Starting phenix.real_space_refine on Sun Nov 19 04:44:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jam_3047/11_2023/3jam_3047.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jam_3047/11_2023/3jam_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_3047/11_2023/3jam_3047.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jam_3047/11_2023/3jam_3047.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jam_3047/11_2023/3jam_3047.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jam_3047/11_2023/3jam_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-1.21rc1-5144/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: 111 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: 29.77, per 1000 atoms: 0.38 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: 30.46 Conformation dependent library (CDL) restraints added in 5.5 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: 25.58 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: 61.97 Time building geometry restraints manager: 33.10 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: 42957 35.94 - 71.88: 3070 71.88 - 107.82: 241 107.82 - 143.76: 29 143.76 - 179.70: 68 Dihedral angle restraints: 46365 sinusoidal: 31796 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 46362 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: 2.310 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: 9.010 Check model and map are aligned: 0.860 Set scattering table: 0.540 Process input model: 219.610 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 236.910 ------------------------------------------------------------------------------- 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 : 21.308 179.704 36963 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 *********************** 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 : 4.262 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 outliers start: 576 outliers final: 114 residues processed: 1742 average time/residue: 0.8525 time to fit residues: 2397.9388 Evaluate side-chains 1027 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 913 time to evaluate : 4.336 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 114 outliers final: 1 residues processed: 114 average time/residue: 0.6828 time to fit residues: 142.2779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 172 optimal weight: 20.0000 chunk 341 optimal weight: 9.9990 chunk 270 optimal weight: 1.9990 chunk 522 optimal weight: 7.9990 chunk 202 optimal weight: 0.0370 chunk 317 optimal weight: 4.9990 chunk 389 optimal weight: 5.9990 chunk 605 optimal weight: 1.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- 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 56 ASN B 99 ASN B 101 HIS B 178 ASN B 209 ASN C 64 HIS C 92 GLN C 99 GLN C 225 ASN C 238 GLN D 67 ASN ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 HIS E 130 GLN E 259 HIS ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN F 226 ASN G 10 ASN G 13 GLN H 30 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 ASN H 170 GLN I 116 HIS J 38 ASN J 142 ASN K 17 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 GLN L 18 HIS L 22 ASN L 81 HIS N 21 ASN N 105 ASN O 12 GLN O 24 ASN O 29 HIS ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 99 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** 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 25 ASN S 78 HIS S 89 GLN T 17 ASN ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS T 93 HIS T 106 GLN ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 HIS X 22 ASN Y 22 GLN Y 31 ASN ** a 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 31 HIS b 42 ASN b 49 HIS ** c 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 10 HIS e 24 GLN ** g 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 55 ASN ** i 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 88 GLN j 81 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 82907 Z= 0.253 Angle : 0.801 14.139 120536 Z= 0.408 Chirality : 0.046 0.354 15025 Planarity : 0.006 0.146 8760 Dihedral : 19.149 179.513 26932 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 1.79 % Allowed : 8.98 % Favored : 89.23 % Rotamer: Outliers : 4.60 % Allowed : 23.18 % Favored : 72.22 % 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: -0.79 (0.12), residues: 4976 helix: 2.60 (0.13), residues: 1570 sheet: -0.92 (0.16), residues: 872 loop : -2.59 (0.11), residues: 2534 *********************** 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 1205 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1008 time to evaluate : 4.497 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 outliers start: 197 outliers final: 93 residues processed: 1145 average time/residue: 0.8153 time to fit residues: 1574.0567 Evaluate side-chains 950 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 857 time to evaluate : 4.267 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 0 residues processed: 93 average time/residue: 0.6136 time to fit residues: 112.3399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 336 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 504 optimal weight: 5.9990 chunk 412 optimal weight: 7.9990 chunk 167 optimal weight: 50.0000 chunk 606 optimal weight: 9.9990 chunk 655 optimal weight: 9.9990 chunk 540 optimal weight: 2.9990 chunk 601 optimal weight: 0.0670 chunk 206 optimal weight: 5.9990 chunk 486 optimal weight: 0.9980 overall best weight: 3.