 153 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 44 through 48 removed outlier: 5.268A pdb=" N ASN I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 62 through 67 removed outlier: 4.106A pdb=" N GLN I 103 " --> pdb=" O THR I 79 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLY I 182 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN I 64 " --> pdb=" O GLY I 182 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE I 184 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER I 66 " --> pdb=" O ILE I 184 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 20 through 24 Processing sheet with id= Y, first strand: chain 'L' and resid 70 through 77 removed outlier: 6.548A pdb=" N VAL L 85 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N PHE L 137 " --> pdb=" O ASN L 106 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL L 139 " --> pdb=" O PRO L 108 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N HIS L 110 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N LYS L 141 " --> pdb=" O HIS L 110 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR L 124 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VAL L 142 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE L 122 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'L' and resid 90 through 94 removed outlier: 3.554A pdb=" N TYR L 90 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 34 through 36 Processing sheet with id= AB, first strand: chain 'M' and resid 53 through 54 removed outlier: 6.015A pdb=" N ALA M 53 " --> pdb=" O ILE M 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'O' and resid 26 through 27 removed outlier: 6.357A pdb=" N GLY O 15 " --> pdb=" O HIS O 80 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS O 82 " --> pdb=" O GLY O 15 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 26 through 27 removed outlier: 5.920A pdb=" N VAL O 79 " --> pdb=" O ILE O 112 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ARG O 114 " --> pdb=" O VAL O 79 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'P' and resid 76 through 78 removed outlier: 3.521A pdb=" N VAL P 94 " --> pdb=" O VAL P 105 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Q' and resid 6 through 13 removed outlier: 6.648A pdb=" N LYS Q 30 " --> pdb=" O VAL Q 67 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL Q 69 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'R' and resid 100 through 102 removed outlier: 3.587A pdb=" N SER R 120 " --> pdb=" O LEU R 100 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'S' and resid 15 through 16 removed outlier: 3.742A pdb=" N LEU S 15 " --> pdb=" O VAL S 22 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'T' and resid 83 through 84 removed outlier: 4.004A pdb=" N LYS T 92 " --> pdb=" O LYS T 84 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'T' and resid 114 through 116 Processing sheet with id= AK, first strand: chain 'U' and resid 113 through 116 removed outlier: 4.636A pdb=" N ASP U 92 " --> pdb=" O GLY U 54 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY U 54 " --> pdb=" O ASP U 92 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU U 94 " --> pdb=" O LYS U 52 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS U 52 " --> pdb=" O GLU U 94 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'U' and resid 51 through 57 removed outlier: 5.951A pdb=" N LYS U 52 " --> pdb=" O GLU U 94 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU U 94 " --> pdb=" O LYS U 52 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLY U 54 " --> pdb=" O ASP U 92 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ASP U 92 " --> pdb=" O GLY U 54 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'U' and resid 61 through 63 removed outlier: 3.561A pdb=" N THR U 67 " --> pdb=" O ASP U 80 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'U' and resid 66 through 68 removed outlier: 3.561A pdb=" N THR U 67 " --> pdb=" O ASP U 80 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'd' and resid 53 through 54 Processing sheet with id= AP, first strand: chain 'V' and resid 32 through 37 Processing sheet with id= AQ, first strand: chain 'W' and resid 109 through 112 removed outlier: 5.109A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'X' and resid 122 through 123 removed outlier: 4.129A pdb=" N PHE X 122 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS X 71 " --> pdb=" O LYS X 56 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS X 56 " --> pdb=" O CYS X 71 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG X 73 " --> pdb=" O LEU X 54 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Y' and resid 7 through 15 removed outlier: 5.624A pdb=" N ILE Y 7 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU Y 28 " --> pdb=" O ILE Y 7 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR Y 9 " --> pdb=" O ASP Y 26 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP Y 26 " --> pdb=" O THR Y 9 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS Y 11 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL Y 24 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Z' and resid 89 through 95 removed outlier: 6.992A pdb=" N ILE Z 100 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS Z 94 " --> pdb=" O GLN Z 98 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN Z 98 " --> pdb=" O LYS Z 94 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'a' and resid 20 through 21 Processing sheet with id= AV, first strand: chain 'a' and resid 37 through 43 Processing sheet with id= AW, first strand: chain 'b' and resid 43 through 47 Processing sheet with id= AX, first strand: chain 'b' and resid 64 through 65 Processing sheet with id= AY, first strand: chain 'd' and resid 30 through 31 Processing sheet with id= AZ, first strand: chain 'f' and resid 106 through 107 Processing sheet with id= BA, first strand: chain 'g' and resid 9 through 14 removed outlier: 6.640A pdb=" N VAL g 319 " --> pdb=" O ARG g 11 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR g 13 " --> pdb=" O ILE g 317 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE g 317 " --> pdb=" O THR g 13 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'g' and resid 23 through 25 removed outlier: 5.918A pdb=" N LEU g 43 " --> pdb=" O SER g 61 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER g 61 " --> pdb=" O LEU g 43 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER g 45 " --> pdb=" O VAL g 59 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG g 47 " --> pdb=" O VAL g 57 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL g 57 " --> pdb=" O ARG g 47 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'g' and resid 69 through 74 removed outlier: 3.563A pdb=" N LEU g 90 " --> pdb=" O PHE g 104 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA g 102 " --> pdb=" O LEU g 92 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASN g 94 " --> pdb=" O SER g 100 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N SER g 100 " --> pdb=" O ASN g 94 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'g' and resid 111 through 116 removed outlier: 6.438A pdb=" N ILE g 132 " --> pdb=" O VAL g 144 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL g 144 " --> pdb=" O ILE g 132 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL g 134 " --> pdb=" O ALA g 142 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'g' and resid 206 through 211 removed outlier: 4.142A pdb=" N GLY g 222 " --> pdb=" O GLN g 226 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLN g 226 " --> pdb=" O GLY g 222 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'g' and resid 249 through 252 removed outlier: 3.712A pdb=" N ALA g 249 " --> pdb=" O ALA g 262 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASP g 271 " --> pdb=" O LEU g 277 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU g 277 " --> pdb=" O ASP g 271 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'i' and resid 33 through 43 removed outlier: 7.091A pdb=" N GLU i 48 " --> pdb=" O THR i 39 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N MET i 41 " --> pdb=" O ARG i 46 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ARG i 46 " --> pdb=" O MET i 41 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS i 89 " --> pdb=" O MET i 58 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU i 78 " --> pdb=" O VAL i 92 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS i 94 " --> pdb=" O ILE i 76 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE i 76 " --> pdb=" O LYS i 94 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'j' and resid 67 through 69 removed outlier: 3.528A pdb=" N ILE j 78 " --> pdb=" O VAL j 42 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE j 26 " --> pdb=" O LYS j 104 " (cutoff:3.500A) 1560 hydrogen bonds defined for protein. 4458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1230 hydrogen bonds 2014 hydrogen bond angles 0 basepair planarities 506 basepair parallelities 885 stacking parallelities Total time for adding SS restraints: 57.83 Time building geometry restraints manager: 32.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10412 1.33 - 1.45: 31009 1.45 - 1.57: 37789 1.57 - 1.69: 3560 1.69 - 1.81: 137 Bond restraints: 82907 Sorted by residual: bond pdb=" CA ILE B 189 " pdb=" CB ILE B 189 " ideal model delta sigma weight residual 1.537 1.567 -0.030 5.00e-03 4.00e+04 3.58e+01 bond pdb=" CA LYS h 14 " pdb=" C LYS h 14 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.30e-02 5.92e+03 1.75e+01 bond pdb=" C ARG N 124 " pdb=" O ARG N 124 " ideal model delta sigma weight residual 1.236 1.280 -0.043 1.15e-02 7.56e+03 1.43e+01 bond pdb=" CA PRO a 97 " pdb=" C PRO a 97 " ideal model delta sigma weight residual 1.514 1.534 -0.020 5.50e-03 3.31e+04 1.30e+01 bond pdb=" N VAL H 64 " pdb=" CA VAL H 64 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.23e-02 6.61e+03 1.28e+01 ... (remaining 82902 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.26: 10534 106.26 - 113.24: 44370 113.24 - 120.22: 32491 120.22 - 127.20: 28915 127.20 - 134.18: 4226 Bond angle restraints: 120536 Sorted by residual: angle pdb=" O3' G 21534 " pdb=" C3' G 21534 " pdb=" C2' G 21534 " ideal model delta sigma weight residual 109.50 123.53 -14.03 1.50e+00 4.44e-01 8.75e+01 angle pdb=" O3' A 2 828 " pdb=" C3' A 2 828 " pdb=" C2' A 2 828 " ideal model delta sigma weight residual 109.50 122.53 -13.03 1.50e+00 4.44e-01 7.55e+01 angle pdb=" O3' U 2 277 " pdb=" C3' U 2 277 " pdb=" C2' U 2 277 " ideal model delta sigma weight residual 109.50 121.96 -12.46 1.50e+00 4.44e-01 6.90e+01 angle pdb=" C GLU D 219 " pdb=" N PRO D 220 " pdb=" CA PRO D 220 " ideal model delta sigma weight residual 119.84 129.75 -9.91 1.25e+00 6.40e-01 6.28e+01 angle pdb=" O3' G 21315 " pdb=" C3' G 21315 " pdb=" C2' G 21315 " ideal model delta sigma weight residual 113.70 125.10 -11.40 1.50e+00 4.44e-01 5.78e+01 ... (remaining 120531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 46096 35.94 - 71.88: 5681 71.88 - 107.82: 581 107.82 - 143.76: 29 143.76 - 179.70: 68 Dihedral angle restraints: 52455 sinusoidal: 37886 harmonic: 14569 Sorted by residual: dihedral pdb=" C5' G 21534 " pdb=" C4' G 21534 " pdb=" C3' G 21534 " pdb=" O3' G 21534 " ideal model delta sinusoidal sigma weight residual 147.00 69.27 77.73 1 8.00e+00 1.56e-02 1.18e+02 dihedral pdb=" C5' A 21243 " pdb=" C4' A 21243 " pdb=" C3' A 21243 " pdb=" O3' A 21243 " ideal model delta sinusoidal sigma weight residual 147.00 70.03 76.97 1 8.00e+00 1.56e-02 1.16e+02 dihedral pdb=" C5' U 2 279 " pdb=" C4' U 2 279 " pdb=" C3' U 2 279 " pdb=" O3' U 2 279 " ideal model delta sinusoidal sigma weight residual 147.00 71.14 75.86 1 8.00e+00 1.56e-02 1.13e+02 ... (remaining 52452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 12497 0.154 - 0.308: 2404 0.308 - 0.463: 92 0.463 - 0.617: 30 0.617 - 0.771: 2 Chirality restraints: 15025 Sorted by residual: chirality pdb=" C3' A 2 828 " pdb=" C4' A 2 828 " pdb=" O3' A 2 828 " pdb=" C2' A 2 828 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" C3' U 2 277 " pdb=" C4' U 2 277 " pdb=" O3' U 2 277 " pdb=" C2' U 2 277 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" C3' C 2 564 " pdb=" C4' C 2 564 " pdb=" O3' C 2 564 " pdb=" C2' C 2 564 " both_signs ideal model delta sigma weight residual False -2.74 -2.13 -0.61 2.00e-01 2.50e+01 9.42e+00 ... (remaining 15022 not shown) Planarity restraints: 8760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 21269 " -0.016 2.00e-02 2.50e+03 3.37e-02 3.41e+01 pdb=" N9 G 21269 " 0.012 2.00e-02 2.50e+03 pdb=" C8 G 21269 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G 21269 " 0.007 2.00e-02 2.50e+03 pdb=" C5 G 21269 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G 21269 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G 21269 " -0.058 2.00e-02 2.50e+03 pdb=" N1 G 21269 " 0.091 2.00e-02 2.50e+03 pdb=" C2 G 21269 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 21269 " -0.038 2.00e-02 2.50e+03 pdb=" N3 G 21269 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G 21269 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21439 " 0.010 2.00e-02 2.50e+03 3.84e-02 3.32e+01 pdb=" N1 C 21439 " -0.006 2.00e-02 2.50e+03 pdb=" C2 C 21439 " 0.003 2.00e-02 2.50e+03 pdb=" O2 C 21439 " 0.041 2.00e-02 2.50e+03 pdb=" N3 C 21439 " -0.092 2.00e-02 2.50e+03 pdb=" C4 C 21439 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C 21439 " 0.054 2.00e-02 2.50e+03 pdb=" C5 C 21439 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C 21439 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21622 " -0.004 2.00e-02 2.50e+03 3.82e-02 3.28e+01 pdb=" N1 C 21622 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C 21622 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C 21622 " -0.041 2.00e-02 2.50e+03 pdb=" N3 C 21622 " 0.095 2.00e-02 2.50e+03 pdb=" C4 C 21622 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C 21622 " -0.048 2.00e-02 2.50e+03 pdb=" C5 C 21622 " 0.007 2.00e-02 2.50e+03 pdb=" C6 C 21622 " 0.001 2.00e-02 2.50e+03 ... (remaining 8757 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 27 2.10 - 2.80: 13216 2.80 - 3.50: 106906 3.50 - 4.20: 232822 4.20 - 4.90: 327141 Nonbonded interactions: 680112 Sorted by model distance: nonbonded pdb=" N1 A 2 991 " pdb=" O4 U 21011 " model vdw 1.398 2.496 nonbonded pdb=" N1 A 2 480 " pdb=" O4 U 2 506 " model vdw 1.621 2.496 nonbonded pdb=" O4 U 21079 " pdb=" N1 A 21090 " model vdw 1.664 2.496 nonbonded pdb=" N3 U 2 628 " pdb=" N6 A 2 969 " model vdw 1.772 2.560 nonbonded pdb=" N1 A 2 864 " pdb=" O4 U 2 964 " model vdw 1.828 2.496 ... (remaining 680107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 9.060 Check model and map are aligned: 0.840 Set scattering table: 0.530 Process input model: 213.230 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 229.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 82907 Z= 0.455 Angle : 1.324 15.121 120536 Z= 0.888 Chirality : 0.104 0.771 15025 Planarity : 0.006 0.130 8760 Dihedral : 25.283 179.704 43053 Min Nonbonded Distance : 1.398 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 3.80 % Allowed : 10.17 % Favored : 86.03 % Rotamer: Outliers : 13.45 % Allowed : 15.60 % Favored : 70.95 % Cbeta Deviations : 1.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.10), residues: 4976 helix: 0.99 (0.10), residues: 1523 sheet: -1.22 (0.16), residues: 901 loop : -2.96 (0.10), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 117 HIS 0.007 0.001 HIS B 160 PHE 0.024 0.002 PHE c 32 TYR 0.017 0.002 TYR K 91 ARG 0.007 0.001 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1966 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 576 poor density : 1390 time to evaluate : 4.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8405 (m-30) cc_final: 0.8121 (m-30) REVERT: A 12 GLU cc_start: 0.7468 (mp0) cc_final: 0.7166 (mp0) REVERT: A 16 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7282 (mp) REVERT: A 21 ARG cc_start: 0.7408 (mtm180) cc_final: 0.7149 (mmt-90) REVERT: A 33 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.7926 (mp10) REVERT: A 38 TYR cc_start: 0.8538 (t80) cc_final: 0.8206 (t80) REVERT: A 62 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8365 (mtp180) REVERT: A 88 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8125 (mmtp) REVERT: A 113 ARG cc_start: 0.8361 (ptp-110) cc_final: 0.7843 (mtp85) REVERT: A 127 ARG cc_start: 0.8086 (tpm170) cc_final: 0.7620 (ttt90) REVERT: A 155 TYR cc_start: 0.9027 (m-80) cc_final: 0.8800 (m-80) REVERT: A 157 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: A 164 ASN cc_start: 0.8442 (m-40) cc_final: 0.7909 (m110) REVERT: B 26 ARG cc_start: 0.6738 (mtm180) cc_final: 0.6290 (ptp-170) REVERT: B 28 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6592 (pm20) REVERT: B 45 LYS cc_start: 0.7883 (mmpt) cc_final: 0.7648 (mmmt) REVERT: B 48 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.7906 (p) REVERT: B 64 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7424 (ttm170) REVERT: B 83 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7800 (ttpp) REVERT: B 96 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8398 (pp) REVERT: B 97 LEU cc_start: 0.8407 (mt) cc_final: 0.8155 (mt) REVERT: B 166 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8280 (ttpt) REVERT: B 207 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8392 (tp) REVERT: B 208 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8615 (pp30) REVERT: C 58 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8689 (tt) REVERT: C 82 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8507 (mmtm) REVERT: C 86 MET cc_start: 0.8499 (mmm) cc_final: 0.8227 (mmm) REVERT: C 95 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8532 (p) REVERT: C 99 GLN cc_start: 0.8988 (pt0) cc_final: 0.8343 (pt0) REVERT: C 109 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8792 (t) REVERT: C 145 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8914 (tpt-90) REVERT: C 148 TYR cc_start: 0.9223 (m-80) cc_final: 0.8900 (m-80) REVERT: C 152 ASN cc_start: 0.8695 (p0) cc_final: 0.7952 (p0) REVERT: C 193 MET cc_start: 0.9224 (mmm) cc_final: 0.8989 (mmp) REVERT: C 206 THR cc_start: 0.9152 (p) cc_final: 0.8880 (m) REVERT: C 223 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8513 (mm) REVERT: C 225 ASN cc_start: 0.8766 (m-40) cc_final: 0.8336 (m-40) REVERT: C 230 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8962 (tp) REVERT: C 237 VAL cc_start: 0.8168 (OUTLIER) cc_final: 0.7935 (p) REVERT: C 248 TYR cc_start: 0.8647 (m-80) cc_final: 0.8307 (m-10) REVERT: D 11 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8405 (mp) REVERT: D 23 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: D 45 LYS cc_start: 0.7635 (mttt) cc_final: 0.7291 (mtmt) REVERT: D 47 GLU cc_start: 0.6461 (mm-30) cc_final: 0.6197 (mp0) REVERT: D 91 VAL cc_start: 0.7155 (t) cc_final: 0.6800 (t) REVERT: D 97 SER cc_start: 0.8657 (t) cc_final: 0.8342 (t) REVERT: D 139 SER cc_start: 0.8046 (t) cc_final: 0.7786 (t) REVERT: D 148 LYS cc_start: 0.8254 (mtmp) cc_final: 0.7838 (mtpt) REVERT: D 150 MET cc_start: 0.7708 (mmt) cc_final: 0.7042 (mmt) REVERT: D 162 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: D 179 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7218 (pm20) REVERT: D 218 LEU cc_start: 0.5089 (mt) cc_final: 0.4773 (pp) REVERT: E 7 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8792 (mttm) REVERT: E 70 VAL cc_start: 0.9277 (t) cc_final: 0.8963 (p) REVERT: E 77 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8626 (mmt180) REVERT: E 97 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8087 (mt-10) REVERT: E 106 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8055 (mmtm) REVERT: E 134 LYS cc_start: 0.8786 (mttt) cc_final: 0.8167 (mttp) REVERT: E 139 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8675 (t) REVERT: E 158 ASP cc_start: 0.8452 (m-30) cc_final: 0.8024 (m-30) REVERT: E 166 THR cc_start: 0.8909 (p) cc_final: 0.8542 (t) REVERT: E 216 ASN cc_start: 0.7867 (t0) cc_final: 0.7394 (m-40) REVERT: E 250 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6523 (tm-30) REVERT: E 254 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7656 (mtt-85) REVERT: F 27 LEU cc_start: 0.7195 (mt) cc_final: 0.6894 (mm) REVERT: F 32 PRO cc_start: 0.7818 (Cg_exo) cc_final: 0.7365 (Cg_endo) REVERT: F 43 LYS cc_start: 0.8119 (mptt) cc_final: 0.7412 (mppt) REVERT: F 44 LEU cc_start: 0.6140 (mt) cc_final: 0.5719 (mp) REVERT: F 47 LYS cc_start: 0.5830 (OUTLIER) cc_final: 0.4649 (mmmt) REVERT: F 48 TRP cc_start: 0.7517 (p90) cc_final: 0.7258 (p90) REVERT: F 50 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6625 (t80) REVERT: F 53 VAL cc_start: 0.8278 (t) cc_final: 0.7847 (p) REVERT: F 84 PHE cc_start: 0.8067 (m-80) cc_final: 0.7713 (m-80) REVERT: F 85 ARG cc_start: 0.8148 (mmt-90) cc_final: 0.7718 (mmt-90) REVERT: F 91 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7497 (mt) REVERT: F 110 LEU cc_start: 0.7870 (mt) cc_final: 0.7637 (mt) REVERT: F 127 THR cc_start: 0.8231 (p) cc_final: 0.7750 (t) REVERT: F 147 ASP cc_start: 0.8055 (m-30) cc_final: 0.7841 (m-30) REVERT: F 188 ASN cc_start: 0.6006 (OUTLIER) cc_final: 0.5344 (t0) REVERT: F 192 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6702 (tp) REVERT: G 4 ASN cc_start: 0.8850 (t0) cc_final: 0.8330 (t0) REVERT: G 19 ASP cc_start: 0.7176 (m-30) cc_final: 0.6750 (m-30) REVERT: G 21 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6119 (pm20) REVERT: G 25 ARG cc_start: 0.8340 (tpp-160) cc_final: 0.7764 (tpp-160) REVERT: G 37 ASP cc_start: 0.7598 (p0) cc_final: 0.6936 (p0) REVERT: G 43 ASP cc_start: 0.6955 (m-30) cc_final: 0.6019 (t0) REVERT: G 149 LYS cc_start: 0.8247 (tttt) cc_final: 0.7913 (ttmm) REVERT: G 154 ARG cc_start: 0.8183 (mtt90) cc_final: 0.7722 (mtt90) REVERT: G 170 THR cc_start: 0.8152 (OUTLIER) cc_final: 0.7825 (p) REVERT: G 183 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8263 (ttt180) REVERT: G 203 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7873 (tt0) REVERT: H 26 ASP cc_start: 0.6800 (m-30) cc_final: 0.6395 (m-30) REVERT: H 30 ASN cc_start: 0.7904 (m-40) cc_final: 0.7663 (m110) REVERT: H 70 TYR cc_start: 0.8086 (m-80) cc_final: 0.7764 (m-80) REVERT: H 72 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8283 (ttmm) REVERT: H 92 PHE cc_start: 0.9069 (m-80) cc_final: 0.8559 (m-80) REVERT: H 133 THR cc_start: 0.9219 (m) cc_final: 0.8933 (p) REVERT: H 134 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7957 (mt-10) REVERT: H 147 ASN cc_start: 0.9055 (p0) cc_final: 0.8721 (p0) REVERT: H 169 PHE cc_start: 0.8521 (m-10) cc_final: 0.8277 (m-10) REVERT: H 175 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8299 (tptp) REVERT: I 20 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7688 (tp-100) REVERT: I 26 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8699 (tptp) REVERT: I 32 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8132 (mt0) REVERT: I 66 SER cc_start: 0.9130 (m) cc_final: 0.8851 (t) REVERT: I 92 ARG cc_start: 0.7163 (ttm110) cc_final: 0.6284 (ttp-110) REVERT: I 107 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8552 (p) REVERT: I 111 GLN cc_start: 0.7931 (mt0) cc_final: 0.7479 (mm-40) REVERT: I 114 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8321 (mt-10) REVERT: I 147 ARG cc_start: 0.6547 (mtt180) cc_final: 0.6206 (mtt180) REVERT: J 9 SER cc_start: 0.9301 (t) cc_final: 0.8847 (m) REVERT: J 17 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.7981 (ttm170) REVERT: J 29 LYS cc_start: 0.8411 (tptt) cc_final: 0.8003 (ttmm) REVERT: J 33 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8212 (mm-30) REVERT: J 90 LYS cc_start: 0.8557 (mttt) cc_final: 0.8237 (mtmt) REVERT: J 106 GLU cc_start: 0.7638 (tp30) cc_final: 0.7293 (tm-30) REVERT: J 107 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8194 (tpt170) REVERT: J 115 LYS cc_start: 0.8602 (mttt) cc_final: 0.7988 (mtmt) REVERT: J 131 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8215 (mm-40) REVERT: J 153 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: J 157 ASP cc_start: 0.8336 (t70) cc_final: 0.7898 (t0) REVERT: K 20 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8545 (m) REVERT: K 44 LYS cc_start: 0.7103 (mtmt) cc_final: 0.6745 (mmtp) REVERT: K 56 LYS cc_start: 0.6906 (mttt) cc_final: 0.6676 (mtmm) REVERT: L 8 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7943 (mp10) REVERT: L 20 PHE cc_start: 0.8399 (t80) cc_final: 0.8061 (t80) REVERT: L 36 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.7355 (pmtt) REVERT: L 79 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7527 (mtm180) REVERT: L 84 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8490 (pt) REVERT: L 87 ARG cc_start: 0.8442 (ttt-90) cc_final: 0.7872 (ttt-90) REVERT: L 111 VAL cc_start: 0.8522 (t) cc_final: 0.8120 (p) REVERT: M 19 ASP cc_start: 0.5183 (OUTLIER) cc_final: 0.4834 (t0) REVERT: M 38 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6738 (pt) REVERT: N 3 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8253 (mmt-90) REVERT: N 4 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8664 (ttp) REVERT: N 9 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8692 (mttt) REVERT: N 11 MET cc_start: 0.8940 (ptp) cc_final: 0.8705 (ptt) REVERT: N 27 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.6586 (mtpp) REVERT: N 53 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7979 (mt) REVERT: N 100 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8338 (tttp) REVERT: N 125 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8265 (tp) REVERT: O 52 ARG cc_start: 0.8379 (ptp90) cc_final: 0.8080 (ptt180) REVERT: O 65 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6643 (mt0) REVERT: O 66 ASP cc_start: 0.8179 (t0) cc_final: 0.7843 (t0) REVERT: O 116 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: O 124 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6783 (t0) REVERT: O 129 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8843 (tttm) REVERT: P 18 LYS cc_start: 0.5206 (mttt) cc_final: 0.4450 (mmtm) REVERT: P 45 PHE cc_start: 0.7435 (m-80) cc_final: 0.7191 (m-80) REVERT: P 49 LEU cc_start: 0.5999 (mp) cc_final: 0.5077 (tp) REVERT: P 83 MET cc_start: 0.7417 (tmm) cc_final: 0.7155 (tpt) REVERT: P 89 MET cc_start: 0.5800 (ptm) cc_final: 0.5502 (ptp) REVERT: P 97 TYR cc_start: 0.7462 (t80) cc_final: 0.5424 (t80) REVERT: P 121 ILE cc_start: 0.7216 (mp) cc_final: 0.6867 (tt) REVERT: P 122 THR cc_start: 0.8117 (p) cc_final: 0.7391 (p) REVERT: P 127 ARG cc_start: 0.5853 (OUTLIER) cc_final: 0.3289 (mmm-85) REVERT: Q 22 VAL cc_start: 0.9081 (m) cc_final: 0.8871 (p) REVERT: Q 45 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7226 (mmm-85) REVERT: Q 68 LYS cc_start: 0.7573 (ttmp) cc_final: 0.7260 (ttpt) REVERT: Q 122 ARG cc_start: 0.8445 (mtp180) cc_final: 0.8234 (mtm180) REVERT: Q 123 ARG cc_start: 0.8648 (ttm110) cc_final: 0.8253 (mmm-85) REVERT: Q 142 TYR cc_start: 0.5274 (OUTLIER) cc_final: 0.3587 (p90) REVERT: R 24 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7561 (tt) REVERT: R 33 ARG cc_start: 0.8302 (mmt90) cc_final: 0.7947 (mmt-90) REVERT: R 48 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7538 (t0) REVERT: R 72 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6808 (mttt) REVERT: R 78 ARG cc_start: 0.7554 (ttm110) cc_final: 0.6954 (mmm-85) REVERT: R 92 ASP cc_start: 0.7725 (t0) cc_final: 0.7196 (t0) REVERT: R 93 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6843 (tt) REVERT: R 94 SER cc_start: 0.8802 (t) cc_final: 0.8036 (p) REVERT: R 106 THR cc_start: 0.9445 (m) cc_final: 0.9050 (p) REVERT: R 125 SER cc_start: 0.7706 (p) cc_final: 0.7380 (t) REVERT: S 14 ILE cc_start: 0.5338 (OUTLIER) cc_final: 0.4855 (tt) REVERT: S 16 ARG cc_start: 0.5604 (OUTLIER) cc_final: 0.5331 (mmt-90) REVERT: S 17 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.4519 (tp) REVERT: S 90 LYS cc_start: 0.3836 (OUTLIER) cc_final: 0.2914 (tmtt) REVERT: S 110 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7594 (mtp-110) REVERT: S 145 ARG cc_start: 0.1685 (OUTLIER) cc_final: 0.0533 (ptp-170) REVERT: T 7 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7083 (ttm-80) REVERT: T 17 ASN cc_start: 0.7471 (m-40) cc_final: 0.7239 (m-40) REVERT: T 68 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.8002 (mpt90) REVERT: T 69 LYS cc_start: 0.7746 (mttt) cc_final: 0.7530 (mtmt) REVERT: T 90 PRO cc_start: 0.8981 (Cg_exo) cc_final: 0.8767 (Cg_endo) REVERT: T 100 ILE cc_start: 0.8186 (mp) cc_final: 0.7930 (mp) REVERT: U 19 ILE cc_start: 0.5553 (mt) cc_final: 0.5049 (mt) REVERT: U 32 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7466 (tptm) REVERT: U 44 ASN cc_start: 0.5884 (OUTLIER) cc_final: 0.5376 (t0) REVERT: U 57 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7370 (mtt180) REVERT: U 61 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7586 (mtmt) REVERT: U 64 LYS cc_start: 0.8527 (tppt) cc_final: 0.8248 (mttm) REVERT: U 77 LYS cc_start: 0.8120 (mttt) cc_final: 0.7894 (mttt) REVERT: U 83 GLU cc_start: 0.8458 (pt0) cc_final: 0.8232 (pt0) REVERT: U 85 ARG cc_start: 0.8494 (ptp-110) cc_final: 0.7898 (ptp-170) REVERT: U 113 ASP cc_start: 0.6807 (t70) cc_final: 0.6543 (t0) REVERT: V 1 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7107 (tpt) REVERT: V 21 ASN cc_start: 0.8616 (t0) cc_final: 0.8240 (t0) REVERT: V 36 ILE cc_start: 0.8833 (mt) cc_final: 0.8480 (mt) REVERT: V 56 SER cc_start: 0.9471 (p) cc_final: 0.9250 (t) REVERT: V 87 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7425 (ttm-80) REVERT: W 22 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8646 (mttp) REVERT: W 24 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: W 25 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8884 (t) REVERT: W 82 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8429 (ttmm) REVERT: W 93 LEU cc_start: 0.9082 (mt) cc_final: 0.8770 (mp) REVERT: W 104 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8824 (pp) REVERT: X 9 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8861 (tp) REVERT: X 21 ASN cc_start: 0.8883 (m-40) cc_final: 0.8665 (m-40) REVERT: X 38 PHE cc_start: 0.8497 (m-80) cc_final: 0.8126 (m-80) REVERT: X 57 ILE cc_start: 0.8781 (mt) cc_final: 0.8420 (pt) REVERT: X 73 ARG cc_start: 0.8398 (ttt90) cc_final: 0.8158 (ttt90) REVERT: X 84 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8792 (m) REVERT: X 107 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.7791 (t80) REVERT: X 109 ARG cc_start: 0.8872 (mmt90) cc_final: 0.8613 (mmm-85) REVERT: X 137 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8055 (mttm) REVERT: Y 8 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7973 (mtm-85) REVERT: Y 20 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8042 (ptp-170) REVERT: Y 44 LEU cc_start: 0.8395 (mt) cc_final: 0.8162 (mt) REVERT: Y 61 ARG cc_start: 0.8893 (mtp85) cc_final: 0.8621 (mtp-110) REVERT: Y 63 GLN cc_start: 0.8622 (tp40) cc_final: 0.8191 (tp-100) REVERT: Y 68 LYS cc_start: 0.8335 (mttt) cc_final: 0.7900 (mtpt) REVERT: Y 84 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8328 (ttpp) REVERT: Y 127 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8085 (ttpt) REVERT: Z 98 GLN cc_start: 0.6301 (OUTLIER) cc_final: 0.4557 (mp10) REVERT: a 18 VAL cc_start: 0.9466 (t) cc_final: 0.9234 (m) REVERT: a 19 LYS cc_start: 0.8641 (tptm) cc_final: 0.8344 (mmmt) REVERT: a 28 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7201 (ttp80) REVERT: a 32 LYS cc_start: 0.8764 (tttm) cc_final: 0.8516 (tptm) REVERT: a 34 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8486 (ttmm) REVERT: a 38 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8757 (mpt180) REVERT: a 39 MET cc_start: 0.8598 (tmm) cc_final: 0.8385 (tpp) REVERT: a 59 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.6614 (p90) REVERT: a 89 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7996 (ttm170) REVERT: a 93 ARG cc_start: 0.8704 (mmm160) cc_final: 0.8363 (mmm160) REVERT: b 24 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8825 (tp) REVERT: b 34 ASP cc_start: 0.7415 (m-30) cc_final: 0.7110 (m-30) REVERT: b 70 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8419 (ttmt) REVERT: c 27 GLN cc_start: 0.8264 (tt0) cc_final: 0.7455 (tp40) REVERT: c 52 ASP cc_start: 0.6022 (m-30) cc_final: 0.5702 (m-30) REVERT: c 57 MET cc_start: 0.4956 (mtm) cc_final: 0.4548 (mmp) REVERT: d 20 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7599 (tm-30) REVERT: d 46 LYS cc_start: 0.9014 (mtmm) cc_final: 0.8671 (mtmm) REVERT: e 21 VAL cc_start: 0.9364 (t) cc_final: 0.9096 (t) REVERT: e 23 LYS cc_start: 0.9083 (mttt) cc_final: 0.8867 (mtpp) REVERT: e 26 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8156 (mtmm) REVERT: e 31 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7841 (mptt) REVERT: e 37 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8498 (ttt180) REVERT: e 46 ASN cc_start: 0.8113 (m110) cc_final: 0.7817 (m-40) REVERT: f 93 HIS cc_start: 0.2872 (OUTLIER) cc_final: 0.2508 (m90) REVERT: f 109 ASP cc_start: 0.1444 (OUTLIER) cc_final: 0.1160 (p0) REVERT: g 55 PHE cc_start: 0.5964 (OUTLIER) cc_final: 0.5517 (t80) REVERT: g 62 TYR cc_start: 0.7015 (m-80) cc_final: 0.6759 (m-10) REVERT: g 63 LYS cc_start: 0.8124 (mttt) cc_final: 0.7890 (mttp) REVERT: g 149 THR cc_start: 0.6332 (p) cc_final: 0.5888 (t) REVERT: g 152 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.7777 (t) REVERT: g 172 ILE cc_start: 0.5338 (OUTLIER) cc_final: 0.4924 (pp) REVERT: g 198 ASP cc_start: 0.6809 (m-30) cc_final: 0.6572 (m-30) REVERT: g 199 PHE cc_start: 0.7507 (m-80) cc_final: 0.7083 (m-10) REVERT: g 269 ILE cc_start: 0.5443 (OUTLIER) cc_final: 0.5205 (mt) REVERT: g 275 GLU cc_start: 0.4155 (OUTLIER) cc_final: 0.3193 (pp20) REVERT: g 284 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: g 293 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7248 (t0) REVERT: g 295 HIS cc_start: 0.8640 (p-80) cc_final: 0.8294 (p-80) REVERT: g 304 ASP cc_start: 0.6477 (OUTLIER) cc_final: 0.6226 (t0) REVERT: g 309 PHE cc_start: 0.7002 (m-80) cc_final: 0.5921 (m-80) REVERT: g 316 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7690 (m) REVERT: h 1 MET cc_start: 0.8435 (ttt) cc_final: 0.8166 (ttt) REVERT: h 16 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5692 (mttt) REVERT: i 71 MET cc_start: 0.7026 (mmt) cc_final: 0.6693 (mmt) REVERT: j 26 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6724 (mt) REVERT: j 62 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.6201 (p90) REVERT: j 74 MET cc_start: 0.5505 (mmm) cc_final: 0.5002 (tpp) outliers start: 576 outliers final: 114 residues processed: 1742 average time/residue: 0.8295 time to fit residues: 2347.2072 Evaluate side-chains 1178 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 952 time to evaluate : 4.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 162 GLN Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 179 GLN Chi-restraints excluded: chain E residue 7 LYS Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 186 PHE Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 183 ARG Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 72 LYS Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 139 ARG Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 32 GLN Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 196 ARG Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 33 GLU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 4 MET Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 100 LYS Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain O residue 65 GLN Chi-restraints excluded: chain O residue 86 THR Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 127 ARG Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 52 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 27 ASP Chi-restraints excluded: chain R residue 38 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain S residue 14 ILE Chi-restraints excluded: chain S residue 16 ARG Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 18 LEU Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 111 ASP Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 145 ARG Chi-restraints excluded: chain T residue 7 ARG Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 61 LYS Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 129 VAL Chi-restraints excluded: chain X residue 9 LEU Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 117 ILE Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 8 ARG Chi-restraints excluded: chain Y residue 20 ARG Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 84 LYS Chi-restraints excluded: chain Y residue 127 LYS Chi-restraints excluded: chain Z residue 60 VAL Chi-restraints excluded: chain Z residue 77 ARG Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 97 LYS Chi-restraints excluded: chain Z residue 98 GLN Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 34 LYS Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 59 TYR Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 37 ARG Chi-restraints excluded: chain f residue 93 HIS Chi-restraints excluded: chain f residue 109 ASP Chi-restraints excluded: chain f residue 129 PHE Chi-restraints excluded: chain g residue 55 PHE Chi-restraints excluded: chain g residue 60 ARG Chi-restraints excluded: chain g residue 152 VAL Chi-restraints excluded: chain g residue 172 ILE Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 208 VAL Chi-restraints excluded: chain g residue 269 ILE Chi-restraints excluded: chain g residue 275 GLU Chi-restraints excluded: chain g residue 284 GLU Chi-restraints excluded: chain g residue 292 GLN Chi-restraints excluded: chain g residue 293 ASP Chi-restraints excluded: chain g residue 304 ASP Chi-restraints excluded: chain g residue 316 VAL Chi-restraints excluded: chain g residue 321 GLN Chi-restraints excluded: chain h residue 16 LYS Chi-restraints excluded: chain i residue 58 MET Chi-restraints excluded: chain i residue 79 VAL Chi-restraints excluded: chain j residue 26 ILE Chi-restraints excluded: chain j residue 62 PHE Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain j residue 105 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 563 optimal weight: 3.9990 chunk 505 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 chunk 341 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 522 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 317 optimal weight: 4.9990 chunk 389 optimal weight: 5.9990 chunk 605 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 131 GLN A 193 GLN B 49 ASN B 56 ASN B 79 HIS B 99 ASN B 101 HIS B 178 ASN B 209 ASN B 211 HIS C 92 GLN C 238 GLN D 67 ASN ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 GLN D 179 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 HIS E 130 GLN E 224 ASN E 259 HIS ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN F 202 ASN F 226 ASN G 4 ASN G 10 ASN G 13 GLN G 199 GLN H 30 ASN H 155 ASN H 170 GLN I 116 HIS J 38 ASN J 131 GLN K 17 GLN K 47 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN L 18 HIS L 22 ASN L 81 HIS M 31 HIS N 5 HIS N 21 ASN N 58 HIS N 105 ASN O 12 GLN O 24 ASN O 29 HIS O 80 HIS O 99 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN Q 83 GLN Q 94 GLN Q 103 ASN R 83 GLN R 105 GLN S 6 GLN S 25 ASN S 78 HIS S 89 GLN ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS T 93 HIS T 106 GLN U 44 ASN U 105 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN W 24 GLN W 92 ASN X 18 HIS X 22 ASN Y 22 GLN Z 98 GLN b 26 GLN b 31 HIS b 42 ASN b 49 HIS d 10 HIS e 24 GLN g 292 GLN ** g 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 55 ASN ** i 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 84 GLN Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 82907 Z= 0.352 Angle : 0.847 14.708 120536 Z= 0.428 Chirality : 0.048 0.364 15025 Planarity : 0.007 0.148 8760 Dihedral : 24.997 179.899 33561 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 1.77 % Allowed : 9.04 % Favored : 89.19 % Rotamer: Outliers : 9.06 % Allowed : 21.36 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.12), residues: 4976 helix: 2.29 (0.13), residues: 1583 sheet: -0.97 (0.16), residues: 873 loop : -2.64 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 149 HIS 0.022 0.002 HIS Z 82 PHE 0.032 0.002 PHE c 32 TYR 0.026 0.002 TYR R 21 ARG 0.009 0.001 ARG d 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 1015 time to evaluate : 4.