Starting phenix.real_space_refine on Fri Mar 15 09:14:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/03_2024/3j7a_2660_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/03_2024/3j7a_2660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/03_2024/3j7a_2660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/03_2024/3j7a_2660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/03_2024/3j7a_2660_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7a_2660/03_2024/3j7a_2660_updated.pdb" } resolution = 3.2 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= 0.044 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 1 6.06 5 P 1681 5.49 5 Mg 67 5.21 5 S 141 5.16 5 C 37011 2.51 5 N 12467 2.21 5 O 17498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "E ARG 13": "NH1" <-> "NH2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 78": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "G GLU 53": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 83": "OE1" <-> "OE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 180": "NH1" <-> "NH2" Residue "G GLU 253": "OE1" <-> "OE2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 154": "NH1" <-> "NH2" Residue "H GLU 200": "OE1" <-> "OE2" Residue "I ARG 46": "NH1" <-> "NH2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I ARG 150": "NH1" <-> "NH2" Residue "I ARG 155": "NH1" <-> "NH2" Residue "I GLU 186": "OE1" <-> "OE2" Residue "I GLU 188": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "J ARG 140": "NH1" <-> "NH2" Residue "J GLU 159": "OE1" <-> "OE2" Residue "J ARG 160": "NH1" <-> "NH2" Residue "J ARG 182": "NH1" <-> "NH2" Residue "K ARG 3": "NH1" <-> "NH2" Residue "K GLU 51": "OE1" <-> "OE2" Residue "K ARG 68": "NH1" <-> "NH2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K GLU 114": "OE1" <-> "OE2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "L ARG 12": "NH1" <-> "NH2" Residue "L ARG 51": "NH1" <-> "NH2" Residue "L ARG 210": "NH1" <-> "NH2" Residue "L ARG 217": "NH1" <-> "NH2" Residue "M ARG 124": "NH1" <-> "NH2" Residue "M ARG 138": "NH1" <-> "NH2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N GLU 71": "OE1" <-> "OE2" Residue "N ARG 78": "NH1" <-> "NH2" Residue "N ARG 82": "NH1" <-> "NH2" Residue "N ARG 86": "NH1" <-> "NH2" Residue "N GLU 112": "OE1" <-> "OE2" Residue "O GLU 67": "OE1" <-> "OE2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "P ARG 55": "NH1" <-> "NH2" Residue "P ARG 66": "NH1" <-> "NH2" Residue "P ARG 117": "NH1" <-> "NH2" Residue "P ARG 121": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ARG 141": "NH1" <-> "NH2" Residue "P ARG 146": "NH1" <-> "NH2" Residue "P ARG 147": "NH1" <-> "NH2" Residue "P ARG 149": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 16": "NH1" <-> "NH2" Residue "Q ARG 19": "NH1" <-> "NH2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q GLU 98": "OE1" <-> "OE2" Residue "Q GLU 138": "OE1" <-> "OE2" Residue "Q GLU 141": "OE1" <-> "OE2" Residue "S GLU 26": "OE1" <-> "OE2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 89": "NH1" <-> "NH2" Residue "S ARG 115": "NH1" <-> "NH2" Residue "S ARG 123": "NH1" <-> "NH2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "U GLU 32": "OE1" <-> "OE2" Residue "U GLU 34": "OE1" <-> "OE2" Residue "U ARG 55": "NH1" <-> "NH2" Residue "U ARG 73": "NH1" <-> "NH2" Residue "U ARG 124": "NH1" <-> "NH2" Residue "U ARG 131": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "V ARG 36": "NH1" <-> "NH2" Residue "V ARG 91": "NH1" <-> "NH2" Residue "V GLU 146": "OE1" <-> "OE2" Residue "W ARG 11": "NH1" <-> "NH2" Residue "W ARG 67": "NH1" <-> "NH2" Residue "W GLU 77": "OE1" <-> "OE2" Residue "X ARG 43": "NH1" <-> "NH2" Residue "X ARG 47": "NH1" <-> "NH2" Residue "X GLU 88": "OE1" <-> "OE2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y ARG 66": "NH1" <-> "NH2" Residue "Y GLU 73": "OE1" <-> "OE2" Residue "Y ARG 79": "NH1" <-> "NH2" Residue "Y ARG 99": "NH1" <-> "NH2" Residue "Y ARG 124": "NH1" <-> "NH2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Y ARG 146": "NH1" <-> "NH2" Residue "Y GLU 152": "OE1" <-> "OE2" Residue "Y ARG 160": "NH1" <-> "NH2" Residue "Z GLU 28": "OE1" <-> "OE2" Residue "Z ARG 70": "NH1" <-> "NH2" Residue "1 ARG 20": "NH1" <-> "NH2" Residue "1 GLU 87": "OE1" <-> "OE2" Residue "1 ARG 91": "NH1" <-> "NH2" Residue "1 ARG 106": "NH1" <-> "NH2" Residue "3 ARG 6": "NH1" <-> "NH2" Residue "3 ARG 42": "NH1" <-> "NH2" Residue "3 ARG 51": "NH1" <-> "NH2" Residue "3 GLU 90": "OE1" <-> "OE2" Residue "3 ARG 92": "NH1" <-> "NH2" Residue "3 ARG 93": "NH1" <-> "NH2" Residue "4 GLU 13": "OE1" <-> "OE2" Residue "4 GLU 82": "OE1" <-> "OE2" Residue "5 ARG 15": "NH1" <-> "NH2" Residue "5 ARG 38": "NH1" <-> "NH2" Residue "6 ARG 33": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68866 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 34277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1608, 34277 Classifications: {'RNA': 1608} Modifications used: {'rna2p_pur': 137, 