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 ASN B 79 HIS B 209 ASN B 211 HIS ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN G 10 ASN H 71 HIS H 110 GLN I 32 GLN I 111 GLN J 123 HIS N 21 ASN ** O 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 HIS Q 83 GLN Q 103 ASN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN T 12 GLN T 17 ASN ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS b 26 GLN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN e 17 GLN ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 292 GLN ** g 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 44 ASN ** i 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 81 GLN j 84 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 82907 Z= 0.265 Angle : 0.736 14.740 120536 Z= 0.371 Chirality : 0.042 0.291 15025 Planarity : 0.006 0.147 8760 Dihedral : 18.742 179.512 26932 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 1.51 % Allowed : 9.79 % Favored : 88.71 % Rotamer: Outliers : 4.76 % Allowed : 24.05 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.55 % 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: -0.93 (0.12), residues: 4976 helix: 2.10 (0.13), residues: 1569 sheet: -0.88 (0.16), residues: 860 loop : -2.43 (0.11), residues: 2547 *********************** 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 1139 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 935 time to evaluate : 4.311 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 outliers start: 204 outliers final: 86 residues processed: 1071 average time/residue: 0.8288 time to fit residues: 1484.0939 Evaluate side-chains 928 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 842 time to evaluate : 4.283 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 0.6023 time to fit residues: 102.4806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 599 optimal weight: 5.9990 chunk 456 optimal weight: 20.0000 chunk 314 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 289 optimal weight: 20.0000 chunk 407 optimal weight: 0.9990 chunk 608 optimal weight: 4.9990 chunk 644 optimal weight: 0.0970 chunk 318 optimal weight: 6.9990 chunk 577 optimal weight: 30.0000 chunk 173 optimal weight: 10.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 74 GLN B 79 HIS ** D 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN E 224 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 ASN H 108 GLN H 161 HIS I 88 ASN K 95 GLN N 5 HIS N 21 ASN ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS Q 32 ASN Q 83 GLN Q 103 ASN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN T 12 GLN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS U 105 GLN W 12 ASN ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 ASN a 17 HIS a 72 HIS b 26 GLN ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 ASN ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 234 HIS i 73 GLN i 88 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 82907 Z= 0.295 Angle : 0.733 14.858 120536 Z= 0.366 Chirality : 0.042 0.332 15025 Planarity : 0.006 0.149 8760 Dihedral : 18.546 179.920 26932 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 1.41 % Allowed : 9.24 % Favored : 89.35 % Rotamer: Outliers : 3.36 % Allowed : 26.76 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % 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: -1.04 (0.12), residues: 4976 helix: 1.84 (0.13), residues: 1567 sheet: -0.85 (0.17), residues: 861 loop : -2.41 (0.11), residues: 2548 *********************** 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 1044 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 900 time to evaluate : 4.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 63 residues processed: 994 average time/residue: 0.8456 time to fit residues: 1399.5963 Evaluate side-chains 918 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 855 time to evaluate : 4.322 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.6130 time to fit residues: 77.0433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 536 optimal weight: 0.0060 chunk 365 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 480 optimal weight: 0.0470 chunk 266 optimal weight: 0.2980 chunk 550 optimal weight: 0.9980 chunk 445 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 329 optimal weight: 8.9990 chunk 578 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN C 225 ASN D 159 HIS ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 HIS F 202 ASN G 4 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 GLN H 108 GLN K 28 ASN N 58 HIS N 78 ASN N 105 ASN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 ASN P 114 HIS Q 32 ASN Q 83 GLN R 56 HIS ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN T 17 ASN ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 189 ASN ** i 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 106 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 82907 Z= 0.157 Angle : 0.652 14.142 120536 Z= 0.326 Chirality : 0.038 0.362 15025 Planarity : 0.005 0.145 8760 Dihedral : 18.343 179.995 26932 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 1.23 % Allowed : 8.64 % Favored : 90.13 % Rotamer: Outliers : 2.45 % Allowed : 26.64 % Favored : 70.91 % Cbeta Deviations : 0.00 % 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: -0.87 (0.12), residues: 4976 helix: 1.92 (0.13), residues: 1566 sheet: -0.77 (0.16), residues: 877 loop : -2.26 (0.12), residues: 2533 *********************** 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 1059 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 954 time to evaluate : 4.