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 GLU cc_start: 0.7672 (mp0) cc_final: 0.7457 (mp0) REVERT: A 15 GLN cc_start: 0.8306 (tt0) cc_final: 0.7804 (tt0) REVERT: A 21 ARG cc_start: 0.7519 (mtm180) cc_final: 0.7127 (mpt-90) REVERT: A 33 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8101 (mp10) REVERT: A 39 LYS cc_start: 0.8567 (mptp) cc_final: 0.8336 (mmmm) REVERT: A 88 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8467 (mmtp) REVERT: A 120 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9013 (tt) REVERT: A 127 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7699 (ttm-80) REVERT: A 150 ASP cc_start: 0.7915 (t0) cc_final: 0.7213 (p0) REVERT: A 157 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: A 164 ASN cc_start: 0.8426 (m-40) cc_final: 0.7630 (m110) REVERT: A 198 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8232 (mtt) REVERT: A 206 ASN cc_start: 0.7106 (p0) cc_final: 0.6882 (p0) REVERT: B 39 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6645 (tp30) REVERT: B 50 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8169 (mtpp) REVERT: B 64 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7854 (mtp85) REVERT: B 83 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7768 (ttpp) REVERT: B 96 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8426 (pp) REVERT: B 105 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8407 (t80) REVERT: C 82 LYS cc_start: 0.8426 (mmtt) cc_final: 0.8122 (mmtm) REVERT: C 83 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: C 86 MET cc_start: 0.8481 (mmm) cc_final: 0.8217 (mmm) REVERT: C 99 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: C 124 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8558 (mtpt) REVERT: C 145 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8932 (tpt-90) REVERT: C 193 MET cc_start: 0.9186 (mmm) cc_final: 0.8906 (mmt) REVERT: C 230 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9069 (tp) REVERT: C 233 ASN cc_start: 0.8540 (p0) cc_final: 0.8249 (p0) REVERT: C 237 VAL cc_start: 0.8580 (t) cc_final: 0.8372 (p) REVERT: C 248 TYR cc_start: 0.8734 (m-80) cc_final: 0.8450 (m-10) REVERT: D 23 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7869 (tp30) REVERT: D 45 LYS cc_start: 0.7786 (mttt) cc_final: 0.7450 (mtmt) REVERT: D 74 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6771 (pt0) REVERT: D 84 ILE cc_start: 0.7747 (mt) cc_final: 0.7512 (tt) REVERT: D 97 SER cc_start: 0.7935 (t) cc_final: 0.7721 (t) REVERT: D 127 MET cc_start: 0.7510 (mmm) cc_final: 0.7272 (mmm) REVERT: D 148 LYS cc_start: 0.8336 (mtmp) cc_final: 0.8129 (mtpt) REVERT: D 150 MET cc_start: 0.7625 (mmt) cc_final: 0.7038 (mmt) REVERT: D 162 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7378 (tm-30) REVERT: E 60 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: E 77 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8609 (mmt180) REVERT: E 97 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8063 (mt-10) REVERT: E 106 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7271 (mptt) REVERT: E 134 LYS cc_start: 0.8938 (mttt) cc_final: 0.8425 (mttt) REVERT: E 166 THR cc_start: 0.8954 (p) cc_final: 0.8258 (t) REVERT: E 168 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8586 (t) REVERT: E 174 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8431 (mmmm) REVERT: E 250 GLU cc_start: 0.7654 (mm-30) cc_final: 0.6575 (tp30) REVERT: E 254 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7701 (mtt-85) REVERT: F 27 LEU cc_start: 0.6899 (mt) cc_final: 0.6662 (mm) REVERT: F 31 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7959 (mt) REVERT: F 32 PRO cc_start: 0.7175 (Cg_exo) cc_final: 0.6152 (Cg_endo) REVERT: F 43 LYS cc_start: 0.7934 (mptt) cc_final: 0.7390 (mppt) REVERT: F 47 LYS cc_start: 0.5807 (OUTLIER) cc_final: 0.5290 (mmmt) REVERT: F 50 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7008 (t80) REVERT: F 56 LYS cc_start: 0.6757 (mttt) cc_final: 0.6547 (mtmm) REVERT: F 85 ARG cc_start: 0.8079 (mmt-90) cc_final: 0.7502 (mmp-170) REVERT: F 91 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7489 (mt) REVERT: F 92 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7240 (m) REVERT: F 105 ASN cc_start: 0.8094 (t0) cc_final: 0.7877 (t0) REVERT: F 144 PRO cc_start: 0.7446 (Cg_exo) cc_final: 0.6885 (Cg_endo) REVERT: F 192 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6358 (tp) REVERT: F 205 LYS cc_start: 0.6947 (mttt) cc_final: 0.6686 (mtpt) REVERT: G 4 ASN cc_start: 0.8631 (OUTLIER) cc_final: 0.8416 (t0) REVERT: G 21 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6774 (pp20) REVERT: G 43 ASP cc_start: 0.6851 (m-30) cc_final: 0.6308 (t0) REVERT: G 121 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7535 (mt) REVERT: H 26 ASP cc_start: 0.6873 (m-30) cc_final: 0.6572 (m-30) REVERT: H 47 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7809 (mtp180) REVERT: H 82 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: H 92 PHE cc_start: 0.9065 (m-80) cc_final: 0.8612 (m-80) REVERT: H 110 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8911 (tt0) REVERT: H 175 LYS cc_start: 0.8659 (mmtt) cc_final: 0.7948 (tptt) REVERT: I 20 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7537 (tp-100) REVERT: I 66 SER cc_start: 0.9095 (m) cc_final: 0.8861 (t) REVERT: I 77 ARG cc_start: 0.8756 (ttm110) cc_final: 0.8534 (ttm110) REVERT: I 89 GLU cc_start: 0.7693 (tp30) cc_final: 0.7391 (tp30) REVERT: I 92 ARG cc_start: 0.7360 (ttm110) cc_final: 0.6951 (ttp80) REVERT: I 114 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8163 (mt-10) REVERT: I 147 ARG cc_start: 0.6513 (mtt180) cc_final: 0.6265 (mtt180) REVERT: J 9 SER cc_start: 0.9422 (t) cc_final: 0.8907 (m) REVERT: J 29 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7986 (mttt) REVERT: J 54 ARG cc_start: 0.8214 (ttm110) cc_final: 0.7976 (ttm110) REVERT: J 70 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9134 (mp) REVERT: J 91 LYS cc_start: 0.8881 (mttt) cc_final: 0.8537 (mtpp) REVERT: J 94 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8490 (m-30) REVERT: J 106 GLU cc_start: 0.7889 (tp30) cc_final: 0.7541 (tm-30) REVERT: J 107 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8531 (tpt170) REVERT: J 131 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8609 (mm-40) REVERT: J 153 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: J 157 ASP cc_start: 0.8194 (t70) cc_final: 0.7671 (t0) REVERT: K 1 MET cc_start: 0.3863 (mtt) cc_final: 0.3476 (mtt) REVERT: K 3 ILE cc_start: 0.7285 (mt) cc_final: 0.7014 (mm) REVERT: K 40 LEU cc_start: 0.7419 (pt) cc_final: 0.7117 (pt) REVERT: K 44 LYS cc_start: 0.7442 (mtmt) cc_final: 0.7161 (mmtt) REVERT: K 56 LYS cc_start: 0.6891 (mttt) cc_final: 0.6618 (mtmm) REVERT: L 8 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7817 (mp-120) REVERT: L 36 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.7385 (pmtt) REVERT: L 53 TYR cc_start: 0.8587 (p90) cc_final: 0.8233 (p90) REVERT: L 93 TYR cc_start: 0.9457 (t80) cc_final: 0.9142 (t80) REVERT: L 123 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8434 (m) REVERT: N 3 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8360 (mmp80) REVERT: N 9 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8791 (mttt) REVERT: N 27 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7439 (mtpp) REVERT: N 53 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8078 (mm) REVERT: N 100 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8495 (tttp) REVERT: O 53 ASP cc_start: 0.8884 (m-30) cc_final: 0.8639 (m-30) REVERT: O 65 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6815 (mt0) REVERT: O 66 ASP cc_start: 0.8557 (t0) cc_final: 0.8215 (t0) REVERT: O 116 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: O 124 ASP cc_start: 0.7244 (t70) cc_final: 0.6806 (t0) REVERT: O 129 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9093 (tttm) REVERT: P 24 LYS cc_start: 0.7247 (mtpp) cc_final: 0.6911 (mtmt) REVERT: P 49 LEU cc_start: 0.6333 (mp) cc_final: 0.5386 (tp) REVERT: P 89 MET cc_start: 0.5934 (ptm) cc_final: 0.5630 (ptp) REVERT: P 94 VAL cc_start: 0.6533 (OUTLIER) cc_final: 0.6183 (m) REVERT: P 97 TYR cc_start: 0.7232 (t80) cc_final: 0.6005 (t80) REVERT: P 127 ARG cc_start: 0.6118 (OUTLIER) cc_final: 0.3644 (mmm-85) REVERT: Q 42 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7069 (tp30) REVERT: Q 122 ARG cc_start: 0.8607 (mtp180) cc_final: 0.8224 (mtm180) REVERT: Q 123 ARG cc_start: 0.8674 (ttm110) cc_final: 0.8397 (mmt-90) REVERT: Q 142 TYR cc_start: 0.5883 (OUTLIER) cc_final: 0.4481 (p90) REVERT: R 33 ARG cc_start: 0.8349 (mmt90) cc_final: 0.7872 (mmt-90) REVERT: R 58 MET cc_start: 0.7463 (mmm) cc_final: 0.7184 (mmt) REVERT: R 72 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7085 (mttp) REVERT: R 92 ASP cc_start: 0.7934 (t0) cc_final: 0.7592 (t0) REVERT: R 94 SER cc_start: 0.8829 (t) cc_final: 0.8262 (p) REVERT: R 103 ASP cc_start: 0.8361 (t70) cc_final: 0.7061 (m-30) REVERT: R 104 THR cc_start: 0.8685 (p) cc_final: 0.8192 (p) REVERT: R 106 THR cc_start: 0.9411 (m) cc_final: 0.9061 (p) REVERT: R 125 SER cc_start: 0.8163 (p) cc_final: 0.7702 (t) REVERT: S 18 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5910 (tt) REVERT: S 106 GLU cc_start: 0.6434 (pt0) cc_final: 0.5702 (pm20) REVERT: S 145 ARG cc_start: 0.1725 (OUTLIER) cc_final: 0.0354 (ptp-110) REVERT: T 17 ASN cc_start: 0.7655 (m-40) cc_final: 0.7384 (m-40) REVERT: U 32 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7654 (tptm) REVERT: U 64 LYS cc_start: 0.8541 (tppt) cc_final: 0.8304 (mttm) REVERT: U 83 GLU cc_start: 0.8465 (pt0) cc_final: 0.7983 (pt0) REVERT: U 84 MET cc_start: 0.8646 (ttm) cc_final: 0.8428 (ttm) REVERT: U 85 ARG cc_start: 0.8704 (ptp-110) cc_final: 0.7848 (mtt-85) REVERT: U 113 ASP cc_start: 0.6829 (t70) cc_final: 0.6486 (t0) REVERT: V 1 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7239 (tpt) REVERT: V 21 ASN cc_start: 0.8902 (t0) cc_final: 0.8518 (t0) REVERT: V 38 GLN cc_start: 0.8551 (mm-40) cc_final: 0.8291 (mt0) REVERT: V 85 TYR cc_start: 0.9093 (t80) cc_final: 0.8873 (t80) REVERT: V 87 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7384 (ttm-80) REVERT: W 22 LYS cc_start: 0.9121 (mmtt) cc_final: 0.8899 (mttp) REVERT: W 26 LEU cc_start: 0.9199 (tm) cc_final: 0.8867 (tp) REVERT: W 82 LYS cc_start: 0.9000 (ttmt) cc_final: 0.8642 (mttt) REVERT: W 93 LEU cc_start: 0.9175 (mt) cc_final: 0.8774 (mp) REVERT: W 111 MET cc_start: 0.8736 (pmm) cc_final: 0.8130 (ptp) REVERT: X 22 ASN cc_start: 0.9128 (m-40) cc_final: 0.8719 (m-40) REVERT: X 34 LEU cc_start: 0.9129 (mt) cc_final: 0.8893 (mp) REVERT: X 38 PHE cc_start: 0.8617 (m-80) cc_final: 0.8354 (m-80) REVERT: X 40 SER cc_start: 0.7681 (p) cc_final: 0.7109 (p) REVERT: X 41 SER cc_start: 0.8183 (t) cc_final: 0.7929 (p) REVERT: X 57 ILE cc_start: 0.8739 (mt) cc_final: 0.8335 (pt) REVERT: X 107 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.7900 (t80) REVERT: Y 38 ASP cc_start: 0.8135 (t70) cc_final: 0.7906 (t0) REVERT: Y 61 ARG cc_start: 0.8917 (mtp85) cc_final: 0.8674 (mtp-110) REVERT: Y 63 GLN cc_start: 0.8767 (tp40) cc_final: 0.8360 (tp-100) REVERT: Y 68 LYS cc_start: 0.8463 (mttt) cc_final: 0.7956 (mtpt) REVERT: Y 98 GLU cc_start: 0.9063 (tt0) cc_final: 0.8579 (mm-30) REVERT: Y 111 ARG cc_start: 0.8509 (ttm-80) cc_final: 0.7648 (ttm-80) REVERT: Y 127 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7966 (ttpt) REVERT: a 18 VAL cc_start: 0.9508 (t) cc_final: 0.9305 (m) REVERT: a 28 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7440 (ttp80) REVERT: a 34 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8680 (ttmm) REVERT: a 38 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8611 (mmt-90) REVERT: a 61 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: b 22 LYS cc_start: 0.9024 (mmtt) cc_final: 0.8785 (mmtp) REVERT: b 24 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8944 (tp) REVERT: b 34 ASP cc_start: 0.7436 (m-30) cc_final: 0.7150 (m-30) REVERT: b 51 GLN cc_start: 0.9172 (mt0) cc_final: 0.8916 (mt0) REVERT: b 70 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8353 (ttmt) REVERT: c 27 GLN cc_start: 0.7978 (tt0) cc_final: 0.7397 (tp40) REVERT: c 58 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7119 (mm-30) REVERT: d 20 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7528 (tm-30) REVERT: d 41 GLN cc_start: 0.8685 (mp10) cc_final: 0.8416 (mp10) REVERT: d 48 ASN cc_start: 0.8912 (m-40) cc_final: 0.8617 (m-40) REVERT: e 26 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8204 (mtmm) REVERT: e 31 LYS cc_start: 0.8387 (mtmt) cc_final: 0.8052 (mptt) REVERT: f 109 ASP cc_start: 0.1386 (OUTLIER) cc_final: 0.1058 (p0) REVERT: g 55 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.5572 (t80) REVERT: g 63 LYS cc_start: 0.8234 (mttt) cc_final: 0.8017 (ttmm) REVERT: g 149 THR cc_start: 0.6339 (p) cc_final: 0.6048 (t) REVERT: g 172 ILE cc_start: 0.4743 (OUTLIER) cc_final: 0.4472 (pp) REVERT: g 199 PHE cc_start: 0.7521 (m-80) cc_final: 0.7303 (m-80) REVERT: g 284 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: g 295 HIS cc_start: 0.8508 (p-80) cc_final: 0.7894 (p90) REVERT: g 309 PHE cc_start: 0.7137 (m-80) cc_final: 0.6510 (m-80) REVERT: h 16 LYS cc_start: 0.6380 (OUTLIER) cc_final: 0.5745 (mttt) REVERT: j 62 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5277 (p90) REVERT: j 73 GLU cc_start: 0.5211 (OUTLIER) cc_final: 0.2913 (pt0) REVERT: j 92 MET cc_start: 0.6832 (mmm) cc_final: 0.6008 (mtm) outliers start: 388 outliers final: 184 residues processed: 1277 average time/residue: 0.8043 time to fit residues: 1703.1681 Evaluate side-chains 1154 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 900 time to evaluate : 4.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 186 PHE Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 4 ASN Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 86 GLN Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 196 ARG Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain K residue 31 LYS Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 100 LYS Chi-restraints excluded: chain N residue 105 ASN Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain O residue 65 GLN Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain O residue 129 LYS Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 127 ARG Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 42 GLU Chi-restraints excluded: chain Q residue 45 ARG Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 55 VAL Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain S residue 18 LEU Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 145 ARG Chi-restraints excluded: chain T residue 37 VAL Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 70 ASN Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 56 LYS Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain Y residue 8 ARG Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 92 VAL Chi-restraints excluded: chain Y residue 124 SER Chi-restraints excluded: chain Y residue 127 LYS Chi-restraints excluded: chain Z residue 78 VAL Chi-restraints excluded: chain Z residue 98 GLN Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 34 LYS Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 54 SER Chi-restraints excluded: chain a residue 61 GLU Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 26 SER Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 109 ASP Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 55 PHE Chi-restraints excluded: chain g residue 67 HIS Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 129 ASP Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 172 ILE Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 195 ILE Chi-restraints excluded: chain g residue 284 GLU Chi-restraints excluded: chain g residue 292 GLN Chi-restraints excluded: chain g residue 293 ASP Chi-restraints excluded: chain g residue 316 VAL Chi-restraints excluded: chain g residue 321 GLN Chi-restraints excluded: chain h residue 16 LYS Chi-restraints excluded: chain i residue 58 MET Chi-restraints excluded: chain i residue 65 LEU Chi-restraints excluded: chain i residue 116 ASN Chi-restraints excluded: chain j residue 62 PHE Chi-restraints excluded: chain j residue 64 CYS Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain j residue 105 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 336 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 504 optimal weight: 0.9990 chunk 412 optimal weight: 5.9990 chunk 167 optimal weight: 50.0000 chunk 606 optimal weight: 10.0000 chunk 655 optimal weight: 30.0000 chunk 540 optimal weight: 3.9990 chunk 601 optimal weight: 0.9990 chunk 206 optimal weight: 10.0000 chunk 486 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 GLN C 64 HIS ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 ASN G 10 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 71 HIS I 32 GLN K 17 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 HIS Q 83 GLN ** Q 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN T 12 GLN T 64 HIS T 91 HIS ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS e 17 GLN ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 44 ASN ** i 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 27 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 82907 Z= 0.227 Angle : 0.712 14.570 120536 Z= 0.360 Chirality : 0.041 0.292 15025 Planarity : 0.006 0.147 8760 Dihedral : 24.742 179.471 33358 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 1.55 % Allowed : 9.32 % Favored : 89.13 % Rotamer: Outliers : 8.08 % Allowed : 23.56 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.12), residues: 4976 helix: 2.25 (0.13), residues: 1575 sheet: -0.87 (0.16), residues: 875 loop : -2.47 (0.11), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 61 HIS 0.016 0.001 HIS H 71 PHE 0.023 0.002 PHE f 129 TYR 0.030 0.002 TYR a 59 ARG 0.008 0.000 ARG R 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1303 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 957 time to evaluate : 4.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8263 (tt0) cc_final: 0.7610 (tp-100) REVERT: A 33 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8082 (mp10) REVERT: A 38 TYR cc_start: 0.8525 (t80) cc_final: 0.8282 (t80) REVERT: A 39 LYS cc_start: 0.8598 (mptp) cc_final: 0.8328 (mmmm) REVERT: A 88 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8446 (mmtp) REVERT: A 108 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7662 (p) REVERT: A 127 ARG cc_start: 0.8179 (ttm170) cc_final: 0.7728 (ttm-80) REVERT: A 150 ASP cc_start: 0.7750 (t0) cc_final: 0.7032 (p0) REVERT: A 157 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7795 (m-30) REVERT: B 62 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8321 (mttm) REVERT: B 64 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7787 (ttm170) REVERT: B 96 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8489 (pp) REVERT: B 105 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8367 (t80) REVERT: C 83 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7538 (m-30) REVERT: C 86 MET cc_start: 0.8395 (mmm) cc_final: 0.8144 (mmm) REVERT: C 124 LYS cc_start: 0.8876 (mtmt) cc_final: 0.8651 (mtpt) REVERT: C 145 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8844 (tpt-90) REVERT: C 193 MET cc_start: 0.9182 (mmm) cc_final: 0.8971 (mmt) REVERT: C 230 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9039 (tp) REVERT: C 236 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7213 (pp20) REVERT: C 237 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8141 (m) REVERT: C 248 TYR cc_start: 0.8707 (m-80) cc_final: 0.8441 (m-10) REVERT: D 17 PHE cc_start: 0.8048 (t80) cc_final: 0.7750 (t80) REVERT: D 45 LYS cc_start: 0.7632 (mttt) cc_final: 0.7334 (mtmt) REVERT: D 74 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6526 (pt0) REVERT: D 105 MET cc_start: 0.8074 (ttt) cc_final: 0.7775 (tpp) REVERT: D 150 MET cc_start: 0.7585 (mmt) cc_final: 0.7101 (mmt) REVERT: D 162 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7353 (tm-30) REVERT: E 60 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7450 (mm-30) REVERT: E 77 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8576 (mmt180) REVERT: E 134 LYS cc_start: 0.8945 (mttt) cc_final: 0.8457 (mttt) REVERT: E 171 ASP cc_start: 0.7976 (t70) cc_final: 0.7639 (t70) REVERT: E 174 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8287 (mmmm) REVERT: F 32 PRO cc_start: 0.6853 (Cg_exo) cc_final: 0.6501 (Cg_endo) REVERT: F 43 LYS cc_start: 0.7882 (mptt) cc_final: 0.7356 (mppt) REVERT: F 47 LYS cc_start: 0.5475 (OUTLIER) cc_final: 0.4872 (mmmt) REVERT: F 50 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.6620 (t80) REVERT: F 85 ARG cc_start: 0.7914 (mmt-90) cc_final: 0.7382 (mmp-170) REVERT: F 91 ILE cc_start: 0.7526 (OUTLIER) cc_final: 0.7095 (mt) REVERT: F 146 GLU cc_start: 0.6421 (pm20) cc_final: 0.6018 (mp0) REVERT: F 192 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6261 (tp) REVERT: F 205 LYS cc_start: 0.6774 (mttt) cc_final: 0.6536 (mtmt) REVERT: G 21 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6737 (pp20) REVERT: G 43 ASP cc_start: 0.6873 (m-30) cc_final: 0.6398 (t0) REVERT: G 56 ASN cc_start: 0.8934 (m110) cc_final: 0.8575 (m-40) REVERT: H 33 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: H 47 ARG cc_start: 0.8270 (ttm170) cc_final: 0.7960 (mtp180) REVERT: H 82 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: H 92 PHE cc_start: 0.8989 (m-80) cc_final: 0.8701 (m-80) REVERT: H 110 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8656 (tt0) REVERT: H 175 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8424 (tptm) REVERT: I 20 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7530 (tp-100) REVERT: I 58 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8568 (mt) REVERT: I 77 ARG cc_start: 0.8751 (ttm110) cc_final: 0.8537 (ttm110) REVERT: I 92 ARG cc_start: 0.7235 (ttm110) cc_final: 0.6795 (ttp80) REVERT: I 113 TYR cc_start: 0.8299 (t80) cc_final: 0.8080 (t80) REVERT: I 114 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8175 (mt-10) REVERT: I 147 ARG cc_start: 0.6431 (mtt180) cc_final: 0.6100 (mtt180) REVERT: I 159 SER cc_start: 0.8925 (m) cc_final: 0.8471 (t) REVERT: I 193 TYR cc_start: 0.8693 (m-80) cc_final: 0.8433 (m-80) REVERT: J 9 SER cc_start: 0.9399 (t) cc_final: 0.8954 (m) REVERT: J 53 ARG cc_start: 0.8416 (ttm110) cc_final: 0.7991 (mtm-85) REVERT: J 70 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9181 (mp) REVERT: J 94 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8447 (m-30) REVERT: J 106 GLU cc_start: 0.7903 (tp30) cc_final: 0.7491 (tm-30) REVERT: J 107 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8552 (tpt170) REVERT: J 153 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: J 157 ASP cc_start: 0.8194 (t70) cc_final: 0.7617 (t0) REVERT: K 20 VAL cc_start: 0.8769 (t) cc_final: 0.8477 (m) REVERT: K 36 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6590 (t0) REVERT: K 40 LEU cc_start: 0.7416 (pt) cc_final: 0.7101 (pt) REVERT: K 44 LYS cc_start: 0.7199 (mtmt) cc_final: 0.6984 (mmtt) REVERT: K 64 TYR cc_start: 0.7421 (m-80) cc_final: 0.6747 (m-80) REVERT: K 68 LEU cc_start: 0.7097 (mt) cc_final: 0.6877 (mt) REVERT: L 8 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7771 (mp-120) REVERT: L 36 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.7671 (pmtt) REVERT: L 55 ASP cc_start: 0.7588 (t0) cc_final: 0.7387 (t0) REVERT: L 93 TYR cc_start: 0.9387 (t80) cc_final: 0.9110 (t80) REVERT: L 123 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8364 (m) REVERT: M 19 ASP cc_start: 0.5654 (OUTLIER) cc_final: 0.5172 (t0) REVERT: M 38 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6417 (pt) REVERT: N 3 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8223 (mmp80) REVERT: N 9 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8736 (mttt) REVERT: N 20 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8023 (mpt90) REVERT: N 27 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7579 (mtpp) REVERT: N 53 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8124 (mm) REVERT: N 115 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9038 (tp) REVERT: O 51 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: O 66 ASP cc_start: 0.8588 (t0) cc_final: 0.8244 (t0) REVERT: O 116 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6900 (mt-10) REVERT: O 124 ASP cc_start: 0.7221 (t70) cc_final: 0.6884 (t0) REVERT: P 28 MET cc_start: 0.3447 (ptt) cc_final: 0.2901 (tpt) REVERT: P 49 LEU cc_start: 0.6352 (mp) cc_final: 0.5470 (tp) REVERT: P 81 ARG cc_start: 0.6897 (ttt-90) cc_final: 0.6607 (ttt-90) REVERT: P 97 TYR cc_start: 0.7180 (t80) cc_final: 0.5942 (t80) REVERT: P 98 ASN cc_start: 0.6746 (t0) cc_final: 0.6490 (t0) REVERT: Q 28 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8135 (tp) REVERT: Q 68 LYS cc_start: 0.7606 (ttmp) cc_final: 0.7359 (ttpt) REVERT: Q 104 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7054 (tp30) REVERT: Q 122 ARG cc_start: 0.8581 (mtp180) cc_final: 0.8060 (mtm180) REVERT: Q 123 ARG cc_start: 0.8638 (ttm110) cc_final: 0.8278 (mmm-85) REVERT: R 24 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8076 (mp) REVERT: R 33 ARG cc_start: 0.8612 (mmt90) cc_final: 0.8234 (mmt-90) REVERT: R 59 LYS cc_start: 0.8503 (mmmm) cc_final: 0.8142 (mtmt) REVERT: R 72 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7035 (mttt) REVERT: R 79 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6534 (mm-30) REVERT: R 92 ASP cc_start: 0.7958 (t0) cc_final: 0.7591 (t0) REVERT: R 94 SER cc_start: 0.8827 (t) cc_final: 0.8377 (p) REVERT: R 103 ASP cc_start: 0.8599 (t70) cc_final: 0.7257 (m-30) REVERT: R 104 THR cc_start: 0.8743 (p) cc_final: 0.8220 (p) REVERT: R 125 SER cc_start: 0.8206 (p) cc_final: 0.7776 (t) REVERT: S 47 CYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6124 (p) REVERT: S 85 PHE cc_start: 0.5702 (p90) cc_final: 0.5452 (p90) REVERT: S 106 GLU cc_start: 0.6453 (pt0) cc_final: 0.5789 (pm20) REVERT: S 145 ARG cc_start: 0.1319 (OUTLIER) cc_final: -0.0167 (ptp-110) REVERT: T 17 ASN cc_start: 0.7522 (m-40) cc_final: 0.7190 (m-40) REVERT: T 21 PHE cc_start: 0.7383 (t80) cc_final: 0.6985 (t80) REVERT: T 24 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6564 (ptm160) REVERT: T 68 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7921 (mpt90) REVERT: T 90 PRO cc_start: 0.8922 (Cg_exo) cc_final: 0.8680 (Cg_endo) REVERT: T 130 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7768 (mtt-85) REVERT: U 32 LYS cc_start: 0.7819 (mmtt) cc_final: 0.7540 (tptm) REVERT: U 64 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8278 (mttm) REVERT: U 83 GLU cc_start: 0.8450 (pt0) cc_final: 0.8124 (pt0) REVERT: V 7 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: V 21 ASN cc_start: 0.8883 (t0) cc_final: 0.8542 (t0) REVERT: V 85 TYR cc_start: 0.9073 (t80) cc_final: 0.8782 (t80) REVERT: V 87 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7429 (ttm-80) REVERT: W 26 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8804 (tp) REVERT: W 90 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8637 (p) REVERT: W 93 LEU cc_start: 0.9158 (mt) cc_final: 0.8865 (mp) REVERT: X 38 PHE cc_start: 0.8652 (m-80) cc_final: 0.8445 (m-80) REVERT: X 56 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7681 (mtpt) REVERT: X 107 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.7905 (t80) REVERT: Y 8 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8431 (tpp80) REVERT: Y 20 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.9009 (ptm160) REVERT: Y 26 ASP cc_start: 0.8923 (t0) cc_final: 0.8623 (t0) REVERT: Y 28 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8199 (mp) REVERT: Y 61 ARG cc_start: 0.8824 (mtp85) cc_final: 0.8596 (mtp-110) REVERT: Y 63 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8339 (tp-100) REVERT: Y 68 LYS cc_start: 0.8432 (mttt) cc_final: 0.7963 (mtpt) REVERT: Y 98 GLU cc_start: 0.9005 (tt0) cc_final: 0.8650 (mm-30) REVERT: Y 111 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.7993 (ttp80) REVERT: Y 127 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8034 (ttpt) REVERT: Z 51 MET cc_start: 0.4736 (OUTLIER) cc_final: 0.3606 (mmm) REVERT: a 28 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7493 (ttp80) REVERT: a 38 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8582 (mmt-90) REVERT: a 59 TYR cc_start: 0.7887 (p90) cc_final: 0.7402 (p90) REVERT: a 62 TYR cc_start: 0.7034 (t80) cc_final: 0.6770 (t80) REVERT: b 24 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9000 (tp) REVERT: b 34 ASP cc_start: 0.7483 (m-30) cc_final: 0.7194 (m-30) REVERT: b 70 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8459 (ttmt) REVERT: d 20 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7576 (tm-30) REVERT: d 48 ASN cc_start: 0.8904 (m-40) cc_final: 0.8626 (m-40) REVERT: d 54 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8104 (ttpp) REVERT: e 26 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8189 (mtmm) REVERT: e 31 LYS cc_start: 0.8374 (mtmt) cc_final: 0.8074 (mttt) REVERT: f 89 LYS cc_start: 0.5264 (tppt) cc_final: 0.4050 (ptmt) REVERT: f 109 ASP cc_start: 0.1461 (OUTLIER) cc_final: 0.1113 (p0) REVERT: g 55 PHE cc_start: 0.6131 (OUTLIER) cc_final: 0.5499 (t80) REVERT: g 99 ASN cc_start: 0.8051 (t0) cc_final: 0.7794 (t0) REVERT: g 149 THR cc_start: 0.6413 (p) cc_final: 0.6035 (t) REVERT: g 238 PHE cc_start: 0.6425 (OUTLIER) cc_final: 0.5990 (t80) REVERT: g 269 ILE cc_start: 0.5611 (OUTLIER) cc_final: 0.5411 (mt) REVERT: g 284 GLU cc_start: 0.6419 (OUTLIER) cc_final: 0.6101 (mp0) REVERT: g 295 HIS cc_start: 0.8424 (p-80) cc_final: 0.7927 (p90) REVERT: g 309 PHE cc_start: 0.7084 (m-80) cc_final: 0.6471 (m-80) REVERT: g 321 GLN cc_start: 0.5580 (OUTLIER) cc_final: 0.5071 (mt0) REVERT: i 41 MET cc_start: 0.6233 (mmp) cc_final: 0.5842 (mmm) REVERT: j 62 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.5356 (p90) REVERT: j 73 GLU cc_start: 0.4956 (OUTLIER) cc_final: 0.3903 (pt0) outliers start: 346 outliers final: 169 residues processed: 1187 average time/residue: 0.8226 time to fit residues: 1640.2979 Evaluate side-chains 1124 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 880 time to evaluate : 4.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 145 ARG Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 259 HIS Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 186 PHE Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 20 GLN Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain I residue 196 ARG Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain O residue 51 ASP Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 116 GLU Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 18 GLU Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 47 CYS Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 145 ARG Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 64 LYS Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 7 GLN Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 56 SER Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 56 LYS Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 8 ARG Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 20 ARG Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 63 GLN Chi-restraints excluded: chain Y residue 124 SER Chi-restraints excluded: chain Y residue 127 LYS Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain d residue 26 SER Chi-restraints excluded: chain d residue 54 LYS Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 109 ASP Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 55 PHE Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 195 ILE Chi-restraints excluded: chain g residue 238 PHE Chi-restraints excluded: chain g residue 269 ILE Chi-restraints excluded: chain g residue 284 GLU Chi-restraints excluded: chain g residue 292 GLN Chi-restraints excluded: chain g residue 293 ASP Chi-restraints excluded: chain g residue 321 GLN Chi-restraints excluded: chain h residue 16 LYS Chi-restraints excluded: chain i residue 44 ASN Chi-restraints excluded: chain i residue 58 MET Chi-restraints excluded: chain i residue 65 LEU Chi-restraints excluded: chain i residue 116 ASN Chi-restraints excluded: chain j residue 62 PHE Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain j residue 105 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 599 optimal weight: 9.9990 chunk 456 optimal weight: 10.0000 chunk 314 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 289 optimal weight: 9.9990 chunk 407 optimal weight: 2.9990 chunk 608 optimal weight: 0.0050 chunk 644 optimal weight: 0.9990 chunk 318 optimal weight: 9.9990 chunk 577 optimal weight: 30.0000 chunk 173 optimal weight: 10.0000 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN C 225 ASN ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN I 88 ASN K 95 GLN N 78 ASN N 105 ASN P 79 HIS P 114 HIS Q 32 ASN Q 77 GLN Q 83 GLN ** Q 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN T 12 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 ASN b 26 GLN c 43 ASN ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 234 HIS ** g 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 GLN ** i 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 82907 Z= 0.313 Angle : 0.739 14.897 120536 Z= 0.370 Chirality : 0.042 0.293 15025 Planarity : 0.006 0.150 8760 Dihedral : 24.574 179.552 33288 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 1.45 % Allowed : 9.53 % Favored : 89.03 % Rotamer: Outliers : 8.48 % Allowed : 24.66 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.12), residues: 4976 helix: 1.93 (0.13), residues: 1573 sheet: -0.83 (0.17), residues: 872 loop : -2.41 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 151 HIS 0.016 0.001 HIS T 91 PHE 0.025 0.002 PHE c 32 TYR 0.028 0.002 TYR a 59 ARG 0.014 0.001 ARG S 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 888 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8283 (tt0) cc_final: 0.7600 (tp-100) REVERT: A 33 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: A 38 TYR cc_start: 0.8573 (t80) cc_final: 0.8295 (t80) REVERT: A 39 LYS cc_start: 0.8570 (mptp) cc_final: 0.8275 (mmmm) REVERT: A 88 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8531 (mmtp) REVERT: A 108 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7600 (p) REVERT: A 127 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7774 (ttm-80) REVERT: A 150 ASP cc_start: 0.7855 (t0) cc_final: 0.7263 (p0) REVERT: A 157 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: A 197 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7299 (mp) REVERT: B 96 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8317 (pp) REVERT: B 105 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8194 (t80) REVERT: C 83 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: C 86 MET cc_start: 0.8541 (mmm) cc_final: 0.8008 (mmm) REVERT: C 99 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: C 193 MET cc_start: 0.9141 (mmm) cc_final: 0.8870 (mmt) REVERT: C 236 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7536 (pp20) REVERT: C 237 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8178 (m) REVERT: C 248 TYR cc_start: 0.8733 (m-80) cc_final: 0.8449 (m-10) REVERT: D 14 ASP cc_start: 0.8404 (t0) cc_final: 0.8110 (t0) REVERT: D 17 PHE cc_start: 0.8087 (t80) cc_final: 0.7765 (t80) REVERT: D 45 LYS cc_start: 0.7588 (mttt) cc_final: 0.7246 (mtmt) REVERT: D 72 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7768 (mm) REVERT: D 127 MET cc_start: 0.7897 (mmm) cc_final: 0.7468 (mmm) REVERT: D 150 MET cc_start: 0.7497 (mmt) cc_final: 0.6976 (mmt) REVERT: D 162 GLN cc_start: 0.7652 (tm-30) cc_final: 0.7344 (tm-30) REVERT: D 217 VAL cc_start: 0.6219 (OUTLIER) cc_final: 0.5985 (t) REVERT: E 42 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8645 (tp) REVERT: E 60 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: E 134 LYS cc_start: 0.8961 (mttt) cc_final: 0.8401 (mttp) REVERT: E 142 HIS cc_start: 0.6553 (OUTLIER) cc_final: 0.5711 (t70) REVERT: E 174 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8318 (mmmm) REVERT: F 32 PRO cc_start: 0.6915 (Cg_exo) cc_final: 0.6404 (Cg_endo) REVERT: F 42 ILE cc_start: 0.6383 (tp) cc_final: 0.5929 (tt) REVERT: F 43 LYS cc_start: 0.7948 (mptt) cc_final: 0.7423 (mppt) REVERT: F 47 LYS cc_start: 0.5646 (OUTLIER) cc_final: 0.5107 (mmmt) REVERT: F 50 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.6601 (t80) REVERT: F 85 ARG cc_start: 0.7916 (mmt-90) cc_final: 0.7391 (mmp-170) REVERT: F 91 ILE cc_start: 0.7756 (OUTLIER) cc_final: 0.7290 (mt) REVERT: F 146 GLU cc_start: 0.6368 (pm20) cc_final: 0.6079 (mp0) REVERT: F 192 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.6317 (tp) REVERT: F 205 LYS cc_start: 0.6780 (mttt) cc_final: 0.6548 (mtmt) REVERT: G 21 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6917 (pp20) REVERT: G 43 ASP cc_start: 0.7049 (m-30) cc_final: 0.6557 (t0) REVERT: G 56 ASN cc_start: 0.8842 (m110) cc_final: 0.8574 (m-40) REVERT: G 112 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8396 (pt) REVERT: G 121 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7648 (mt) REVERT: G 170 THR cc_start: 0.7927 (p) cc_final: 0.7679 (p) REVERT: H 33 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: H 47 ARG cc_start: 0.8259 (ttm170) cc_final: 0.7972 (mtp180) REVERT: H 82 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: H 92 PHE cc_start: 0.8964 (m-80) cc_final: 0.8647 (m-80) REVERT: H 110 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8654 (tt0) REVERT: H 175 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8335 (tptm) REVERT: I 22 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.6536 (ptm160) REVERT: I 23 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8203 (ptpt) REVERT: I 25 ARG cc_start: 0.9561 (OUTLIER) cc_final: 0.9160 (mmm160) REVERT: I 32 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8515 (mm-40) REVERT: I 58 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8536 (mt) REVERT: I 61 GLU cc_start: 0.8026 (tt0) cc_final: 0.7809 (tt0) REVERT: I 77 ARG cc_start: 0.8751 (ttm110) cc_final: 0.8517 (ttm110) REVERT: I 95 THR cc_start: 0.9116 (m) cc_final: 0.8751 (m) REVERT: I 147 ARG cc_start: 0.6533 (mtt180) cc_final: 0.6129 (mtm180) REVERT: I 152 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7867 (ptpp) REVERT: I 158 ASP cc_start: 0.8256 (m-30) cc_final: 0.7885 (m-30) REVERT: I 159 SER cc_start: 0.8934 (m) cc_final: 0.8497 (t) REVERT: I 193 TYR cc_start: 0.8715 (m-80) cc_final: 0.8509 (m-80) REVERT: J 9 SER cc_start: 0.9415 (t) cc_final: 0.8971 (m) REVERT: J 29 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8042 (mttt) REVERT: J 53 ARG cc_start: 0.8526 (ttm110) cc_final: 0.8194 (mtm-85) REVERT: J 60 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8921 (mt) REVERT: J 94 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8536 (m-30) REVERT: J 106 GLU cc_start: 0.7981 (tp30) cc_final: 0.7575 (tm-30) REVERT: J 107 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8610 (tpt170) REVERT: J 153 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: J 157 ASP cc_start: 0.8232 (t70) cc_final: 0.7683 (t0) REVERT: K 1 MET cc_start: 0.3004 (mtt) cc_final: 0.2738 (mtt) REVERT: K 20 VAL cc_start: 0.8656 (t) cc_final: 0.8361 (m) REVERT: K 33 GLU cc_start: 0.7593 (tp30) cc_final: 0.7285 (tp30) REVERT: K 40 LEU cc_start: 0.7602 (pt) cc_final: 0.7273 (pt) REVERT: K 44 LYS cc_start: 0.7233 (mtmt) cc_final: 0.6980 (mmtt) REVERT: K 64 TYR cc_start: 0.7534 (m-80) cc_final: 0.6963 (m-80) REVERT: K 81 ASN cc_start: 0.5660 (m110) cc_final: 0.5363 (m-40) REVERT: L 8 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7599 (mp-120) REVERT: L 36 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.7404 (pmtt) REVERT: L 55 ASP cc_start: 0.7702 (t0) cc_final: 0.7464 (t0) REVERT: L 93 TYR cc_start: 0.9349 (t80) cc_final: 0.9038 (t80) REVERT: L 123 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8416 (m) REVERT: M 19 ASP cc_start: 0.5575 (OUTLIER) cc_final: 0.5116 (t0) REVERT: M 38 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6464 (pt) REVERT: N 3 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.8385 (mmp80) REVERT: N 9 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8768 (mttt) REVERT: N 20 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7998 (mpt90) REVERT: N 27 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.7597 (mtpp) REVERT: N 53 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8313 (mm) REVERT: N 78 ASN cc_start: 0.8724 (t0) cc_final: 0.8483 (t0) REVERT: N 115 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8987 (tp) REVERT: O 66 ASP cc_start: 0.8638 (t0) cc_final: 0.8336 (t0) REVERT: O 99 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7759 (mm-40) REVERT: O 124 ASP cc_start: 0.7180 (t70) cc_final: 0.6826 (t0) REVERT: P 35 LYS cc_start: 0.8017 (mmmm) cc_final: 0.7490 (pttt) REVERT: P 49 LEU cc_start: 0.6572 (mp) cc_final: 0.5536 (tp) REVERT: P 52 LYS cc_start: 0.6468 (tptm) cc_final: 0.6140 (tptm) REVERT: P 57 MET cc_start: 0.7012 (mmm) cc_final: 0.6810 (mmm) REVERT: P 89 MET cc_start: 0.5851 (ptp) cc_final: 0.5524 (pmm) REVERT: P 98 ASN cc_start: 0.6727 (t0) cc_final: 0.6492 (t0) REVERT: P 127 ARG cc_start: 0.6635 (pmm150) cc_final: 0.4329 (mmm-85) REVERT: Q 99 GLU cc_start: 0.8541 (tp30) cc_final: 0.8333 (mm-30) REVERT: Q 104 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7083 (tp30) REVERT: Q 122 ARG cc_start: 0.8603 (mtp180) cc_final: 0.8172 (mtm180) REVERT: Q 123 ARG cc_start: 0.8697 (ttm110) cc_final: 0.8249 (mmm-85) REVERT: R 33 ARG cc_start: 0.8715 (mmt90) cc_final: 0.8448 (mmt-90) REVERT: R 41 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7121 (pp) REVERT: R 58 MET cc_start: 0.7385 (mmm) cc_final: 0.6958 (mmt) REVERT: R 59 LYS cc_start: 0.8520 (mmmm) cc_final: 0.8229 (mtmt) REVERT: R 72 LYS cc_start: 0.7982 (pptt) cc_final: 0.7079 (mttp) REVERT: R 79 GLU cc_start: 0.6654 (mm-30) cc_final: 0.6002 (mm-30) REVERT: R 92 ASP cc_start: 0.8030 (t0) cc_final: 0.7697 (t0) REVERT: R 94 SER cc_start: 0.8928 (t) cc_final: 0.8407 (p) REVERT: R 104 THR cc_start: 0.8780 (p) cc_final: 0.8483 (p) REVERT: S 106 GLU cc_start: 0.6637 (pt0) cc_final: 0.5963 (pm20) REVERT: S 145 ARG cc_start: 0.1323 (OUTLIER) cc_final: -0.0400 (ptp-110) REVERT: T 17 ASN cc_start: 0.7418 (m-40) cc_final: 0.7055 (m-40) REVERT: T 21 PHE cc_start: 0.7482 (t80) cc_final: 0.7064 (t80) REVERT: T 24 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6766 (ptm160) REVERT: T 68 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7137 (mtm-85) REVERT: T 90 PRO cc_start: 0.8906 (Cg_exo) cc_final: 0.8631 (Cg_endo) REVERT: T 130 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7503 (mtt-85) REVERT: U 32 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7711 (tptm) REVERT: U 64 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8321 (mttm) REVERT: V 1 MET cc_start: 0.7129 (tpt) cc_final: 0.6846 (tpt) REVERT: V 7 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8109 (pm20) REVERT: V 21 ASN cc_start: 0.8957 (t0) cc_final: 0.8581 (t0) REVERT: V 53 TYR cc_start: 0.8796 (m-10) cc_final: 0.8480 (m-10) REVERT: V 87 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7389 (ttm-80) REVERT: W 26 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8836 (tp) REVERT: W 90 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8604 (p) REVERT: W 111 MET cc_start: 0.8759 (ptp) cc_final: 0.8531 (ptp) REVERT: X 16 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7926 (ttp80) REVERT: X 107 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8019 (t80) REVERT: Y 20 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.9070 (ptm160) REVERT: Y 26 ASP cc_start: 0.8938 (t0) cc_final: 0.8618 (t0) REVERT: Y 61 ARG cc_start: 0.8871 (mtp85) cc_final: 0.8641 (mtp-110) REVERT: Y 63 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8303 (tp-100) REVERT: Y 68 LYS cc_start: 0.8507 (mttt) cc_final: 0.8010 (mtpt) REVERT: Y 98 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8671 (mm-30) REVERT: Y 111 ARG cc_start: 0.8577 (ttm-80) cc_final: 0.8120 (ttp80) REVERT: Y 127 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8091 (ttpt) REVERT: Z 51 MET cc_start: 0.4956 (OUTLIER) cc_final: 0.4188 (mmm) REVERT: a 28 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7573 (ttp80) REVERT: a 38 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8633 (mmt-90) REVERT: b 17 ARG cc_start: 0.8449 (mtp-110) cc_final: 0.8120 (mtp85) REVERT: b 34 ASP cc_start: 0.7362 (m-30) cc_final: 0.7026 (m-30) REVERT: b 70 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8554 (ttmt) REVERT: c 27 GLN cc_start: 0.8154 (tt0) cc_final: 0.7460 (tp40) REVERT: d 20 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7600 (tm-30) REVERT: d 48 ASN cc_start: 0.8900 (m-40) cc_final: 0.8612 (m-40) REVERT: e 26 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8154 (mtmm) REVERT: e 31 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7904 (mptt) REVERT: g 7 MET cc_start: 0.7521 (tmm) cc_final: 0.7291 (tmm) REVERT: g 55 PHE cc_start: 0.5851 (OUTLIER) cc_final: 0.5342 (t80) REVERT: g 99 ASN cc_start: 0.8113 (t0) cc_final: 0.7836 (t0) REVERT: g 149 THR cc_start: 0.6233 (p) cc_final: 0.5926 (t) REVERT: g 151 TRP cc_start: 0.6516 (m100) cc_final: 0.5869 (m100) REVERT: g 295 HIS cc_start: 0.8437 (p-80) cc_final: 0.8005 (p90) REVERT: g 309 PHE cc_start: 0.7034 (m-80) cc_final: 0.6430 (m-80) REVERT: g 321 GLN cc_start: 0.5312 (OUTLIER) cc_final: 0.4850 (mt0) REVERT: i 41 MET cc_start: 0.6191 (mmp) cc_final: 0.5779 (mmm) REVERT: i 44 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7437 (p0) REVERT: j 62 PHE cc_start: 0.6928 (OUTLIER) cc_final: 0.5405 (p90) REVERT: j 73 GLU cc_start: 0.4870 (OUTLIER) cc_final: 0.3912 (pt0) REVERT: j 104 LYS cc_start: 0.5617 (OUTLIER) cc_final: 0.4884 (tptm) outliers start: 363 outliers final: 209 residues processed: 1137 average time/residue: 0.7855 time to fit residues: 1488.7396 Evaluate side-chains 1138 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 858 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 89 LYS Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 178 ARG Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 PHE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 186 PHE Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 153 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 123 SER Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 145 ARG Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 64 LYS Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 7 GLN Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 50 TYR Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain V residue 86 SER Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 56 LYS Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 20 ARG Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 63 GLN Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain Y residue 124 SER Chi-restraints excluded: chain Y residue 127 LYS Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain Z residue 65 LEU Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 36 ILE Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 54 SER Chi-restraints excluded: chain a residue 58 VAL Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 55 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain d residue 26 SER Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 55 PHE Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 292 GLN Chi-restraints excluded: chain g residue 293 ASP Chi-restraints excluded: chain g residue 321 GLN Chi-restraints excluded: chain h residue 16 LYS Chi-restraints excluded: chain i residue 44 ASN Chi-restraints excluded: chain i residue 58 MET Chi-restraints excluded: chain i residue 65 LEU Chi-restraints excluded: chain i residue 116 ASN Chi-restraints excluded: chain j residue 62 PHE Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain j residue 104 LYS Chi-restraints excluded: chain j residue 105 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 536 optimal weight: 0.6980 chunk 365 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 480 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 chunk 550 optimal weight: 2.9990 chunk 445 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 329 optimal weight: 10.0000 chunk 578 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 209 ASN ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN G 4 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 HIS P 114 HIS Q 83 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN T 12 GLN T 91 HIS ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN W 80 ASN Y 22 GLN ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 106 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 82907 Z= 0.240 Angle : 0.689 14.633 120536 Z= 0.344 Chirality : 0.040 0.420 15025 Planarity : 0.006 0.149 8760 Dihedral : 24.460 179.862 33255 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 1.31 % Allowed : 9.24 % Favored : 89.45 % Rotamer: Outliers : 8.13 % Allowed : 25.73 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.12), residues: 4976 helix: 1.88 (0.13), residues: 1572 sheet: -0.77 (0.17), residues: 873 loop : -2.30 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 61 HIS 0.007 0.001 HIS E 16 PHE 0.022 0.002 PHE R 71 TYR 0.018 0.002 TYR K 64 ARG 0.007 0.000 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 912 time to evaluate : 4.