'rna2p_pyr': 92, 'rna3p_pur': 738, 'rna3p_pyr': 641} Link IDs: {'rna2p': 228, 'rna3p': 1379} Chain breaks: 22 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1713 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 4, 'TRANS': 205} Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "D" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1228 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain breaks: 3 Chain: "E" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1508 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2061 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain: "G" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1757 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "H" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1644 Classifications: {'peptide': 204} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1424 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "J" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1528 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 6, 'TRANS': 181} Chain: "K" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1037 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "L" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1392 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 2 Chain: "M" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1098 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 3, 'TRANS': 134} Chain: "N" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 772 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "O" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 686 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "P" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 953 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "Q" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "R" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 746 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain breaks: 2 Chain: "S" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1042 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 404 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "U" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 141} Chain: "V" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1206 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain breaks: 1 Chain: "W" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain breaks: 1 Chain: "X" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 776 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain breaks: 1 Chain: "Y" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1266 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain: "Z" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 556 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "1" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 981 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "2" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 320 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 2 Chain: "3" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 781 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "4" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 586 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 69} Chain: "5" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 451 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain breaks: 1 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: "6" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 345 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "7" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1571 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 62} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 102 Unusual residues: {' MG': 67, '34G': 1} Classifications: {'undetermined': 68} Link IDs: {None: 67} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 57636 SG CYS T 19 55.402 88.444 75.019 1.00119.06 S ATOM 57660 SG CYS T 22 58.256 92.212 74.720 1.00187.39 S ATOM 57784 SG CYS T 37 58.819 87.359 76.500 1.00132.78 S ATOM 57810 SG CYS T 40 58.234 90.449 77.786 1.00141.95 S Time building chain proxies: 27.36, per 1000 atoms: 0.40 Number of scatterers: 68866 At special positions: 0 Unit cell: (218.42, 226.46, 192.96, 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 1 29.99 S 141 16.00 P 1681 15.00 Mg 67 11.99 O 17498 8.00 N 12467 7.00 C 37011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 3 26 " - pdb=" SG CYS 3 77 " distance=2.04 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: 28.31 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 100 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 40 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 37 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 22 " pdb="ZN ZN T 100 " - pdb=" SG CYS T 19 " Number of angles added : 6 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 142 helices and 45 sheets defined 33.3% alpha, 