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 45 residues processed: 1015 average time/residue: 0.7994 time to fit residues: 1359.5188 Evaluate side-chains 879 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 834 time to evaluate : 4.346 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.5985 time to fit residues: 56.2687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 216 optimal weight: 6.9990 chunk 580 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 378 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 645 optimal weight: 0.0570 chunk 535 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 213 optimal weight: 0.7980 chunk 338 optimal weight: 2.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 ASN C 194 GLN C 225 ASN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN E 216 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 HIS ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN H 122 HIS K 29 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 HIS N 78 ASN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS Q 83 GLN Q 103 ASN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 25 ASN T 12 GLN T 91 HIS ** U 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 ASN X 89 ASN Y 22 GLN a 72 HIS b 51 GLN ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 82907 Z= 0.188 Angle : 0.650 14.423 120536 Z= 0.323 Chirality : 0.038 0.300 15025 Planarity : 0.005 0.144 8760 Dihedral : 18.142 179.890 26932 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 1.19 % Allowed : 8.52 % Favored : 90.29 % Rotamer: Outliers : 2.01 % Allowed : 28.13 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % 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: -0.78 (0.12), residues: 4976 helix: 1.97 (0.13), residues: 1556 sheet: -0.68 (0.17), residues: 871 loop : -2.17 (0.12), residues: 2549 *********************** 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 972 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 886 time to evaluate : 4.399 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 outliers start: 86 outliers final: 45 residues processed: 938 average time/residue: 0.8047 time to fit residues: 1262.6104 Evaluate side-chains 863 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 818 time to evaluate : 4.262 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.6004 time to fit residues: 56.1069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 622 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 367 optimal weight: 9.9990 chunk 471 optimal weight: 20.0000 chunk 365 optimal weight: 10.0000 chunk 543 optimal weight: 5.9990 chunk 360 optimal weight: 7.9990 chunk 642 optimal weight: 20.0000 chunk 402 optimal weight: 4.9990 chunk 391 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN ** E 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 HIS ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 GLN H 108 GLN ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS Q 83 GLN ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 ASN S 89 GLN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 GLN W 80 ASN Y 22 GLN b 26 GLN ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 GLN ** i 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 82907 Z= 0.519 Angle : 0.860 15.139 120536 Z= 0.425 Chirality : 0.047 0.292 15025 Planarity : 0.007 0.152 8760 Dihedral : 18.332 179.271 26932 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 1.37 % Allowed : 10.31 % Favored : 88.32 % Rotamer: Outliers : 2.73 % Allowed : 28.98 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % 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: -1.28 (0.12), residues: 4976 helix: 1.32 (0.13), residues: 1566 sheet: -0.89 (0.17), residues: 876 loop : -2.36 (0.12), residues: 2534 *********************** 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 943 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 826 time to evaluate : 4.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 67 residues processed: 896 average time/residue: 0.8153 time to fit residues: 1219.1203 Evaluate side-chains 839 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 772 time to evaluate : 4.280 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.6021 time to fit residues: 81.4431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 397 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 383 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 408 optimal weight: 10.0000 chunk 437 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 505 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN E 50 ASN E 216 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 HIS ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN H 108 GLN ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS Q 83 GLN ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 GLN S 89 GLN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS X 75 GLN b 26 GLN ** g 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 82907 Z= 0.280 Angle : 0.720 14.842 120536 Z= 0.358 Chirality : 0.041 0.293 15025 Planarity : 0.006 0.150 8760 Dihedral : 18.200 179.401 26932 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 1.33 % Allowed : 9.24 % Favored : 89.43 % Rotamer: Outliers : 1.40 % Allowed : 29.51 % Favored : 69.09 % Cbeta Deviations : 0.00 % 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: -1.13 (0.12), residues: 4976 helix: 1.46 (0.13), residues: 1555 sheet: -0.75 (0.17), residues: 864 loop : -2.27 (0.12), residues: 2557 *********************** 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 868 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 808 time to evaluate : 4.