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8292 (tt0) cc_final: 0.7640 (tp-100) REVERT: A 33 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: A 38 TYR cc_start: 0.8585 (t80) cc_final: 0.8322 (t80) REVERT: A 88 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8470 (mmtp) REVERT: A 127 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7748 (ttm-80) REVERT: A 150 ASP cc_start: 0.7776 (t0) cc_final: 0.7143 (p0) REVERT: A 157 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7686 (m-30) REVERT: A 197 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7340 (mp) REVERT: B 89 ASP cc_start: 0.7993 (m-30) cc_final: 0.7564 (t0) REVERT: B 96 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8410 (pp) REVERT: B 105 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8212 (t80) REVERT: B 224 ASP cc_start: 0.7167 (t0) cc_final: 0.6869 (t0) REVERT: C 51 LYS cc_start: 0.8806 (ttmt) cc_final: 0.8394 (tttp) REVERT: C 86 MET cc_start: 0.8542 (mmm) cc_final: 0.8073 (mmm) REVERT: C 99 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: C 193 MET cc_start: 0.9127 (mmm) cc_final: 0.8892 (mmt) REVERT: C 248 TYR cc_start: 0.8704 (m-80) cc_final: 0.8454 (m-10) REVERT: D 14 ASP cc_start: 0.8337 (t0) cc_final: 0.8056 (t0) REVERT: D 17 PHE cc_start: 0.8119 (t80) cc_final: 0.7891 (t80) REVERT: D 72 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7736 (mm) REVERT: D 162 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7318 (tm-30) REVERT: E 19 MET cc_start: 0.8710 (mmm) cc_final: 0.8388 (mmm) REVERT: E 42 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8605 (tp) REVERT: E 60 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: E 127 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8329 (ttpp) REVERT: E 134 LYS cc_start: 0.8903 (mttt) cc_final: 0.8389 (mttp) REVERT: E 142 HIS cc_start: 0.6454 (OUTLIER) cc_final: 0.5616 (t70) REVERT: E 250 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6808 (tp30) REVERT: F 32 PRO cc_start: 0.6886 (Cg_exo) cc_final: 0.6412 (Cg_endo) REVERT: F 47 LYS cc_start: 0.5643 (OUTLIER) cc_final: 0.5238 (mmmt) REVERT: F 85 ARG cc_start: 0.7854 (mmt-90) cc_final: 0.7333 (mmp-170) REVERT: F 91 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7276 (mt) REVERT: F 165 SER cc_start: 0.8627 (t) cc_final: 0.8373 (p) REVERT: F 192 ILE cc_start: 0.6877 (OUTLIER) cc_final: 0.6290 (tp) REVERT: G 10 ASN cc_start: 0.7254 (OUTLIER) cc_final: 0.6191 (p0) REVERT: G 21 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6928 (pp20) REVERT: G 43 ASP cc_start: 0.7028 (m-30) cc_final: 0.6555 (t0) REVERT: G 56 ASN cc_start: 0.8769 (m110) cc_final: 0.8479 (m-40) REVERT: G 105 ASP cc_start: 0.8721 (p0) cc_final: 0.8506 (p0) REVERT: H 47 ARG cc_start: 0.8329 (ttm170) cc_final: 0.7962 (mtp180) REVERT: H 81 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7759 (mt) REVERT: H 82 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: H 92 PHE cc_start: 0.8918 (m-80) cc_final: 0.8642 (m-10) REVERT: H 110 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: H 175 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8376 (tptm) REVERT: I 22 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.6570 (ptm160) REVERT: I 25 ARG cc_start: 0.9544 (OUTLIER) cc_final: 0.9141 (mmm160) REVERT: I 58 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8492 (mt) REVERT: I 77 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8545 (ttm110) REVERT: I 92 ARG cc_start: 0.6818 (ttp-110) cc_final: 0.6406 (ttp80) REVERT: I 95 THR cc_start: 0.9151 (m) cc_final: 0.8788 (m) REVERT: I 114 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8144 (mt-10) REVERT: I 117 TYR cc_start: 0.8114 (m-80) cc_final: 0.7801 (m-80) REVERT: I 147 ARG cc_start: 0.6582 (mtt180) cc_final: 0.6196 (mtm180) REVERT: I 158 ASP cc_start: 0.8229 (m-30) cc_final: 0.7791 (m-30) REVERT: I 159 SER cc_start: 0.8923 (m) cc_final: 0.8482 (t) REVERT: J 9 SER cc_start: 0.9393 (t) cc_final: 0.8909 (m) REVERT: J 29 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8003 (mttt) REVERT: J 53 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8108 (mtm-85) REVERT: J 60 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8796 (mt) REVERT: J 94 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8539 (m-30) REVERT: J 106 GLU cc_start: 0.7989 (tp30) cc_final: 0.7527 (tm-30) REVERT: J 107 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8552 (tpt170) REVERT: J 157 ASP cc_start: 0.8166 (t70) cc_final: 0.7697 (t0) REVERT: J 174 ARG cc_start: 0.7664 (mtp-110) cc_final: 0.7356 (mtm-85) REVERT: K 33 GLU cc_start: 0.7571 (tp30) cc_final: 0.7251 (tp30) REVERT: K 40 LEU cc_start: 0.7560 (pt) cc_final: 0.7265 (pt) REVERT: K 44 LYS cc_start: 0.6978 (mtmt) cc_final: 0.6716 (mmtt) REVERT: K 64 TYR cc_start: 0.7471 (m-80) cc_final: 0.6800 (m-80) REVERT: K 79 TYR cc_start: 0.5721 (t80) cc_final: 0.5433 (t80) REVERT: K 81 ASN cc_start: 0.5553 (m110) cc_final: 0.5285 (m-40) REVERT: L 8 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7773 (mp-120) REVERT: L 36 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.7483 (pmtt) REVERT: L 93 TYR cc_start: 0.9322 (t80) cc_final: 0.9027 (t80) REVERT: L 123 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8334 (m) REVERT: M 19 ASP cc_start: 0.5621 (OUTLIER) cc_final: 0.5169 (t0) REVERT: M 38 LEU cc_start: 0.6846 (OUTLIER) cc_final: 0.6510 (pt) REVERT: N 3 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8243 (mmp80) REVERT: N 9 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8757 (mttt) REVERT: N 27 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7560 (mtpp) REVERT: N 53 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8312 (mm) REVERT: N 115 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9057 (tp) REVERT: O 66 ASP cc_start: 0.8652 (t0) cc_final: 0.8359 (t0) REVERT: O 72 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8157 (mmmt) REVERT: O 99 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7746 (mm-40) REVERT: O 124 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6851 (t0) REVERT: P 23 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.5877 (mp0) REVERT: P 49 LEU cc_start: 0.6686 (mp) cc_final: 0.5638 (tp) REVERT: P 89 MET cc_start: 0.5920 (ptp) cc_final: 0.5565 (pmm) REVERT: P 127 ARG cc_start: 0.6592 (pmm150) cc_final: 0.4387 (mmm-85) REVERT: Q 47 LYS cc_start: 0.8281 (mmpt) cc_final: 0.8031 (tppt) REVERT: Q 99 GLU cc_start: 0.8595 (tp30) cc_final: 0.8354 (mm-30) REVERT: Q 104 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7139 (tp30) REVERT: Q 122 ARG cc_start: 0.8637 (mtp180) cc_final: 0.8203 (mtm180) REVERT: Q 123 ARG cc_start: 0.8584 (ttm110) cc_final: 0.8158 (mmm-85) REVERT: R 17 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7484 (mt) REVERT: R 41 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7210 (pp) REVERT: R 58 MET cc_start: 0.7234 (mmm) cc_final: 0.6875 (mmt) REVERT: R 72 LYS cc_start: 0.7923 (pptt) cc_final: 0.7039 (mttp) REVERT: R 79 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6127 (mm-30) REVERT: R 92 ASP cc_start: 0.8032 (t0) cc_final: 0.7719 (t0) REVERT: R 94 SER cc_start: 0.8916 (t) cc_final: 0.8649 (p) REVERT: S 73 MET cc_start: 0.6673 (ptt) cc_final: 0.6365 (mmm) REVERT: S 101 LEU cc_start: 0.7994 (mt) cc_final: 0.7648 (mm) REVERT: S 106 GLU cc_start: 0.6460 (pt0) cc_final: 0.5846 (pm20) REVERT: S 145 ARG cc_start: 0.1410 (OUTLIER) cc_final: -0.0497 (ptp-110) REVERT: T 17 ASN cc_start: 0.7492 (m-40) cc_final: 0.7082 (m-40) REVERT: T 21 PHE cc_start: 0.7494 (t80) cc_final: 0.7082 (t80) REVERT: T 24 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6718 (ptm160) REVERT: T 68 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.6805 (mtm-85) REVERT: T 90 PRO cc_start: 0.8961 (Cg_exo) cc_final: 0.8751 (Cg_endo) REVERT: T 130 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7504 (mtt-85) REVERT: U 32 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7533 (tptm) REVERT: V 1 MET cc_start: 0.6928 (tpt) cc_final: 0.6715 (tpt) REVERT: V 21 ASN cc_start: 0.8927 (t0) cc_final: 0.8533 (t0) REVERT: V 53 TYR cc_start: 0.8816 (m-10) cc_final: 0.8465 (m-10) REVERT: V 87 ARG cc_start: 0.7817 (ttm110) cc_final: 0.7291 (ttm-80) REVERT: W 26 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8807 (tp) REVERT: W 90 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8584 (p) REVERT: X 16 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7875 (ttp80) REVERT: X 107 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8232 (t80) REVERT: X 137 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8365 (mttm) REVERT: Y 22 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8991 (mt0) REVERT: Y 26 ASP cc_start: 0.8972 (t0) cc_final: 0.8571 (t0) REVERT: Y 61 ARG cc_start: 0.8830 (mtp85) cc_final: 0.8615 (mtp-110) REVERT: Y 63 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8247 (tp-100) REVERT: Y 68 LYS cc_start: 0.8585 (mttt) cc_final: 0.8107 (mtpt) REVERT: Y 98 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8556 (mm-30) REVERT: Y 111 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8132 (ttp80) REVERT: Y 127 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7992 (tttp) REVERT: Z 51 MET cc_start: 0.4468 (OUTLIER) cc_final: 0.3848 (mmm) REVERT: a 28 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.7611 (ttp80) REVERT: a 38 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8576 (mmt-90) REVERT: b 34 ASP cc_start: 0.7432 (m-30) cc_final: 0.7115 (m-30) REVERT: b 70 LYS cc_start: 0.8717 (ttmt) cc_final: 0.8484 (ttmt) REVERT: c 27 GLN cc_start: 0.8135 (tt0) cc_final: 0.7477 (tp40) REVERT: d 20 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7826 (tm-30) REVERT: d 48 ASN cc_start: 0.8856 (m-40) cc_final: 0.8528 (m-40) REVERT: e 26 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8133 (mtmm) REVERT: e 31 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7856 (mptt) REVERT: g 55 PHE cc_start: 0.5677 (OUTLIER) cc_final: 0.5043 (t80) REVERT: g 99 ASN cc_start: 0.8144 (t0) cc_final: 0.7930 (t0) REVERT: g 258 TRP cc_start: 0.4746 (m100) cc_final: 0.4363 (m100) REVERT: g 309 PHE cc_start: 0.6950 (m-80) cc_final: 0.6264 (m-80) REVERT: g 321 GLN cc_start: 0.4435 (OUTLIER) cc_final: 0.3772 (mt0) REVERT: i 41 MET cc_start: 0.6217 (mmp) cc_final: 0.5863 (mmm) REVERT: j 73 GLU cc_start: 0.4887 (OUTLIER) cc_final: 0.4595 (pt0) REVERT: j 92 MET cc_start: 0.6241 (mmm) cc_final: 0.5300 (mtp) REVERT: j 104 LYS cc_start: 0.5590 (OUTLIER) cc_final: 0.4868 (tptm) outliers start: 348 outliers final: 217 residues processed: 1148 average time/residue: 0.7819 time to fit residues: 1498.7008 Evaluate side-chains 1129 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 850 time to evaluate : 4.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 82 GLU Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 87 PHE Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 123 SER Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 88 GLU Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain S residue 18 LEU Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 47 CYS Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 145 ARG Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 56 LYS Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 22 GLN Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 63 GLN Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain Y residue 124 SER Chi-restraints excluded: chain Y residue 127 LYS Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 54 SER Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain d residue 26 SER Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain f residue 142 CYS Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 55 PHE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 110 ASP Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 195 ILE Chi-restraints excluded: chain g residue 292 GLN Chi-restraints excluded: chain g residue 293 ASP Chi-restraints excluded: chain g residue 321 GLN Chi-restraints excluded: chain h residue 16 LYS Chi-restraints excluded: chain i residue 58 MET Chi-restraints excluded: chain i residue 116 ASN Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain j residue 104 LYS Chi-restraints excluded: chain j residue 105 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 216 optimal weight: 1.9990 chunk 580 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 378 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 645 optimal weight: 10.0000 chunk 535 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 213 optimal weight: 7.9990 chunk 338 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS Q 83 GLN S 89 GLN T 91 HIS W 80 ASN Y 22 GLN b 26 GLN ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 GLN ** g 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 82907 Z= 0.287 Angle : 0.707 14.724 120536 Z= 0.352 Chirality : 0.041 0.351 15025 Planarity : 0.006 0.150 8760 Dihedral : 24.383 179.858 33236 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 1.29 % Allowed : 9.47 % Favored : 89.25 % Rotamer: Outliers : 8.59 % Allowed : 25.52 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.12), residues: 4976 helix: 1.73 (0.13), residues: 1572 sheet: -0.80 (0.17), residues: 878 loop : -2.27 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 29 HIS 0.025 0.001 HIS T 91 PHE 0.024 0.002 PHE D 24 TYR 0.020 0.002 TYR a 59 ARG 0.008 0.000 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1214 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 846 time to evaluate : 4.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8309 (tt0) cc_final: 0.7674 (tp-100) REVERT: A 33 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: A 88 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8519 (mmtp) REVERT: A 127 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7799 (ttm-80) REVERT: A 150 ASP cc_start: 0.7787 (t0) cc_final: 0.7195 (p0) REVERT: A 157 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: A 197 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7543 (mp) REVERT: B 89 ASP cc_start: 0.8042 (m-30) cc_final: 0.7667 (t0) REVERT: B 96 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8339 (pp) REVERT: B 105 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8138 (t80) REVERT: B 207 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8093 (mp) REVERT: B 224 ASP cc_start: 0.7049 (t0) cc_final: 0.6800 (t0) REVERT: C 86 MET cc_start: 0.8640 (mmm) cc_final: 0.8169 (mmm) REVERT: C 99 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: C 193 MET cc_start: 0.9111 (mmm) cc_final: 0.8818 (mmt) REVERT: C 210 ARG cc_start: 0.8562 (mtm110) cc_final: 0.8342 (mtm180) REVERT: C 236 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7539 (pp20) REVERT: C 248 TYR cc_start: 0.8719 (m-80) cc_final: 0.8457 (m-10) REVERT: D 72 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7651 (mm) REVERT: D 104 SER cc_start: 0.7571 (p) cc_final: 0.7170 (p) REVERT: D 162 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7447 (tm-30) REVERT: D 170 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8619 (t) REVERT: D 217 VAL cc_start: 0.6099 (OUTLIER) cc_final: 0.5864 (t) REVERT: E 19 MET cc_start: 0.8762 (mmm) cc_final: 0.8203 (mmm) REVERT: E 60 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7486 (mm-30) REVERT: E 134 LYS cc_start: 0.8939 (mttt) cc_final: 0.8474 (mttp) REVERT: E 142 HIS cc_start: 0.6544 (OUTLIER) cc_final: 0.5693 (t70) REVERT: E 171 ASP cc_start: 0.8133 (t70) cc_final: 0.7808 (t70) REVERT: F 71 TYR cc_start: 0.7404 (m-80) cc_final: 0.6700 (m-10) REVERT: F 85 ARG cc_start: 0.7862 (mmt-90) cc_final: 0.7324 (mmp-170) REVERT: F 91 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7281 (mt) REVERT: F 192 ILE cc_start: 0.6900 (OUTLIER) cc_final: 0.6263 (tp) REVERT: G 21 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6944 (pp20) REVERT: G 43 ASP cc_start: 0.6862 (m-30) cc_final: 0.6442 (t0) REVERT: G 105 ASP cc_start: 0.8788 (p0) cc_final: 0.8475 (p0) REVERT: H 47 ARG cc_start: 0.8347 (ttm170) cc_final: 0.7968 (mtp180) REVERT: H 60 VAL cc_start: 0.9002 (m) cc_final: 0.8544 (p) REVERT: H 81 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7734 (mt) REVERT: H 92 PHE cc_start: 0.8895 (m-80) cc_final: 0.8552 (m-10) REVERT: H 110 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8570 (tt0) REVERT: H 175 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8370 (tptm) REVERT: I 22 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.6549 (ptm160) REVERT: I 25 ARG cc_start: 0.9539 (OUTLIER) cc_final: 0.9142 (mmm160) REVERT: I 58 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8578 (mt) REVERT: I 92 ARG cc_start: 0.6804 (ttp-110) cc_final: 0.6456 (ttp80) REVERT: I 95 THR cc_start: 0.9169 (m) cc_final: 0.8787 (m) REVERT: I 114 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8122 (mt-10) REVERT: I 147 ARG cc_start: 0.6626 (mtt180) cc_final: 0.6254 (mtm180) REVERT: I 152 LYS cc_start: 0.8319 (mmmt) cc_final: 0.7831 (ptpp) REVERT: I 158 ASP cc_start: 0.8259 (m-30) cc_final: 0.7902 (m-30) REVERT: I 159 SER cc_start: 0.8921 (m) cc_final: 0.8495 (t) REVERT: J 9 SER cc_start: 0.9364 (t) cc_final: 0.8893 (m) REVERT: J 29 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8040 (mttt) REVERT: J 53 ARG cc_start: 0.8498 (ttm110) cc_final: 0.7930 (mtm180) REVERT: J 60 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8819 (mt) REVERT: J 94 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8520 (m-30) REVERT: J 106 GLU cc_start: 0.7975 (tp30) cc_final: 0.7478 (tm-30) REVERT: J 107 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8564 (tpt170) REVERT: J 157 ASP cc_start: 0.8213 (t70) cc_final: 0.7734 (t0) REVERT: K 1 MET cc_start: 0.3051 (mtt) cc_final: 0.2277 (mtt) REVERT: K 33 GLU cc_start: 0.7902 (tp30) cc_final: 0.7561 (tp30) REVERT: K 40 LEU cc_start: 0.7657 (pt) cc_final: 0.7349 (pt) REVERT: K 44 LYS cc_start: 0.7003 (mtmt) cc_final: 0.6717 (mmtt) REVERT: K 64 TYR cc_start: 0.7384 (m-80) cc_final: 0.6636 (m-80) REVERT: K 79 TYR cc_start: 0.5697 (t80) cc_final: 0.5420 (t80) REVERT: K 81 ASN cc_start: 0.5633 (m110) cc_final: 0.5369 (m-40) REVERT: L 8 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7734 (mp-120) REVERT: L 36 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.7335 (pmtt) REVERT: L 93 TYR cc_start: 0.9317 (t80) cc_final: 0.8997 (t80) REVERT: L 123 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8284 (m) REVERT: M 19 ASP cc_start: 0.5583 (OUTLIER) cc_final: 0.5137 (t0) REVERT: M 38 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6528 (pt) REVERT: M 57 GLU cc_start: 0.6253 (mt-10) cc_final: 0.5485 (mp0) REVERT: M 116 ASN cc_start: 0.5108 (OUTLIER) cc_final: 0.4881 (p0) REVERT: N 3 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8265 (mmp80) REVERT: N 9 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8767 (mttt) REVERT: N 27 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7613 (mtpp) REVERT: N 53 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8316 (mm) REVERT: N 115 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8967 (tp) REVERT: O 66 ASP cc_start: 0.8690 (t0) cc_final: 0.8429 (t0) REVERT: O 72 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8204 (mmmt) REVERT: O 99 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7770 (mm-40) REVERT: O 124 ASP cc_start: 0.7104 (t70) cc_final: 0.6791 (t0) REVERT: P 23 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.5539 (mp0) REVERT: P 35 LYS cc_start: 0.8112 (mmmm) cc_final: 0.7406 (pttt) REVERT: P 49 LEU cc_start: 0.6580 (mp) cc_final: 0.5569 (tp) REVERT: P 57 MET cc_start: 0.6496 (mmm) cc_final: 0.6283 (mmm) REVERT: P 81 ARG cc_start: 0.5990 (ttt-90) cc_final: 0.5658 (ttt-90) REVERT: P 89 MET cc_start: 0.5686 (ptp) cc_final: 0.5326 (pmm) REVERT: P 127 ARG cc_start: 0.6216 (pmm150) cc_final: 0.4340 (mmm-85) REVERT: Q 47 LYS cc_start: 0.8299 (mmpt) cc_final: 0.8068 (tppt) REVERT: Q 104 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7138 (tp30) REVERT: Q 122 ARG cc_start: 0.8660 (mtp180) cc_final: 0.8263 (mtm180) REVERT: Q 123 ARG cc_start: 0.8540 (ttm110) cc_final: 0.8141 (mmm-85) REVERT: R 24 LEU cc_start: 0.8204 (tp) cc_final: 0.7979 (tt) REVERT: R 41 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7290 (pp) REVERT: R 72 LYS cc_start: 0.7973 (pptt) cc_final: 0.7117 (mttp) REVERT: R 79 GLU cc_start: 0.6568 (mm-30) cc_final: 0.6000 (mm-30) REVERT: R 92 ASP cc_start: 0.8076 (t0) cc_final: 0.7736 (t0) REVERT: R 94 SER cc_start: 0.8968 (t) cc_final: 0.8719 (p) REVERT: S 53 ASP cc_start: 0.5373 (OUTLIER) cc_final: 0.5035 (p0) REVERT: S 73 MET cc_start: 0.6627 (ptt) cc_final: 0.6298 (mmm) REVERT: S 101 LEU cc_start: 0.7937 (mt) cc_final: 0.7576 (mm) REVERT: S 106 GLU cc_start: 0.6377 (pt0) cc_final: 0.5737 (pm20) REVERT: S 145 ARG cc_start: 0.1552 (OUTLIER) cc_final: -0.0485 (ptp-110) REVERT: T 21 PHE cc_start: 0.7595 (t80) cc_final: 0.7212 (t80) REVERT: T 24 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6816 (ptm160) REVERT: T 68 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.6868 (mtm-85) REVERT: T 90 PRO cc_start: 0.8611 (Cg_exo) cc_final: 0.8391 (Cg_endo) REVERT: T 130 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7664 (mtp85) REVERT: U 85 ARG cc_start: 0.8689 (ptp-110) cc_final: 0.7892 (mtt-85) REVERT: V 1 MET cc_start: 0.6898 (tpt) cc_final: 0.6674 (tpt) REVERT: V 21 ASN cc_start: 0.8927 (t0) cc_final: 0.8475 (t0) REVERT: V 53 TYR cc_start: 0.8813 (m-10) cc_final: 0.8499 (m-10) REVERT: V 87 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7219 (ttm-80) REVERT: X 16 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7916 (ttp80) REVERT: X 89 ASN cc_start: 0.8338 (m-40) cc_final: 0.8122 (m110) REVERT: X 107 PHE cc_start: 0.9325 (OUTLIER) cc_final: 0.8250 (t80) REVERT: Y 26 ASP cc_start: 0.8985 (t0) cc_final: 0.8617 (t0) REVERT: Y 63 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8227 (tp-100) REVERT: Y 68 LYS cc_start: 0.8602 (mttt) cc_final: 0.8104 (mtpt) REVERT: Y 98 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8531 (mm-30) REVERT: Y 111 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8172 (ttp80) REVERT: Y 127 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8032 (tttp) REVERT: Z 51 MET cc_start: 0.4538 (OUTLIER) cc_final: 0.3854 (mmm) REVERT: a 15 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7741 (mtm-85) REVERT: a 28 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7615 (ttp80) REVERT: a 38 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8530 (mmt-90) REVERT: b 34 ASP cc_start: 0.7307 (m-30) cc_final: 0.6974 (m-30) REVERT: b 70 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8504 (ttmt) REVERT: c 27 GLN cc_start: 0.8212 (tt0) cc_final: 0.7553 (tp40) REVERT: c 38 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.5691 (mmm-85) REVERT: d 20 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7773 (tm-30) REVERT: d 34 TYR cc_start: 0.9161 (m-80) cc_final: 0.8778 (m-80) REVERT: d 48 ASN cc_start: 0.8851 (m-40) cc_final: 0.8493 (m-40) REVERT: e 26 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8149 (mtmm) REVERT: e 31 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7845 (mptt) REVERT: g 7 MET cc_start: 0.7160 (tmm) cc_final: 0.6067 (mmm) REVERT: g 55 PHE cc_start: 0.5899 (OUTLIER) cc_final: 0.5123 (t80) REVERT: g 239 MET cc_start: 0.5679 (ptp) cc_final: 0.5458 (ptt) REVERT: g 258 TRP cc_start: 0.4680 (m100) cc_final: 0.4352 (m100) REVERT: g 321 GLN cc_start: 0.4510 (OUTLIER) cc_final: 0.3862 (mt0) REVERT: i 41 MET cc_start: 0.6308 (mmp) cc_final: 0.6092 (mmm) REVERT: i 58 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6918 (tmm) REVERT: j 73 GLU cc_start: 0.4812 (OUTLIER) cc_final: 0.4588 (pt0) REVERT: j 74 MET cc_start: 0.4915 (mmm) cc_final: 0.3883 (mtm) REVERT: j 92 MET cc_start: 0.6061 (mmm) cc_final: 0.5164 (mtp) REVERT: j 104 LYS cc_start: 0.5596 (OUTLIER) cc_final: 0.4850 (tptm) outliers start: 368 outliers final: 244 residues processed: 1091 average time/residue: 0.7818 time to fit residues: 1427.9472 Evaluate side-chains 1130 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 825 time to evaluate : 4.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 87 ASP Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 115 SER Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 10 LYS Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 87 PHE Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 104 HIS Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 123 VAL Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 99 GLN Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain P residue 12 PHE Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 124 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 106 LYS Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain S residue 18 LEU Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 53 ASP Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 145 ARG Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 69 LEU Chi-restraints excluded: chain W residue 75 ILE Chi-restraints excluded: chain W residue 90 THR Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 56 LYS Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 63 GLN Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain Y residue 124 SER Chi-restraints excluded: chain Y residue 127 LYS Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain a residue 15 ARG Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 54 SER Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 9 HIS Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 55 THR Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 38 ARG Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain d residue 26 SER Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 55 PHE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 110 ASP Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 275 GLU Chi-restraints excluded: chain g residue 279 ASP Chi-restraints excluded: chain g residue 292 GLN Chi-restraints excluded: chain g residue 293 ASP Chi-restraints excluded: chain g residue 321 GLN Chi-restraints excluded: chain h residue 16 LYS Chi-restraints excluded: chain i residue 44 ASN Chi-restraints excluded: chain i residue 58 MET Chi-restraints excluded: chain i residue 65 LEU Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 116 ASN Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain j residue 104 LYS Chi-restraints excluded: chain j residue 105 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 622 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 chunk 471 optimal weight: 2.9990 chunk 365 optimal weight: 7.9990 chunk 543 optimal weight: 2.9990 chunk 360 optimal weight: 9.9990 chunk 642 optimal weight: 0.6980 chunk 402 optimal weight: 0.6980 chunk 391 optimal weight: 1.9990 chunk 296 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN N 21 ASN ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 ASN P 114 HIS Q 83 GLN Q 139 GLN R 56 HIS S 89 GLN T 91 HIS Y 22 GLN b 26 GLN ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 82907 Z= 0.190 Angle : 0.653 14.385 120536 Z= 0.325 Chirality : 0.038 0.323 15025 Planarity : 0.005 0.148 8760 Dihedral : 24.282 179.957 33230 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 1.19 % Allowed : 9.12 % Favored : 89.69 % Rotamer: Outliers : 7.07 % Allowed : 26.76 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.12), residues: 4976 helix: 1.88 (0.13), residues: 1561 sheet: -0.69 (0.17), residues: 881 loop : -2.17 (0.12), residues: 2534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 112 HIS 0.038 0.001 HIS T 91 PHE 0.023 0.002 PHE R 71 TYR 0.017 0.001 TYR T 66 ARG 0.009 0.000 ARG T 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 904 time to evaluate : 4.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8249 (tt0) cc_final: 0.7621 (tp-100) REVERT: A 18 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7936 (mm) REVERT: A 33 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: A 71 GLU cc_start: 0.7948 (pm20) cc_final: 0.7744 (pm20) REVERT: A 88 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8426 (mmtp) REVERT: A 127 ARG cc_start: 0.8237 (ttm170) cc_final: 0.7821 (ttm-80) REVERT: A 150 ASP cc_start: 0.7574 (t0) cc_final: 0.7080 (p0) REVERT: A 157 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: B 89 ASP cc_start: 0.7984 (m-30) cc_final: 0.7661 (t0) REVERT: B 96 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8332 (pp) REVERT: B 105 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8155 (t80) REVERT: B 224 ASP cc_start: 0.6771 (t0) cc_final: 0.6368 (t0) REVERT: C 51 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8406 (tttp) REVERT: C 86 MET cc_start: 0.8452 (mmm) cc_final: 0.7795 (mmm) REVERT: C 99 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: C 193 MET cc_start: 0.9097 (mmm) cc_final: 0.8892 (mmt) REVERT: C 194 GLN cc_start: 0.8664 (mt0) cc_final: 0.8350 (mt0) REVERT: C 248 TYR cc_start: 0.8676 (m-80) cc_final: 0.8414 (m-10) REVERT: D 17 PHE cc_start: 0.8086 (t80) cc_final: 0.7684 (t80) REVERT: D 38 GLU cc_start: 0.8039 (tt0) cc_final: 0.7762 (tt0) REVERT: D 72 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7505 (mm) REVERT: D 159 HIS cc_start: 0.8882 (m-70) cc_final: 0.8656 (m170) REVERT: D 162 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7350 (tm-30) REVERT: D 170 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8598 (t) REVERT: E 19 MET cc_start: 0.8621 (mmm) cc_final: 0.8311 (mmm) REVERT: E 77 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8641 (mmt180) REVERT: E 97 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7931 (mt-10) REVERT: E 134 LYS cc_start: 0.8931 (mttt) cc_final: 0.8446 (mttt) REVERT: E 142 HIS cc_start: 0.6365 (OUTLIER) cc_final: 0.5506 (t70) REVERT: E 171 ASP cc_start: 0.8124 (t70) cc_final: 0.7778 (t70) REVERT: E 174 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8367 (mmmm) REVERT: E 250 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6770 (tp30) REVERT: F 85 ARG cc_start: 0.7703 (mmt-90) cc_final: 0.7193 (mmp-170) REVERT: F 91 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7493 (mt) REVERT: F 165 SER cc_start: 0.8600 (t) cc_final: 0.8379 (p) REVERT: F 192 ILE cc_start: 0.6765 (OUTLIER) cc_final: 0.6131 (tp) REVERT: G 15 CYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7705 (t) REVERT: G 21 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6947 (pp20) REVERT: G 43 ASP cc_start: 0.6924 (m-30) cc_final: 0.6545 (t0) REVERT: G 56 ASN cc_start: 0.8582 (m110) cc_final: 0.7997 (m-40) REVERT: G 105 ASP cc_start: 0.8479 (p0) cc_final: 0.8153 (p0) REVERT: H 47 ARG cc_start: 0.8342 (ttm170) cc_final: 0.8005 (mtp180) REVERT: H 60 VAL cc_start: 0.8937 (m) cc_final: 0.8604 (p) REVERT: H 81 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7732 (mt) REVERT: H 92 PHE cc_start: 0.8909 (m-80) cc_final: 0.8602 (m-10) REVERT: H 110 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: H 175 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8367 (tptm) REVERT: I 22 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.6497 (ptm160) REVERT: I 58 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8457 (mt) REVERT: I 92 ARG cc_start: 0.6741 (ttp-110) cc_final: 0.6446 (ttp80) REVERT: I 95 THR cc_start: 0.9131 (m) cc_final: 0.8771 (m) REVERT: I 147 ARG cc_start: 0.6602 (mtt180) cc_final: 0.6224 (mtm180) REVERT: I 152 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7873 (mmmm) REVERT: I 158 ASP cc_start: 0.8223 (m-30) cc_final: 0.7787 (m-30) REVERT: I 159 SER cc_start: 0.8902 (m) cc_final: 0.8439 (t) REVERT: J 9 SER cc_start: 0.9281 (t) cc_final: 0.8881 (m) REVERT: J 29 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8009 (mttt) REVERT: J 53 ARG cc_start: 0.8351 (ttm110) cc_final: 0.7815 (mtm180) REVERT: J 60 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8811 (mt) REVERT: J 106 GLU cc_start: 0.7863 (tp30) cc_final: 0.7308 (tm-30) REVERT: J 107 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8559 (tpt170) REVERT: J 157 ASP cc_start: 0.8156 (t70) cc_final: 0.7661 (t0) REVERT: K 1 MET cc_start: 0.2789 (mtt) cc_final: 0.2403 (mtt) REVERT: K 33 GLU cc_start: 0.7781 (tp30) cc_final: 0.7517 (tp30) REVERT: K 40 LEU cc_start: 0.7609 (pt) cc_final: 0.7316 (pt) REVERT: K 44 LYS cc_start: 0.6800 (mtmt) cc_final: 0.6488 (mmtt) REVERT: K 64 TYR cc_start: 0.7308 (m-80) cc_final: 0.6513 (m-80) REVERT: K 79 TYR cc_start: 0.5569 (t80) cc_final: 0.5285 (t80) REVERT: K 81 ASN cc_start: 0.5814 (m110) cc_final: 0.5542 (m-40) REVERT: L 8 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7542 (mp-120) REVERT: L 36 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.7386 (pmtt) REVERT: L 93 TYR cc_start: 0.9297 (t80) cc_final: 0.9017 (t80) REVERT: M 19 ASP cc_start: 0.5760 (OUTLIER) cc_final: 0.5368 (t0) REVERT: M 57 GLU cc_start: 0.6104 (mt-10) cc_final: 0.5503 (mp0) REVERT: N 3 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8156 (mmp80) REVERT: N 9 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8718 (mttt) REVERT: N 27 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7663 (mtpp) REVERT: N 53 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8259 (mm) REVERT: N 115 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9006 (tp) REVERT: O 66 ASP cc_start: 0.8647 (t0) cc_final: 0.8404 (t0) REVERT: O 124 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6779 (t0) REVERT: P 23 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.5413 (mp0) REVERT: P 35 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7417 (pttt) REVERT: P 49 LEU cc_start: 0.6658 (mp) cc_final: 0.5630 (tp) REVERT: P 52 LYS cc_start: 0.6190 (tptm) cc_final: 0.5932 (tptm) REVERT: P 89 MET cc_start: 0.5610 (ptp) cc_final: 0.5321 (pmm) REVERT: P 127 ARG cc_start: 0.6153 (pmm150) cc_final: 0.4236 (mmm-85) REVERT: Q 104 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7104 (tp30) REVERT: Q 122 ARG cc_start: 0.8622 (mtp180) cc_final: 0.8170 (mtm180) REVERT: Q 123 ARG cc_start: 0.8513 (ttm110) cc_final: 0.8135 (mmm-85) REVERT: R 24 LEU cc_start: 0.8288 (tp) cc_final: 0.8063 (tt) REVERT: R 41 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7284 (pp) REVERT: R 72 LYS cc_start: 0.7931 (pptt) cc_final: 0.7075 (mttp) REVERT: R 79 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6244 (mm-30) REVERT: R 92 ASP cc_start: 0.8083 (t0) cc_final: 0.7818 (t70) REVERT: R 94 SER cc_start: 0.8957 (t) cc_final: 0.8714 (p) REVERT: S 54 LEU cc_start: 0.5893 (mm) cc_final: 0.5534 (mt) REVERT: S 73 MET cc_start: 0.6693 (ptt) cc_final: 0.6423 (mmm) REVERT: S 101 LEU cc_start: 0.7887 (mt) cc_final: 0.7469 (mm) REVERT: S 145 ARG cc_start: 0.1612 (OUTLIER) cc_final: -0.0519 (ptp-110) REVERT: T 13 ASP cc_start: 0.8106 (m-30) cc_final: 0.7859 (t0) REVERT: T 21 PHE cc_start: 0.7621 (t80) cc_final: 0.7229 (t80) REVERT: T 24 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6842 (ptm160) REVERT: T 68 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.6483 (mtm-85) REVERT: T 115 GLU cc_start: 0.7437 (pt0) cc_final: 0.6490 (pm20) REVERT: T 130 ARG cc_start: 0.7885 (mtp180) cc_final: 0.7644 (mtp85) REVERT: U 85 ARG cc_start: 0.8656 (ptp-110) cc_final: 0.7932 (mtt-85) REVERT: U 113 ASP cc_start: 0.7043 (t0) cc_final: 0.6777 (t0) REVERT: V 21 ASN cc_start: 0.8932 (t0) cc_final: 0.8459 (t0) REVERT: V 53 TYR cc_start: 0.8799 (m-10) cc_final: 0.8443 (m-10) REVERT: V 87 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7423 (ttm-80) REVERT: W 26 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8759 (tp) REVERT: W 90 THR cc_start: 0.8912 (m) cc_final: 0.8476 (p) REVERT: X 56 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7545 (mtpt) REVERT: X 89 ASN cc_start: 0.8154 (m-40) cc_final: 0.7795 (m-40) REVERT: X 107 PHE cc_start: 0.9321 (OUTLIER) cc_final: 0.8290 (t80) REVERT: X 137 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8364 (mttm) REVERT: Y 26 ASP cc_start: 0.8897 (t0) cc_final: 0.8523 (t0) REVERT: Y 63 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8281 (tp40) REVERT: Y 68 LYS cc_start: 0.8597 (mttt) cc_final: 0.8096 (mtpt) REVERT: Y 98 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8530 (mm-30) REVERT: Y 111 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8158 (ttp80) REVERT: Y 127 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8004 (tttp) REVERT: Z 51 MET cc_start: 0.4434 (OUTLIER) cc_final: 0.3717 (mmm) REVERT: a 28 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7491 (ttp80) REVERT: a 38 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8746 (mmt-90) REVERT: b 34 ASP cc_start: 0.7387 (m-30) cc_final: 0.7102 (m-30) REVERT: b 70 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8428 (ttmt) REVERT: c 27 GLN cc_start: 0.8260 (tt0) cc_final: 0.7562 (tp40) REVERT: c 32 PHE cc_start: 0.3906 (OUTLIER) cc_final: 0.3704 (p90) REVERT: d 14 PHE cc_start: 0.7640 (p90) cc_final: 0.7298 (p90) REVERT: d 20 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7905 (tm-30) REVERT: d 34 TYR cc_start: 0.9154 (m-80) cc_final: 0.8839 (m-80) REVERT: d 48 ASN cc_start: 0.8858 (m-40) cc_final: 0.8511 (m-40) REVERT: e 26 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8116 (mtmm) REVERT: e 31 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7806 (mptt) REVERT: g 7 MET cc_start: 0.7196 (tmm) cc_final: 0.5936 (mmm) REVERT: g 55 PHE cc_start: 0.5867 (OUTLIER) cc_final: 0.5027 (t80) REVERT: g 69 VAL cc_start: 0.8000 (t) cc_final: 0.7733 (p) REVERT: g 239 MET cc_start: 0.6119 (ptp) cc_final: 0.5894 (ptt) REVERT: g 258 TRP cc_start: 0.4507 (m100) cc_final: 0.4303 (m100) REVERT: g 275 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.5214 (pt0) REVERT: g 279 ASP cc_start: 0.3534 (m-30) cc_final: 0.1358 (t0) REVERT: g 295 HIS cc_start: 0.8661 (p90) cc_final: 0.8102 (p90) REVERT: g 321 GLN cc_start: 0.4745 (OUTLIER) cc_final: 0.4164 (mt0) REVERT: i 41 MET cc_start: 0.6119 (mmp) cc_final: 0.5889 (mmm) REVERT: i 58 MET cc_start: 0.7492 (ttt) cc_final: 0.6927 (tmm) REVERT: j 74 MET cc_start: 0.4908 (mmm) cc_final: 0.3837 (mtm) REVERT: j 92 MET cc_start: 0.6046 (mmm) cc_final: 0.5447 (mtm) REVERT: j 104 LYS cc_start: 0.5576 (OUTLIER) cc_final: 0.4867 (tptm) outliers start: 303 outliers final: 189 residues processed: 1100 average time/residue: 0.7693 time to fit residues: 1427.0627 Evaluate side-chains 1091 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 850 time to evaluate : 4.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 208 GLN Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 87 PHE Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 104 HIS Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain P residue 12 PHE Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain Q residue 139 GLN Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 145 ARG Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 80 LYS Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 56 LYS Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 63 GLN Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain Y residue 124 SER Chi-restraints excluded: chain Y residue 127 LYS Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain d residue 26 SER Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain f residue 142 CYS Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 55 PHE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 110 ASP Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 195 ILE Chi-restraints excluded: chain g residue 275 GLU Chi-restraints excluded: chain g residue 292 GLN Chi-restraints excluded: chain g residue 293 ASP Chi-restraints excluded: chain g residue 321 GLN Chi-restraints excluded: chain h residue 16 LYS Chi-restraints excluded: chain i residue 44 ASN Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 116 ASN Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain j residue 104 LYS Chi-restraints excluded: chain j residue 105 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 397 optimal weight: 8.9990 chunk 256 optimal weight: 9.9990 chunk 383 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 408 optimal weight: 0.9990 chunk 437 optimal weight: 0.5980 chunk 317 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 505 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN M 116 ASN ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 ASN P 114 HIS Q 83 GLN ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN T 91 HIS b 26 GLN ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 82907 Z= 0.229 Angle : 0.668 15.437 120536 Z= 0.331 Chirality : 0.039 0.299 15025 Planarity : 0.006 0.147 8760 Dihedral : 24.193 179.889 33204 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 1.19 % Allowed : 9.26 % Favored : 89.55 % Rotamer: Outliers : 7.26 % Allowed : 27.13 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.12), residues: 4976 helix: 1.84 (0.13), residues: 1560 sheet: -0.64 (0.17), residues: 869 loop : -2.12 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 29 HIS 0.020 0.001 HIS T 91 PHE 0.026 0.002 PHE D 77 TYR 0.022 0.002 TYR T 66 ARG 0.008 0.000 ARG J 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 863 time to evaluate : 4.