11.5% beta 482 base pairs and 897 stacking pairs defined. Time for finding SS restraints: 28.35 Creating SS restraints... Processing helix chain 'B' and resid 58 through 61 No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 71 through 74 No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 158 through 178 Processing helix chain 'B' and resid 181 through 189 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'C' and resid 11 through 19 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 51 through 66 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 80 through 92 removed outlier: 4.579A pdb=" N ARG C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA C 85 " --> pdb=" O PHE C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 139 removed outlier: 3.616A pdb=" N ALA C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 184 Processing helix chain 'D' and resid 7 through 28 Processing helix chain 'D' and resid 67 through 77 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'E' and resid 21 through 34 Processing helix chain 'E' and resid 40 through 61 removed outlier: 3.538A pdb=" N ILE E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 83 Processing helix chain 'E' and resid 101 through 107 removed outlier: 3.877A pdb=" N ARG E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 122 through 130 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'E' and resid 173 through 185 Processing helix chain 'F' and resid 16 through 18 No H-bonds generated for 'chain 'F' and resid 16 through 18' Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing helix chain 'F' and resid 44 through 49 Processing helix chain 'F' and resid 58 through 66 Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.582A pdb=" N LYS F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 116 through 120' Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 248 through 256 Processing helix chain 'G' and resid 46 through 52 Processing helix chain 'G' and resid 59 through 64 Processing helix chain 'G' and resid 72 through 78 Processing helix chain 'G' and resid 133 through 147 Processing helix chain 'G' and resid 194 through 203 Processing helix chain 'G' and resid 219 through 233 Processing helix chain 'G' and resid 239 through 242 removed outlier: 3.817A pdb=" N TRP G 242 " --> pdb=" O PRO G 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 239 through 242' Processing helix chain 'G' and resid 251 through 254 No H-bonds generated for 'chain 'G' and resid 251 through 254' Processing helix chain 'G' and resid 256 through 259 No H-bonds generated for 'chain 'G' and resid 256 through 259' Processing helix chain 'H' and resid 21 through 24 No H-bonds generated for 'chain 'H' and resid 21 through 24' Processing helix chain 'H' and resid 38 through 40 No H-bonds generated for 'chain 'H' and resid 38 through 40' Processing helix chain 'H' and resid 138 through 145 Processing helix chain 'H' and resid 181 through 212 Processing helix chain 'I' and resid 25 through 29 Processing helix chain 'I' and resid 53 through 56 No H-bonds generated for 'chain 'I' and resid 53 through 56' Processing helix chain 'I' and resid 59 through 67 Processing helix chain 'I' and resid 71 through 73 No H-bonds generated for 'chain 'I' and resid 71 through 73' Processing helix chain 'I' and resid 77 through 93 Processing helix chain 'I' and resid 99 through 110 Processing helix chain 'I' and resid 134 through 153 Processing helix chain 'I' and resid 160 through 173 Processing helix chain 'I' and resid 179 through 194 Processing helix chain 'J' and resid 17 through 30 Processing helix chain 'J' and resid 38 through 41 No H-bonds generated for 'chain 'J' and resid 38 through 41' Processing helix chain 'J' and resid 66 through 71 Processing helix chain 'J' and resid 77 through 87 Processing helix chain 'J' and resid 119 through 130 Processing helix chain 'J' and resid 165 through 180 Processing helix chain 'K' and resid 6 through 20 Processing helix chain 'K' and resid 32 through 43 Processing helix chain 'K' and resid 86 through 93 Processing helix chain 'K' and resid 113 through 119 Processing helix chain 'L' and resid 88 through 93 Processing helix chain 'L' and resid 107 through 116 Processing helix chain 'L' and resid 170 through 178 removed outlier: 3.547A pdb=" N GLN L 178 " --> pdb=" O GLU L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 192 No H-bonds generated for 'chain 'L' and resid 189 through 192' Processing helix chain 'L' and resid 203 through 212 Processing helix chain 'M' and resid 45 through 56 removed outlier: 4.240A pdb=" N GLU M 51 " --> pdb=" O LYS M 48 " (cutoff:3.500A) Proline residue: M 52 - end of helix Processing helix chain 'M' and resid 76 through 97 removed outlier: 3.529A pdb=" N ILE M 91 " --> pdb=" O GLY M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 113 Processing helix chain 'N' and resid 28 through 44 removed outlier: 3.505A pdb=" N