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 29 residues processed: 843 average time/residue: 0.8140 time to fit residues: 1144.6966 Evaluate side-chains 805 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 776 time to evaluate : 4.309 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.6012 time to fit residues: 38.0485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 584 optimal weight: 0.1980 chunk 615 optimal weight: 4.9990 chunk 561 optimal weight: 3.9990 chunk 599 optimal weight: 9.9990 chunk 360 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 470 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 541 optimal weight: 0.5980 chunk 566 optimal weight: 5.9990 chunk 596 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 216 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN H 108 GLN J 131 GLN K 17 GLN K 28 ASN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS Q 83 GLN ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN S 122 HIS ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN ** W 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 189 ASN ** i 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 82907 Z= 0.205 Angle : 0.677 14.421 120536 Z= 0.336 Chirality : 0.038 0.298 15025 Planarity : 0.005 0.148 8760 Dihedral : 18.044 179.707 26932 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 1.11 % Allowed : 9.75 % Favored : 89.15 % Rotamer: Outliers : 1.21 % Allowed : 29.84 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % 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: -1.02 (0.12), residues: 4976 helix: 1.57 (0.13), residues: 1559 sheet: -0.69 (0.17), residues: 861 loop : -2.23 (0.12), residues: 2556 *********************** 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 873 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 821 time to evaluate : 4.314 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 outliers start: 52 outliers final: 30 residues processed: 848 average time/residue: 0.8192 time to fit residues: 1156.9528 Evaluate side-chains 816 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 786 time to evaluate : 4.267 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5944 time to fit residues: 39.2169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 393 optimal weight: 3.9990 chunk 633 optimal weight: 20.0000 chunk 386 optimal weight: 5.9990 chunk 300 optimal weight: 8.9990 chunk 440 optimal weight: 6.9990 chunk 664 optimal weight: 10.0000 chunk 611 optimal weight: 0.0010 chunk 529 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 408 optimal weight: 3.9990 chunk 324 optimal weight: 6.9990 overall best weight: 2.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN E 216 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS Q 83 GLN ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 89 GLN S 99 HIS T 17 ASN T 25 GLN ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 82907 Z= 0.245 Angle : 0.691 15.837 120536 Z= 0.342 Chirality : 0.039 0.305 15025 Planarity : 0.006 0.149 8760 Dihedral : 17.976 179.923 26932 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 1.17 % Allowed : 9.49 % Favored : 89.35 % Rotamer: Outliers : 0.54 % Allowed : 30.56 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % 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: -1.04 (0.12), residues: 4976 helix: 1.52 (0.13), residues: 1564 sheet: -0.70 (0.17), residues: 874 loop : -2.23 (0.12), residues: 2538 ********************** 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 833 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 810 time to evaluate : 4.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 823 average time/residue: 0.8442 time to fit residues: 1161.6054 Evaluate side-chains 797 residues out of total 4295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 783 time to evaluate : 4.335 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.6525 time to fit residues: 21.9685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 667 random chunks: chunk 420 optimal weight: 9.9990 chunk 563 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 487 optimal weight: 0.2980 chunk 78 optimal weight: 8.9990 chunk 147 optimal weight: 20.0000 chunk 529 optimal weight: 0.8980 chunk 221 optimal weight: 2.9990 chunk 544 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN D 56 GLN E 216 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN K 17 GLN K 28 ASN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 GLN g 306 GLN ** i 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.158303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115511 restraints weight = 122913.697| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.30 r_work: 0.3038 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 82907 Z= 0.216 Angle : 0.673 15.493 120536 Z= 0.333 Chirality : 0.038 0.304 15025 Planarity : 0.005 0.148 8760 Dihedral : 17.919 179.995 26932 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 1.09 % Allowed : 9.77 % Favored : 89.15 % Rotamer: Outliers : 0.54 % Allowed : 31.01 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.07 % 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: -1.02 (0.12), residues: 4976 helix: 1.51 (0.13), residues: 1565 sheet: -0.66 (0.17), residues: 872 loop : -2.20 (0.12), residues: 2539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21467.51 seconds wall clock time: 376 minutes 51.48 seconds (22611.48 seconds total)