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8262 (tt0) cc_final: 0.7636 (tp-100) REVERT: A 18 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7959 (mm) REVERT: A 33 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: A 39 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7950 (mmmm) REVERT: A 88 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8458 (mmtp) REVERT: A 127 ARG cc_start: 0.8242 (ttm170) cc_final: 0.7795 (ttm170) REVERT: A 150 ASP cc_start: 0.7669 (t0) cc_final: 0.7121 (p0) REVERT: A 157 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7667 (m-30) REVERT: A 197 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7451 (mp) REVERT: B 82 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7767 (ttp-110) REVERT: B 89 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7674 (t0) REVERT: B 96 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8272 (pp) REVERT: B 105 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8046 (t80) REVERT: B 224 ASP cc_start: 0.6745 (t0) cc_final: 0.6320 (t0) REVERT: C 51 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8492 (tttp) REVERT: C 86 MET cc_start: 0.8541 (mmm) cc_final: 0.7791 (mmm) REVERT: C 99 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7988 (pt0) REVERT: C 141 VAL cc_start: 0.8848 (t) cc_final: 0.8552 (t) REVERT: C 193 MET cc_start: 0.9098 (mmm) cc_final: 0.8824 (mmt) REVERT: C 248 TYR cc_start: 0.8685 (m-80) cc_final: 0.8424 (m-10) REVERT: D 38 GLU cc_start: 0.8092 (tt0) cc_final: 0.7826 (tt0) REVERT: D 72 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7681 (mm) REVERT: D 162 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7434 (tm-30) REVERT: D 170 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8583 (t) REVERT: D 217 VAL cc_start: 0.5956 (OUTLIER) cc_final: 0.5752 (t) REVERT: E 19 MET cc_start: 0.8665 (mmm) cc_final: 0.8203 (mmm) REVERT: E 77 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8683 (mmt180) REVERT: E 97 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7952 (mt-10) REVERT: E 134 LYS cc_start: 0.8942 (mttt) cc_final: 0.8406 (mttp) REVERT: E 142 HIS cc_start: 0.6419 (OUTLIER) cc_final: 0.5590 (t70) REVERT: E 171 ASP cc_start: 0.8188 (t70) cc_final: 0.7809 (t70) REVERT: E 174 LYS cc_start: 0.8676 (mmtt) cc_final: 0.8354 (mmmm) REVERT: E 250 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6826 (tp30) REVERT: F 85 ARG cc_start: 0.7805 (mmt-90) cc_final: 0.7274 (mmp-170) REVERT: F 91 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7696 (mt) REVERT: F 100 MET cc_start: 0.8195 (mtp) cc_final: 0.7981 (ttm) REVERT: F 165 SER cc_start: 0.8592 (t) cc_final: 0.8380 (p) REVERT: F 192 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.6151 (tp) REVERT: G 15 CYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7594 (t) REVERT: G 43 ASP cc_start: 0.6927 (m-30) cc_final: 0.6561 (t0) REVERT: G 56 ASN cc_start: 0.8547 (m110) cc_final: 0.8102 (m-40) REVERT: G 105 ASP cc_start: 0.8452 (p0) cc_final: 0.8029 (p0) REVERT: H 47 ARG cc_start: 0.8343 (ttm170) cc_final: 0.8019 (mtp180) REVERT: H 81 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7768 (mt) REVERT: H 110 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: H 175 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8368 (tptm) REVERT: I 22 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.6517 (ptm160) REVERT: I 25 ARG cc_start: 0.9514 (OUTLIER) cc_final: 0.9127 (mmm160) REVERT: I 58 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8490 (mt) REVERT: I 92 ARG cc_start: 0.6764 (ttp-110) cc_final: 0.6459 (ttp80) REVERT: I 95 THR cc_start: 0.9085 (m) cc_final: 0.8697 (m) REVERT: I 114 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8098 (mt-10) REVERT: I 116 HIS cc_start: 0.8760 (t-90) cc_final: 0.8196 (t-90) REVERT: I 147 ARG cc_start: 0.6569 (mtt180) cc_final: 0.6151 (mtt180) REVERT: I 152 LYS cc_start: 0.8298 (mmmt) cc_final: 0.7880 (mmmm) REVERT: I 158 ASP cc_start: 0.8228 (m-30) cc_final: 0.7870 (m-30) REVERT: I 159 SER cc_start: 0.8915 (m) cc_final: 0.8477 (t) REVERT: J 9 SER cc_start: 0.9309 (t) cc_final: 0.8874 (m) REVERT: J 29 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8026 (mttt) REVERT: J 53 ARG cc_start: 0.8402 (ttm110) cc_final: 0.7807 (mtm180) REVERT: J 106 GLU cc_start: 0.7905 (tp30) cc_final: 0.7346 (tm-30) REVERT: J 107 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8536 (tpt170) REVERT: J 157 ASP cc_start: 0.8183 (t70) cc_final: 0.7703 (t0) REVERT: K 1 MET cc_start: 0.2960 (mtt) cc_final: 0.2357 (mtt) REVERT: K 40 LEU cc_start: 0.7657 (pt) cc_final: 0.7355 (pt) REVERT: K 44 LYS cc_start: 0.7053 (mtmt) cc_final: 0.6657 (mmtt) REVERT: K 46 LEU cc_start: 0.7845 (mm) cc_final: 0.7440 (mm) REVERT: K 64 TYR cc_start: 0.7301 (m-80) cc_final: 0.6547 (m-80) REVERT: K 79 TYR cc_start: 0.5619 (t80) cc_final: 0.5330 (t80) REVERT: K 81 ASN cc_start: 0.5783 (m110) cc_final: 0.5515 (m-40) REVERT: L 8 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7561 (mp-120) REVERT: L 36 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.7378 (pmtt) REVERT: L 93 TYR cc_start: 0.9296 (t80) cc_final: 0.9016 (t80) REVERT: M 19 ASP cc_start: 0.5778 (OUTLIER) cc_final: 0.5381 (t0) REVERT: N 3 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8238 (mmp80) REVERT: N 27 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7681 (mtpp) REVERT: N 53 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8275 (mm) REVERT: N 115 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9038 (tp) REVERT: O 66 ASP cc_start: 0.8702 (t0) cc_final: 0.8449 (t0) REVERT: O 72 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8315 (mmmt) REVERT: O 124 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6738 (t0) REVERT: P 23 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.5390 (mp0) REVERT: P 35 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7419 (pttt) REVERT: P 89 MET cc_start: 0.5580 (ptp) cc_final: 0.5265 (pmm) REVERT: P 90 ILE cc_start: 0.7373 (mm) cc_final: 0.7091 (mm) REVERT: P 127 ARG cc_start: 0.6190 (pmm150) cc_final: 0.4266 (mmm-85) REVERT: Q 68 LYS cc_start: 0.7562 (ttmp) cc_final: 0.7275 (tttt) REVERT: Q 104 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7033 (tp30) REVERT: Q 122 ARG cc_start: 0.8646 (mtp180) cc_final: 0.8263 (mtm180) REVERT: Q 123 ARG cc_start: 0.8479 (ttm110) cc_final: 0.8114 (mmm-85) REVERT: R 24 LEU cc_start: 0.8337 (tp) cc_final: 0.8033 (tt) REVERT: R 41 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7241 (pp) REVERT: R 72 LYS cc_start: 0.7859 (pptt) cc_final: 0.6983 (mttp) REVERT: R 79 GLU cc_start: 0.6497 (mm-30) cc_final: 0.5963 (mm-30) REVERT: R 92 ASP cc_start: 0.8151 (t0) cc_final: 0.7916 (t70) REVERT: R 94 SER cc_start: 0.8916 (t) cc_final: 0.8477 (p) REVERT: S 54 LEU cc_start: 0.5906 (mm) cc_final: 0.5544 (mt) REVERT: S 101 LEU cc_start: 0.7912 (mt) cc_final: 0.7475 (mm) REVERT: S 106 GLU cc_start: 0.8256 (tp30) cc_final: 0.7375 (pt0) REVERT: S 145 ARG cc_start: 0.1558 (OUTLIER) cc_final: -0.0456 (ptp-110) REVERT: T 13 ASP cc_start: 0.8106 (m-30) cc_final: 0.7849 (t0) REVERT: T 21 PHE cc_start: 0.7644 (t80) cc_final: 0.7260 (t80) REVERT: T 24 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6835 (ptm160) REVERT: T 29 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6283 (tm-30) REVERT: T 115 GLU cc_start: 0.7490 (pt0) cc_final: 0.6658 (pm20) REVERT: T 130 ARG cc_start: 0.7884 (mtp180) cc_final: 0.7630 (mtp85) REVERT: U 85 ARG cc_start: 0.8661 (ptp-110) cc_final: 0.7904 (mtt-85) REVERT: V 21 ASN cc_start: 0.8948 (t0) cc_final: 0.8477 (t0) REVERT: V 53 TYR cc_start: 0.8778 (m-10) cc_final: 0.8456 (m-10) REVERT: V 69 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8831 (tm) REVERT: V 87 ARG cc_start: 0.7779 (ttm110) cc_final: 0.7368 (ttm-80) REVERT: W 90 THR cc_start: 0.8927 (m) cc_final: 0.8455 (p) REVERT: W 111 MET cc_start: 0.8619 (ptp) cc_final: 0.8355 (ptp) REVERT: X 16 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7868 (ttp80) REVERT: X 89 ASN cc_start: 0.8251 (m-40) cc_final: 0.7833 (m-40) REVERT: X 107 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8378 (t80) REVERT: Y 26 ASP cc_start: 0.8978 (t0) cc_final: 0.8531 (t0) REVERT: Y 63 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8244 (tp40) REVERT: Y 68 LYS cc_start: 0.8604 (mttt) cc_final: 0.8142 (mtpt) REVERT: Y 98 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8520 (mm-30) REVERT: Y 111 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.8173 (ttp80) REVERT: Y 127 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7996 (tttp) REVERT: Z 51 MET cc_start: 0.4478 (OUTLIER) cc_final: 0.3730 (mtm) REVERT: a 38 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8707 (mpt180) REVERT: b 34 ASP cc_start: 0.7383 (m-30) cc_final: 0.7085 (m-30) REVERT: b 70 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8460 (ttmt) REVERT: c 27 GLN cc_start: 0.8422 (tt0) cc_final: 0.7767 (tp40) REVERT: c 32 PHE cc_start: 0.3961 (OUTLIER) cc_final: 0.3396 (p90) REVERT: d 14 PHE cc_start: 0.7672 (p90) cc_final: 0.7335 (p90) REVERT: d 20 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7868 (tm-30) REVERT: d 34 TYR cc_start: 0.9149 (m-80) cc_final: 0.8837 (m-80) REVERT: d 48 ASN cc_start: 0.8860 (m-40) cc_final: 0.8507 (m-40) REVERT: e 26 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8073 (mtmm) REVERT: e 31 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7793 (mptt) REVERT: g 7 MET cc_start: 0.7560 (tmm) cc_final: 0.6208 (mmm) REVERT: g 55 PHE cc_start: 0.5869 (OUTLIER) cc_final: 0.4956 (t80) REVERT: g 69 VAL cc_start: 0.7996 (t) cc_final: 0.7726 (p) REVERT: g 258 TRP cc_start: 0.4487 (m100) cc_final: 0.4276 (m100) REVERT: g 295 HIS cc_start: 0.8637 (p90) cc_final: 0.8138 (p90) REVERT: g 309 PHE cc_start: 0.6888 (m-80) cc_final: 0.6160 (m-80) REVERT: g 321 GLN cc_start: 0.4988 (OUTLIER) cc_final: 0.4331 (mt0) REVERT: i 44 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.7029 (m-40) REVERT: i 58 MET cc_start: 0.7672 (ttt) cc_final: 0.7100 (tmm) REVERT: j 74 MET cc_start: 0.4929 (mmm) cc_final: 0.3863 (mtm) REVERT: j 92 MET cc_start: 0.5993 (mmm) cc_final: 0.5378 (mtm) REVERT: j 104 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.4867 (tptm) outliers start: 311 outliers final: 224 residues processed: 1073 average time/residue: 0.7685 time to fit residues: 1378.9882 Evaluate side-chains 1111 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 835 time to evaluate : 4.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 43 PHE Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 87 PHE Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 104 HIS Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain O residue 124 ASP Chi-restraints excluded: chain P residue 12 PHE Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 141 SER Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 17 ILE Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 145 ARG Chi-restraints excluded: chain T residue 24 ARG Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 80 LYS Chi-restraints excluded: chain V residue 82 VAL Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain W residue 107 SER Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 56 LYS Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 63 GLN Chi-restraints excluded: chain Y residue 70 THR Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain Y residue 124 SER Chi-restraints excluded: chain Y residue 127 LYS Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 36 ILE Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 21 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain d residue 26 SER Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain f residue 142 CYS Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 55 PHE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 110 ASP Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 275 GLU Chi-restraints excluded: chain g residue 292 GLN Chi-restraints excluded: chain g residue 293 ASP Chi-restraints excluded: chain g residue 321 GLN Chi-restraints excluded: chain h residue 16 LYS Chi-restraints excluded: chain i residue 44 ASN Chi-restraints excluded: chain i residue 65 LEU Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 116 ASN Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain j residue 104 LYS Chi-restraints excluded: chain j residue 105 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 584 optimal weight: 9.9990 chunk 615 optimal weight: 5.9990 chunk 561 optimal weight: 1.9990 chunk 599 optimal weight: 3.9990 chunk 360 optimal weight: 6.9990 chunk 260 optimal weight: 0.0050 chunk 470 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 541 optimal weight: 0.7980 chunk 566 optimal weight: 6.9990 chunk 596 optimal weight: 7.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 GLN ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN M 116 ASN ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 ASN P 114 HIS Q 83 GLN ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 82907 Z= 0.175 Angle : 0.642 14.698 120536 Z= 0.317 Chirality : 0.037 0.299 15025 Planarity : 0.005 0.146 8760 Dihedral : 24.136 179.849 33188 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 1.13 % Allowed : 9.16 % Favored : 89.71 % Rotamer: Outliers : 6.54 % Allowed : 27.81 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.12), residues: 4976 helix: 1.83 (0.13), residues: 1563 sheet: -0.56 (0.17), residues: 869 loop : -2.09 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 29 HIS 0.037 0.001 HIS T 91 PHE 0.023 0.001 PHE R 71 TYR 0.023 0.001 TYR I 117 ARG 0.009 0.000 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 875 time to evaluate : 4.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8332 (tt0) cc_final: 0.7677 (tp-100) REVERT: A 18 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7944 (mm) REVERT: A 33 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: A 39 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7958 (mmmm) REVERT: A 88 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8392 (mmtp) REVERT: A 108 THR cc_start: 0.7544 (OUTLIER) cc_final: 0.7122 (m) REVERT: A 127 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7795 (ttm170) REVERT: A 150 ASP cc_start: 0.7430 (t0) cc_final: 0.6994 (p0) REVERT: B 26 ARG cc_start: 0.7127 (mtm180) cc_final: 0.6490 (ptp-170) REVERT: B 70 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8731 (tp) REVERT: B 82 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8319 (ttm170) REVERT: B 89 ASP cc_start: 0.8024 (m-30) cc_final: 0.7658 (t0) REVERT: B 96 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8317 (pp) REVERT: B 105 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8058 (t80) REVERT: B 224 ASP cc_start: 0.6681 (t0) cc_final: 0.6293 (t0) REVERT: C 51 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8306 (tttp) REVERT: C 86 MET cc_start: 0.8508 (mmm) cc_final: 0.7761 (mmm) REVERT: C 99 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: C 141 VAL cc_start: 0.8805 (t) cc_final: 0.8510 (t) REVERT: C 193 MET cc_start: 0.9096 (mmm) cc_final: 0.8894 (mmt) REVERT: C 194 GLN cc_start: 0.8659 (mt0) cc_final: 0.8345 (mt0) REVERT: D 38 GLU cc_start: 0.8060 (tt0) cc_final: 0.7825 (tt0) REVERT: D 72 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7747 (mm) REVERT: D 156 PHE cc_start: 0.7624 (t80) cc_final: 0.7337 (t80) REVERT: D 159 HIS cc_start: 0.8864 (m-70) cc_final: 0.8624 (m170) REVERT: D 162 GLN cc_start: 0.7557 (tm-30) cc_final: 0.7342 (tm-30) REVERT: D 170 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8581 (t) REVERT: E 77 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8650 (mmt180) REVERT: E 97 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7896 (mt-10) REVERT: E 134 LYS cc_start: 0.8945 (mttt) cc_final: 0.8461 (mttt) REVERT: E 142 HIS cc_start: 0.6298 (OUTLIER) cc_final: 0.5455 (t70) REVERT: E 171 ASP cc_start: 0.8017 (t70) cc_final: 0.7686 (t70) REVERT: E 174 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8339 (mmmm) REVERT: E 250 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6794 (tp30) REVERT: F 85 ARG cc_start: 0.7642 (mmt-90) cc_final: 0.7132 (mmp-170) REVERT: F 93 GLU cc_start: 0.7942 (tp30) cc_final: 0.7376 (tp30) REVERT: F 100 MET cc_start: 0.8095 (mtp) cc_final: 0.7846 (ttm) REVERT: F 165 SER cc_start: 0.8588 (t) cc_final: 0.8376 (p) REVERT: F 192 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.6118 (tp) REVERT: G 15 CYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7696 (t) REVERT: G 21 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7025 (pp20) REVERT: G 43 ASP cc_start: 0.6978 (m-30) cc_final: 0.6664 (t0) REVERT: G 56 ASN cc_start: 0.8457 (m110) cc_final: 0.8013 (m-40) REVERT: G 105 ASP cc_start: 0.8332 (p0) cc_final: 0.7901 (p0) REVERT: H 47 ARG cc_start: 0.8313 (ttm170) cc_final: 0.8037 (mtp180) REVERT: H 110 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: H 175 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8358 (tptm) REVERT: I 22 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.6476 (ptm160) REVERT: I 25 ARG cc_start: 0.9464 (OUTLIER) cc_final: 0.9092 (mmm160) REVERT: I 53 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8095 (pt0) REVERT: I 58 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8419 (mt) REVERT: I 92 ARG cc_start: 0.6819 (ttp-110) cc_final: 0.6541 (ttp80) REVERT: I 95 THR cc_start: 0.9059 (m) cc_final: 0.8669 (m) REVERT: I 116 HIS cc_start: 0.8605 (t-90) cc_final: 0.8262 (t-90) REVERT: I 147 ARG cc_start: 0.6476 (mtt180) cc_final: 0.6065 (mtt180) REVERT: I 158 ASP cc_start: 0.8204 (m-30) cc_final: 0.7768 (m-30) REVERT: I 159 SER cc_start: 0.8903 (m) cc_final: 0.8449 (t) REVERT: J 9 SER cc_start: 0.9237 (t) cc_final: 0.8841 (m) REVERT: J 29 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8019 (mttt) REVERT: J 53 ARG cc_start: 0.8367 (ttm110) cc_final: 0.7824 (mtm180) REVERT: J 60 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8790 (mt) REVERT: J 106 GLU cc_start: 0.7878 (tp30) cc_final: 0.7311 (tm-30) REVERT: J 107 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8535 (tpt170) REVERT: J 157 ASP cc_start: 0.8122 (t70) cc_final: 0.7650 (t0) REVERT: K 1 MET cc_start: 0.3125 (mtt) cc_final: 0.2200 (mtt) REVERT: K 40 LEU cc_start: 0.7630 (pt) cc_final: 0.7338 (pt) REVERT: K 44 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6774 (mmtt) REVERT: K 46 LEU cc_start: 0.7993 (mm) cc_final: 0.7630 (mm) REVERT: K 64 TYR cc_start: 0.7281 (m-80) cc_final: 0.6644 (m-80) REVERT: K 79 TYR cc_start: 0.5820 (t80) cc_final: 0.5545 (t80) REVERT: K 81 ASN cc_start: 0.5845 (m110) cc_final: 0.5595 (m-40) REVERT: L 8 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7552 (mp-120) REVERT: L 36 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.7385 (pmtt) REVERT: L 93 TYR cc_start: 0.9279 (t80) cc_final: 0.9017 (t80) REVERT: M 19 ASP cc_start: 0.5747 (OUTLIER) cc_final: 0.5389 (t0) REVERT: M 38 LEU cc_start: 0.6782 (mp) cc_final: 0.6457 (mt) REVERT: N 3 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8102 (mmp80) REVERT: N 27 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7692 (mtpp) REVERT: N 53 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8308 (mm) REVERT: N 115 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8997 (tp) REVERT: O 72 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8241 (mmmt) REVERT: O 124 ASP cc_start: 0.6760 (t70) cc_final: 0.6485 (t0) REVERT: P 23 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5224 (mp0) REVERT: P 35 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7537 (pttt) REVERT: P 90 ILE cc_start: 0.7319 (mm) cc_final: 0.6995 (mm) REVERT: P 127 ARG cc_start: 0.6070 (pmm150) cc_final: 0.4113 (mmm-85) REVERT: Q 54 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8075 (mm) REVERT: Q 68 LYS cc_start: 0.7643 (ttmp) cc_final: 0.7399 (tttt) REVERT: Q 104 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7030 (tp30) REVERT: Q 122 ARG cc_start: 0.8629 (mtp180) cc_final: 0.8177 (mtm180) REVERT: Q 123 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7866 (mmm-85) REVERT: R 24 LEU cc_start: 0.8425 (tp) cc_final: 0.8155 (tt) REVERT: R 41 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7257 (pp) REVERT: R 72 LYS cc_start: 0.7657 (pptt) cc_final: 0.6764 (mttp) REVERT: R 79 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6423 (mm-30) REVERT: R 92 ASP cc_start: 0.8120 (t0) cc_final: 0.7742 (t70) REVERT: R 94 SER cc_start: 0.8905 (t) cc_final: 0.8364 (p) REVERT: S 54 LEU cc_start: 0.6097 (mm) cc_final: 0.5827 (mt) REVERT: S 101 LEU cc_start: 0.7839 (mt) cc_final: 0.7400 (mm) REVERT: S 106 GLU cc_start: 0.8287 (tp30) cc_final: 0.7348 (pt0) REVERT: S 145 ARG cc_start: 0.1864 (OUTLIER) cc_final: -0.0385 (ptp-110) REVERT: T 13 ASP cc_start: 0.8102 (m-30) cc_final: 0.7847 (t0) REVERT: T 21 PHE cc_start: 0.7629 (t80) cc_final: 0.7326 (t80) REVERT: T 29 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6497 (tm-30) REVERT: T 115 GLU cc_start: 0.7476 (pt0) cc_final: 0.6677 (pm20) REVERT: T 130 ARG cc_start: 0.7849 (mtp180) cc_final: 0.7421 (mtt-85) REVERT: U 85 ARG cc_start: 0.8679 (ptp-110) cc_final: 0.8024 (mtt-85) REVERT: V 21 ASN cc_start: 0.8952 (t0) cc_final: 0.8469 (t0) REVERT: V 53 TYR cc_start: 0.8768 (m-10) cc_final: 0.8438 (m-10) REVERT: V 69 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8814 (tm) REVERT: V 87 ARG cc_start: 0.7722 (ttm110) cc_final: 0.7339 (ttm-80) REVERT: W 90 THR cc_start: 0.8921 (m) cc_final: 0.8466 (p) REVERT: W 111 MET cc_start: 0.8576 (ptp) cc_final: 0.8071 (ptp) REVERT: X 16 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7811 (ttp80) REVERT: X 56 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7510 (mtpt) REVERT: X 89 ASN cc_start: 0.8138 (m-40) cc_final: 0.7770 (m-40) REVERT: X 107 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8325 (t80) REVERT: X 137 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8362 (mttm) REVERT: Y 63 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8190 (tp40) REVERT: Y 98 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8519 (mm-30) REVERT: Y 111 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.8152 (ttp80) REVERT: Y 127 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7978 (tttp) REVERT: Z 51 MET cc_start: 0.4277 (OUTLIER) cc_final: 0.3412 (mtm) REVERT: a 28 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8478 (ttt-90) REVERT: a 38 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8588 (mpt180) REVERT: a 99 GLN cc_start: 0.4043 (OUTLIER) cc_final: 0.2190 (tm-30) REVERT: b 34 ASP cc_start: 0.7361 (m-30) cc_final: 0.6723 (m-30) REVERT: b 70 LYS cc_start: 0.8642 (ttmt) cc_final: 0.8419 (ttmt) REVERT: b 80 ARG cc_start: 0.7887 (tmm160) cc_final: 0.7456 (tmm-80) REVERT: c 27 GLN cc_start: 0.8415 (tt0) cc_final: 0.7754 (tp40) REVERT: d 14 PHE cc_start: 0.7638 (p90) cc_final: 0.7306 (p90) REVERT: d 20 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7831 (tm-30) REVERT: d 34 TYR cc_start: 0.9143 (m-80) cc_final: 0.8890 (m-80) REVERT: d 48 ASN cc_start: 0.8855 (m-40) cc_final: 0.8527 (m-40) REVERT: e 10 ARG cc_start: 0.7322 (mmp-170) cc_final: 0.7001 (mtp85) REVERT: e 26 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8079 (mtmm) REVERT: e 31 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7727 (mptt) REVERT: g 7 MET cc_start: 0.7571 (tmm) cc_final: 0.6141 (mmm) REVERT: g 55 PHE cc_start: 0.5873 (OUTLIER) cc_final: 0.4996 (t80) REVERT: g 69 VAL cc_start: 0.7992 (t) cc_final: 0.7729 (p) REVERT: g 239 MET cc_start: 0.6668 (ptp) cc_final: 0.6080 (ptp) REVERT: g 275 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.5188 (pt0) REVERT: g 279 ASP cc_start: 0.3646 (m-30) cc_final: 0.1744 (t0) REVERT: g 295 HIS cc_start: 0.8597 (p90) cc_final: 0.8104 (p90) REVERT: g 309 PHE cc_start: 0.6858 (m-80) cc_final: 0.6153 (m-80) REVERT: i 41 MET cc_start: 0.6337 (mmm) cc_final: 0.6081 (mmt) REVERT: i 58 MET cc_start: 0.7605 (ttt) cc_final: 0.7004 (tmm) REVERT: j 26 ILE cc_start: 0.6417 (OUTLIER) cc_final: 0.6140 (mt) REVERT: j 92 MET cc_start: 0.5993 (mmm) cc_final: 0.5450 (mtm) REVERT: j 104 LYS cc_start: 0.5567 (OUTLIER) cc_final: 0.4872 (tptm) outliers start: 280 outliers final: 191 residues processed: 1058 average time/residue: 0.8070 time to fit residues: 1433.4328 Evaluate side-chains 1091 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 845 time to evaluate : 4.