GLU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 101 Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 50 through 63 Processing helix chain 'O' and resid 81 through 88 Processing helix chain 'P' and resid 71 through 88 Processing helix chain 'P' and resid 110 through 122 removed outlier: 4.225A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 25 removed outlier: 4.433A pdb=" N TRP Q 24 " --> pdb=" O ARG Q 20 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA Q 25 " --> pdb=" O THR Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 33 Processing helix chain 'Q' and resid 35 through 39 removed outlier: 3.529A pdb=" N LYS Q 39 " --> pdb=" O THR Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 132 through 137 Processing helix chain 'R' and resid 23 through 35 removed outlier: 4.191A pdb=" N LYS R 27 " --> pdb=" O THR R 23 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 49 Processing helix chain 'R' and resid 67 through 77 Processing helix chain 'R' and resid 91 through 96 Processing helix chain 'R' and resid 129 through 134 removed outlier: 3.701A pdb=" N SER R 134 " --> pdb=" O ASP R 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 34 Processing helix chain 'S' and resid 41 through 50 Processing helix chain 'S' and resid 63 through 73 Processing helix chain 'S' and resid 102 through 119 removed outlier: 3.825A pdb=" N ASP S 106 " --> pdb=" O ALA S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 129 Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 38 through 48 removed outlier: 5.230A pdb=" N ASP T 46 " --> pdb=" O ARG T 42 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE T 47 " --> pdb=" O GLU T 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 42 Processing helix chain 'U' and resid 47 through 56 Processing helix chain 'U' and resid 63 through 66 No H-bonds generated for 'chain 'U' and resid 63 through 66' Processing helix chain 'U' and resid 71 through 78 Processing helix chain 'U' and resid 86 through 104 Processing helix chain 'U' and resid 109 through 131 Processing helix chain 'U' and resid 146 through 149 No H-bonds generated for 'chain 'U' and resid 146 through 149' Processing helix chain 'V' and resid 49 through 52 No H-bonds generated for 'chain 'V' and resid 49 through 52' Processing helix chain 'V' and resid 154 through 156 No H-bonds generated for 'chain 'V' and resid 154 through 156' Processing helix chain 'W' and resid 7 through 18 removed outlier: 4.215A pdb=" N VAL W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU W 18 " --> pdb=" O ARG W 14 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 38 Processing helix chain 'W' and resid 45 through 60 Processing helix chain 'W' and resid 72 through 82 Processing helix chain 'W' and resid 100 through 109 Processing helix chain 'X' and resid 22 through 27 Processing helix chain 'X' and resid 30 through 36 Processing helix chain 'X' and resid 39 through 47 Processing helix chain 'X' and resid 50 through 66 removed outlier: 3.996A pdb=" N LYS X 54 " --> pdb=" O SER X 50 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER X 55 " --> pdb=" O LYS X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 89 No H-bonds generated for 'chain 'X' and resid 87 through 89' Processing helix chain 'Y' and resid 29 through 31 No H-bonds generated for 'chain 'Y' and resid 29 through 31' Processing helix chain 'Y' and resid 34 through 48 Processing helix chain 'Y' and resid 56 through 59 Processing helix chain 'Y' and resid 64 through 66 No H-bonds generated for 'chain 'Y' and resid 64 through 66' Processing helix chain 'Y' and resid 75 through 89 Processing helix chain 'Y' and resid 95 through 101 Processing helix chain 'Y' and resid 120 through 133 Processing helix chain 'Y' and resid 149 through 167 Processing helix chain 'Z' and resid 26 through 28 No H-bonds generated for 'chain 'Z' and resid 26 through 28' Processing helix chain 'Z' and resid 56 through 61 Processing helix chain 'Z' and resid 64 through 74 Processing helix chain '1' and resid 37 through 47 Processing helix chain '1' and resid 53 through 55 No H-bonds generated for 'chain '1' and resid 53 through 55' Processing helix chain '1' and resid 80 through 86 Processing helix chain '1' and resid 89 through 95 Processing helix chain '1' and resid 108 through 113 Processing helix chain '2' and resid 61 through 68 Processing helix chain '2' and resid 72 through 83 Processing helix chain '3' and resid 48 through 56 Processing helix chain '3' and resid 75 through 80 Processing helix chain '3' and resid 89 through 93 removed outlier: 4.056A pdb=" N ARG 3 93 " --> pdb=" O ARG 3 89 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 89 through 93' Processing helix chain '6' and resid 13 through 17 Processing helix chain '6' and resid 33 through 43 Processing sheet with id= A, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.614A pdb=" N SER B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N PHE B 100 