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 18 TRP Chi-restraints excluded: chain E residue 69 HIS Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain E residue 146 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 52 ILE Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 76 THR Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain J residue 20 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 44 LYS Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 87 PHE Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 83 THR Chi-restraints excluded: chain L residue 104 HIS Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 124 THR Chi-restraints excluded: chain M residue 19 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain P residue 12 PHE Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 113 ASP Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 123 ARG Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 145 ARG Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 56 LYS Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 127 VAL Chi-restraints excluded: chain X residue 128 SER Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain X residue 137 LYS Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 63 GLN Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 98 GLU Chi-restraints excluded: chain Y residue 124 SER Chi-restraints excluded: chain Y residue 127 LYS Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 28 ARG Chi-restraints excluded: chain a residue 36 ILE Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 99 GLN Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 14 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 52 THR Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 55 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain d residue 26 SER Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 139 CYS Chi-restraints excluded: chain f residue 142 CYS Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 55 PHE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 110 ASP Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 275 GLU Chi-restraints excluded: chain g residue 292 GLN Chi-restraints excluded: chain g residue 293 ASP Chi-restraints excluded: chain g residue 321 GLN Chi-restraints excluded: chain h residue 16 LYS Chi-restraints excluded: chain i residue 87 ASP Chi-restraints excluded: chain i residue 116 ASN Chi-restraints excluded: chain j residue 26 ILE Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain j residue 104 LYS Chi-restraints excluded: chain j residue 105 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 393 optimal weight: 0.5980 chunk 633 optimal weight: 30.0000 chunk 386 optimal weight: 6.9990 chunk 300 optimal weight: 8.9990 chunk 440 optimal weight: 0.0060 chunk 664 optimal weight: 0.4980 chunk 611 optimal weight: 0.5980 chunk 529 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 408 optimal weight: 0.0970 chunk 324 optimal weight: 6.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 ASN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS E 16 HIS ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 HIS G 185 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 HIS N 78 ASN O 24 ASN P 114 HIS Q 83 GLN ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 11 ASN a 17 HIS g 189 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 82907 Z= 0.151 Angle : 0.623 14.085 120536 Z= 0.307 Chirality : 0.036 0.300 15025 Planarity : 0.005 0.143 8760 Dihedral : 24.001 179.993 33177 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 1.13 % Allowed : 8.82 % Favored : 90.05 % Rotamer: Outliers : 4.90 % Allowed : 29.56 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.12), residues: 4976 helix: 1.91 (0.13), residues: 1563 sheet: -0.48 (0.17), residues: 875 loop : -2.01 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 29 HIS 0.055 0.001 HIS T 91 PHE 0.034 0.001 PHE D 24 TYR 0.030 0.001 TYR T 66 ARG 0.016 0.000 ARG S 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1170 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 960 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8116 (tt0) cc_final: 0.7489 (tp-100) REVERT: A 18 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7999 (mm) REVERT: A 33 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: A 88 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8206 (mmtp) REVERT: A 108 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.7122 (m) REVERT: A 127 ARG cc_start: 0.8080 (ttm170) cc_final: 0.7673 (ttm170) REVERT: A 150 ASP cc_start: 0.7171 (t0) cc_final: 0.6690 (p0) REVERT: B 26 ARG cc_start: 0.7022 (mtm180) cc_final: 0.6573 (ptp-170) REVERT: B 41 ARG cc_start: 0.7187 (mmm160) cc_final: 0.6768 (mmm160) REVERT: B 105 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.7997 (t80) REVERT: B 137 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8573 (pt) REVERT: C 51 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8326 (tttp) REVERT: C 86 MET cc_start: 0.8325 (mmm) cc_final: 0.7669 (mmm) REVERT: C 99 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7884 (pt0) REVERT: C 141 VAL cc_start: 0.8735 (t) cc_final: 0.8438 (t) REVERT: C 194 GLN cc_start: 0.8540 (mt0) cc_final: 0.8243 (mt0) REVERT: D 38 GLU cc_start: 0.7912 (tt0) cc_final: 0.7670 (tt0) REVERT: D 71 LEU cc_start: 0.8433 (mp) cc_final: 0.8156 (mt) REVERT: D 72 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7746 (mm) REVERT: D 156 PHE cc_start: 0.7599 (t80) cc_final: 0.7344 (t80) REVERT: E 77 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8555 (mmt180) REVERT: E 97 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7905 (mt-10) REVERT: E 134 LYS cc_start: 0.8928 (mttt) cc_final: 0.8422 (mttt) REVERT: E 142 HIS cc_start: 0.6018 (OUTLIER) cc_final: 0.5179 (t70) REVERT: E 228 ILE cc_start: 0.8977 (mm) cc_final: 0.8713 (mm) REVERT: F 65 GLN cc_start: 0.6832 (tp40) cc_final: 0.6532 (tm-30) REVERT: F 85 ARG cc_start: 0.7651 (mmt-90) cc_final: 0.7133 (mmp-170) REVERT: F 96 THR cc_start: 0.9188 (m) cc_final: 0.8965 (m) REVERT: F 100 MET cc_start: 0.7913 (mtp) cc_final: 0.7658 (ttp) REVERT: F 165 SER cc_start: 0.8555 (t) cc_final: 0.8354 (p) REVERT: F 192 ILE cc_start: 0.6661 (OUTLIER) cc_final: 0.6063 (tp) REVERT: G 10 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.6936 (p0) REVERT: G 21 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6879 (pp20) REVERT: G 43 ASP cc_start: 0.6857 (m-30) cc_final: 0.6650 (t0) REVERT: G 105 ASP cc_start: 0.8170 (p0) cc_final: 0.7593 (p0) REVERT: H 47 ARG cc_start: 0.8287 (ttm170) cc_final: 0.8047 (mtp180) REVERT: H 64 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.8083 (t) REVERT: H 110 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: H 147 ASN cc_start: 0.8936 (p0) cc_final: 0.8616 (p0) REVERT: H 175 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8409 (tptm) REVERT: I 14 THR cc_start: 0.9057 (p) cc_final: 0.8805 (p) REVERT: I 22 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.6457 (ptm160) REVERT: I 58 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8404 (mt) REVERT: I 77 ARG cc_start: 0.8630 (ttm110) cc_final: 0.8071 (ttp80) REVERT: I 92 ARG cc_start: 0.6806 (ttp-110) cc_final: 0.6554 (ttp80) REVERT: I 95 THR cc_start: 0.8951 (m) cc_final: 0.8549 (m) REVERT: I 114 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8281 (mt-10) REVERT: I 116 HIS cc_start: 0.8434 (t-90) cc_final: 0.8153 (t-90) REVERT: I 147 ARG cc_start: 0.6297 (mtt180) cc_final: 0.5969 (mtt180) REVERT: I 152 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7940 (ptmt) REVERT: I 158 ASP cc_start: 0.8134 (m-30) cc_final: 0.7709 (m-30) REVERT: I 159 SER cc_start: 0.8911 (m) cc_final: 0.8420 (t) REVERT: I 196 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.6913 (tpm-80) REVERT: J 9 SER cc_start: 0.9061 (t) cc_final: 0.8710 (m) REVERT: J 29 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7964 (mttt) REVERT: J 60 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8653 (mt) REVERT: J 106 GLU cc_start: 0.7717 (tp30) cc_final: 0.7084 (tm-30) REVERT: J 157 ASP cc_start: 0.7979 (t70) cc_final: 0.7530 (t0) REVERT: K 40 LEU cc_start: 0.7653 (pt) cc_final: 0.7383 (pt) REVERT: K 46 LEU cc_start: 0.8024 (mm) cc_final: 0.7736 (mm) REVERT: K 64 TYR cc_start: 0.7209 (m-80) cc_final: 0.6482 (m-80) REVERT: K 79 TYR cc_start: 0.5728 (t80) cc_final: 0.5488 (t80) REVERT: K 81 ASN cc_start: 0.5852 (m110) cc_final: 0.5598 (m-40) REVERT: L 8 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7033 (mp-120) REVERT: L 10 GLU cc_start: 0.7980 (pm20) cc_final: 0.7625 (pm20) REVERT: L 36 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.7336 (pmtt) REVERT: L 93 TYR cc_start: 0.9258 (t80) cc_final: 0.9024 (t80) REVERT: L 123 VAL cc_start: 0.8302 (m) cc_final: 0.7989 (m) REVERT: M 38 LEU cc_start: 0.6928 (mp) cc_final: 0.6601 (mt) REVERT: M 61 GLU cc_start: 0.4361 (mm-30) cc_final: 0.3990 (mt-10) REVERT: N 3 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7799 (mmp80) REVERT: N 27 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7583 (mtpp) REVERT: N 53 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8187 (mm) REVERT: N 115 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8841 (tp) REVERT: P 23 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.5458 (mp0) REVERT: P 72 LYS cc_start: 0.5198 (ptpt) cc_final: 0.4811 (mttp) REVERT: P 81 ARG cc_start: 0.5753 (ttt-90) cc_final: 0.5499 (ttt90) REVERT: P 90 ILE cc_start: 0.7243 (mm) cc_final: 0.6929 (mm) REVERT: P 127 ARG cc_start: 0.5821 (pmm150) cc_final: 0.3964 (mmm-85) REVERT: Q 54 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8097 (mm) REVERT: Q 65 ILE cc_start: 0.8094 (mm) cc_final: 0.7775 (mm) REVERT: Q 68 LYS cc_start: 0.7885 (ttmp) cc_final: 0.7497 (tttt) REVERT: Q 104 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7215 (tp30) REVERT: Q 122 ARG cc_start: 0.8561 (mtp180) cc_final: 0.8092 (mtm180) REVERT: Q 123 ARG cc_start: 0.8426 (ttm110) cc_final: 0.8117 (mmm-85) REVERT: R 24 LEU cc_start: 0.8313 (tp) cc_final: 0.8090 (tt) REVERT: R 41 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7384 (pp) REVERT: R 72 LYS cc_start: 0.7693 (pptt) cc_final: 0.6798 (mttp) REVERT: R 79 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6595 (mm-30) REVERT: R 92 ASP cc_start: 0.8082 (t0) cc_final: 0.7647 (t70) REVERT: R 94 SER cc_start: 0.8972 (t) cc_final: 0.8373 (p) REVERT: S 14 ILE cc_start: 0.5028 (mt) cc_final: 0.4808 (tt) REVERT: S 93 ASN cc_start: 0.7057 (t0) cc_final: 0.6778 (t0) REVERT: S 101 LEU cc_start: 0.7752 (mt) cc_final: 0.7182 (mm) REVERT: S 106 GLU cc_start: 0.8057 (tp30) cc_final: 0.7316 (pt0) REVERT: S 112 ASP cc_start: 0.5974 (m-30) cc_final: 0.5718 (m-30) REVERT: S 145 ARG cc_start: 0.1944 (OUTLIER) cc_final: -0.0277 (ptp-110) REVERT: T 13 ASP cc_start: 0.8032 (m-30) cc_final: 0.7402 (t0) REVERT: T 17 ASN cc_start: 0.7593 (m-40) cc_final: 0.6977 (m-40) REVERT: T 21 PHE cc_start: 0.7591 (t80) cc_final: 0.7289 (t80) REVERT: T 29 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6659 (tm-30) REVERT: T 68 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.6449 (mtm-85) REVERT: T 115 GLU cc_start: 0.7451 (pt0) cc_final: 0.6775 (pm20) REVERT: U 85 ARG cc_start: 0.8630 (ptp-110) cc_final: 0.7927 (mtt-85) REVERT: V 21 ASN cc_start: 0.9121 (t0) cc_final: 0.8628 (t0) REVERT: V 53 TYR cc_start: 0.8773 (m-10) cc_final: 0.8398 (m-10) REVERT: V 69 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8801 (tm) REVERT: V 87 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7295 (ttm-80) REVERT: W 54 ASP cc_start: 0.9108 (t70) cc_final: 0.8618 (t0) REVERT: W 90 THR cc_start: 0.8910 (m) cc_final: 0.8465 (p) REVERT: W 111 MET cc_start: 0.8584 (ptp) cc_final: 0.8118 (ptp) REVERT: X 56 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7077 (mtpt) REVERT: X 60 GLU cc_start: 0.7864 (pm20) cc_final: 0.7282 (pt0) REVERT: X 89 ASN cc_start: 0.7715 (m-40) cc_final: 0.7467 (m-40) REVERT: X 93 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7371 (tp) REVERT: X 107 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8410 (t80) REVERT: Y 63 GLN cc_start: 0.8183 (tp40) cc_final: 0.7871 (tt0) REVERT: Y 111 ARG cc_start: 0.8567 (ttm-80) cc_final: 0.8069 (ttp80) REVERT: Y 127 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7977 (tttp) REVERT: Z 51 MET cc_start: 0.4090 (OUTLIER) cc_final: 0.3166 (mtt) REVERT: a 38 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8497 (mpt180) REVERT: a 99 GLN cc_start: 0.3665 (OUTLIER) cc_final: 0.1818 (tm-30) REVERT: b 17 ARG cc_start: 0.8438 (mtp-110) cc_final: 0.8108 (mtp85) REVERT: b 34 ASP cc_start: 0.7339 (m-30) cc_final: 0.6729 (m-30) REVERT: b 70 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8396 (ttmt) REVERT: b 80 ARG cc_start: 0.7866 (tmm160) cc_final: 0.7501 (tmm-80) REVERT: c 27 GLN cc_start: 0.8398 (tt0) cc_final: 0.7645 (tp40) REVERT: d 14 PHE cc_start: 0.7598 (p90) cc_final: 0.7196 (p90) REVERT: d 34 TYR cc_start: 0.9076 (m-80) cc_final: 0.8861 (m-80) REVERT: d 48 ASN cc_start: 0.8780 (m-40) cc_final: 0.8465 (m-40) REVERT: e 10 ARG cc_start: 0.7379 (mmp-170) cc_final: 0.7052 (mtp85) REVERT: e 26 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8151 (ptmm) REVERT: e 31 LYS cc_start: 0.8004 (mtmt) cc_final: 0.7679 (mptt) REVERT: g 7 MET cc_start: 0.7546 (tmm) cc_final: 0.6057 (mmm) REVERT: g 55 PHE cc_start: 0.6091 (OUTLIER) cc_final: 0.4982 (t80) REVERT: g 69 VAL cc_start: 0.7991 (t) cc_final: 0.7720 (p) REVERT: g 239 MET cc_start: 0.6669 (ptp) cc_final: 0.6454 (ptp) REVERT: g 256 ARG cc_start: 0.7398 (ttp-170) cc_final: 0.6988 (ttt180) REVERT: g 275 GLU cc_start: 0.5363 (OUTLIER) cc_final: 0.4618 (pp20) REVERT: g 279 ASP cc_start: 0.3577 (m-30) cc_final: 0.2004 (t0) REVERT: g 309 PHE cc_start: 0.6857 (m-80) cc_final: 0.6414 (m-80) REVERT: i 41 MET cc_start: 0.6222 (mmm) cc_final: 0.5868 (mmt) REVERT: j 92 MET cc_start: 0.5946 (mmm) cc_final: 0.5456 (mtm) REVERT: j 104 LYS cc_start: 0.5649 (OUTLIER) cc_final: 0.4980 (tptm) outliers start: 210 outliers final: 127 residues processed: 1098 average time/residue: 0.7598 time to fit residues: 1401.9095 Evaluate side-chains 1039 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 869 time to evaluate : 4.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 32 HIS Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 140 ASN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 235 TRP Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain E residue 108 ARG Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 142 HIS Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 192 ILE Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 217 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain I residue 22 ARG Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 115 SER Chi-restraints excluded: chain I residue 196 ARG Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 45 ILE Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 107 ARG Chi-restraints excluded: chain J residue 151 GLU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain L residue 8 GLN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 104 HIS Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 3 ARG Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 27 LYS Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 49 LYS Chi-restraints excluded: chain O residue 112 ILE Chi-restraints excluded: chain P residue 23 GLU Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain P residue 56 LEU Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 79 HIS Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 48 VAL Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 54 LEU Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 142 TYR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 ASN Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain S residue 90 LYS Chi-restraints excluded: chain S residue 140 THR Chi-restraints excluded: chain S residue 145 ARG Chi-restraints excluded: chain T residue 68 ARG Chi-restraints excluded: chain T residue 91 HIS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 116 ILE Chi-restraints excluded: chain U residue 31 VAL Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 100 VAL Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain W residue 26 LEU Chi-restraints excluded: chain W residue 49 GLU Chi-restraints excluded: chain W residue 104 LEU Chi-restraints excluded: chain W residue 105 THR Chi-restraints excluded: chain X residue 56 LYS Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 94 ASN Chi-restraints excluded: chain X residue 107 PHE Chi-restraints excluded: chain X residue 132 LEU Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 127 LYS Chi-restraints excluded: chain Z residue 51 MET Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 50 ILE Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 99 GLN Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 55 THR Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 32 PHE Chi-restraints excluded: chain c residue 54 LEU Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 48 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 142 CYS Chi-restraints excluded: chain g residue 43 LEU Chi-restraints excluded: chain g residue 55 PHE Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 108 THR Chi-restraints excluded: chain g residue 119 ASN Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 153 THR Chi-restraints excluded: chain g residue 175 VAL Chi-restraints excluded: chain g residue 275 GLU Chi-restraints excluded: chain g residue 292 GLN Chi-restraints excluded: chain g residue 293 ASP Chi-restraints excluded: chain g residue 321 GLN Chi-restraints excluded: chain h residue 16 LYS Chi-restraints excluded: chain i residue 116 ASN Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain j residue 104 LYS Chi-restraints excluded: chain j residue 105 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 420 optimal weight: 3.9990 chunk 563 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 487 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 529 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 544 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN H 150 GLN J 131 GLN ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 47 GLN O 24 ASN P 114 HIS Q 83 GLN Q 94 GLN Q 103 ASN ** S 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.160508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117894 restraints weight = 123230.418| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.21 r_work: 0.3141 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 82907 Z= 0.186 Angle : 0.633 14.309 120536 Z= 0.312 Chirality : 0.037 0.299 15025 Planarity : 0.005 0.143 8760 Dihedral : 23.914 179.948 33153 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 1.07 % Allowed : 8.86 % Favored : 90.07 % Rotamer: Outliers : 4.34 % Allowed : 30.00 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.12), residues: 4976 helix: 1.85 (0.13), residues: 1567 sheet: -0.43 (0.17), residues: 866 loop : -1.96 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 18 HIS 0.012 0.001 HIS T 91 PHE 0.032 0.002 PHE D 77 TYR 0.034 0.001 TYR S 42 ARG 0.008 0.000 ARG E 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22804.22 seconds wall clock time: 399 minutes 34.83 seconds (23974.83 seconds total)