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 126 through 128 removed outlier: 3.953A pdb=" N HIS B 134 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B 219 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG B 136 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ILE B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 28 through 33 removed outlier: 4.194A pdb=" N GLY B 44 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 73 through 76 removed outlier: 6.171A pdb=" N LEU C 120 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 76 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE C 122 " --> pdb=" O VAL C 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 144 through 147 removed outlier: 6.676A pdb=" N ILE C 158 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N CYS C 147 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE C 160 " --> pdb=" O CYS C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 37 through 40 removed outlier: 7.060A pdb=" N ILE C 47 " --> pdb=" O TYR C 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 151 through 154 removed outlier: 3.651A pdb=" N GLY D 134 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY D 181 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 70 through 72 Processing sheet with id= I, first strand: chain 'F' and resid 101 through 103 Processing sheet with id= J, first strand: chain 'F' and resid 121 through 125 removed outlier: 3.533A pdb=" N THR F 159 " --> pdb=" O LEU F 173 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU F 171 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ASP F 163 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.508A pdb=" N LEU F 136 " --> pdb=" O ARG F 132 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS F 128 " --> pdb=" O VAL F 140 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 181 through 183 Processing sheet with id= M, first strand: chain 'F' and resid 207 through 211 Processing sheet with id= N, first strand: chain 'G' and resid 89 through 91 Processing sheet with id= O, first strand: chain 'G' and resid 94 through 99 removed outlier: 3.846A pdb=" N LYS G 94 " --> pdb=" O PHE G 113 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 170 through 174 Processing sheet with id= Q, first strand: chain 'H' and resid 2 through 7 Processing sheet with id= R, first strand: chain 'H' and resid 35 through 37 removed outlier: 5.757A pdb=" N ARG H 51 " --> pdb=" O LEU H 113 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU H 113 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 72 through 76 Processing sheet with id= T, first strand: chain 'I' and resid 114 through 117 Processing sheet with id= U, first strand: chain 'J' and resid 46 through 51 removed outlier: 6.798A pdb=" N TYR J 91 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE J 62 " --> pdb=" O TYR J 91 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL J 93 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE J 64 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL J 95 " --> pdb=" O ILE J 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 141 through 143 Processing sheet with id= W, first strand: chain 'K' and resid 24 through 27 removed outlier: 3.754A pdb=" N VAL K 62 " --> pdb=" O GLU K 51 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 72 through 74 removed outlier: 6.709A pdb=" N ILE K 103 " --> pdb=" O LEU K 126 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE K 128 " --> pdb=" O HIS K 101 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N HIS K 101 " --> pdb=" O PHE K 128 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 64 through 67 Processing sheet with id= Z, first strand: chain 'L' and resid 197 through 199 removed outlier: 3.680A pdb=" N ASP L 80 " --> pdb=" O VAL L 103 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP L 105 " --> pdb=" O ILE L 78 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE L 78 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'L' and resid 42 through 48 removed outlier: 6.372A pdb=" N HIS L 44 " --> pdb=" O ALA L 57 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ALA L 57 " --> pdb=" O HIS L 44 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL L 46 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N TYR L 55 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLY L 48 " --> pdb=" O TYR L 53 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR L 53 " --> pdb=" O GLY L 48 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 7 through 11 Processing sheet with id= AC, first strand: chain 'N' and resid 84 through 87 Processing sheet with id= AD, first strand: chain 'N' and resid 59 through 65 removed outlier: 3.513A pdb=" N THR N 64 " --> pdb=" O ASP N 77 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 66 through 68 Processing sheet with id= AF, first strand: chain 'P' and resid 92 through 98 Processing sheet with id= AG, first strand: chain 'Q' and resid 122 through 124 removed outlier: 6.608A pdb=" N ARG Q 73 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS Q 56 " --> pdb=" O CYS Q 71 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N CYS Q 71 " --> pdb=" O LYS Q 56 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA Q 58 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG Q 69 " --> pdb=" O ALA Q 58 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'R' and resid 38 through 40 Processing sheet with id= AI, first strand: chain 'V' and resid 105 through 113 removed outlier: 3.555A pdb=" N ILE V 88 " --> pdb=" O SER V 80 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER V 80 " --> pdb=" O ILE V 88 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG V 90 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL V 78 " --> pdb=" O ARG V 90 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN V 92 " --> pdb=" O GLY V 76 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLY V 76 " --> pdb=" O ASN V 92 " (cutoff:3.500A) removed outlier: 14.056A pdb=" N LEU V 94 " --> pdb=" O LEU V 74 " (cutoff:3.500A) removed outlier: 16.190A pdb=" N LEU V 74 " --> pdb=" O LEU V 94 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY V 129 " --> pdb=" O VAL V 142 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL V 142 " --> pdb=" O GLY V 129 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Y' and resid 104 through 106 Processing sheet with id= AK, first strand: chain 'Z' and resid 32 through 37 Processing sheet with id= AL, first strand: chain '1' and resid 6 through 10 Processing sheet with id= AM, first strand: chain '1' and resid 13 through 15 Processing sheet with id= AN, first strand: chain '3' and resid 20 through 22 Processing sheet with id= AO, first strand: chain '3' and resid 36 through 38 Processing sheet with id= AP, first strand: chain '3' and resid 41 through 43 Processing sheet with id= AQ, first strand: chain '4' and resid 31 through 34 removed outlier: 3.537A pdb=" N SER 4 76 " --> pdb=" O LYS 4 34 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain '5' and resid 53 through 56 removed outlier: 3.623A pdb=" N ALA 5 7 " --> pdb=" O LEU 5 54 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG 5 26 " --> pdb=" O GLU 5 10 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL 5 12 " --> pdb=" O GLN 5 24 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLN 5 24 " --> pdb=" O VAL 5 12 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain '5' and resid 14 through 16 removed outlier: 3.655A pdb=" N GLY 5 14 " --> pdb=" O GLN 5 24 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL 5 22 " --> pdb=" O THR 5 16 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3030 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1143 hydrogen bonds 1864 hydrogen bond angles 0 basepair planarities 482 basepair parallelities 897 stacking parallelities Total time for adding SS restraints: 51.53 Time building geometry restraints manager: 30.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7756 1.32 - 1.45: 29017 1.45 - 1.57: 33241 1.57 - 1.70: 3343 1.70 - 1.83: 208 Bond restraints: 73565 Sorted by residual: bond pdb=" C1' U A 789 " pdb=" N1 U A 789 " ideal model delta sigma weight residual 1.480 1.587 -0.107 1.50e-02 4.44e+03 5.08e+01 bond pdb=" O3' A A 788 " pdb=" P U A 789 " ideal model delta sigma weight residual 1.607 1.703 -0.096 1.50e-02 4.44e+03 4.11e+01 bond pdb=" CAM 34G A2168 " pdb=" CAX 34G A2168 " ideal model delta sigma weight residual 1.504 1.377 0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C1' A A 788 " pdb=" N9 A A 788 " ideal model delta sigma weight residual 1.475 1.391 0.084 1.50e-02 4.44e+03 3.13e+01 bond pdb=" CAL 34G A2168 " pdb=" CAW 34G A2168 " ideal model delta sigma weight residual 1.505 1.412 0.093 2.00e-02 2.50e+03 2.17e+01 ... (remaining 73560 not shown) Histogram of bond angle deviations from ideal: 93.53 - 101.75: 2313 101.75 - 109.97: 25715 109.97 - 118.18: 39457 118.18 - 126.40: 34605 126.40 - 134.62: 5148 Bond angle restraints: 107238 Sorted by residual: angle pdb=" O3' U A2053 " pdb=" C3' U A2053 " pdb=" C2' U A2053 " ideal model delta sigma weight residual 109.50 126.57 -17.07 1.50e+00 4.44e-01 1.30e+02 angle pdb=" O3' U A1386 " pdb=" C3' U A1386 " pdb=" C2' U A1386 " ideal model delta sigma weight residual 109.50 125.28 -15.78 1.50e+00 4.44e-01 1.11e+02 angle pdb=" O3' G A 465 " pdb=" C3' G A 465 " pdb=" C2' G A 465 " ideal model delta sigma weight residual 109.50 123.81 -14.31 1.50e+00 4.44e-01 9.09e+01 angle pdb=" C3' A A 788 " pdb=" O3' A A 788 " pdb=" P U A 789 " ideal model delta sigma weight residual 120.20 106.69 13.51 1.50e+00 4.44e-01 8.12e+01 angle pdb=" C4' A A1897 " pdb=" C3' A A1897 " pdb=" O3' A A1897 " ideal model delta sigma weight residual 109.40 122.36 -12.96 1.50e+00 4.44e-01 7.46e+01 ... (remaining 107233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 41120 35.91 - 71.82: 4764 71.82 - 107.72: 437 107.72 - 143.63: 20 143.63 - 179.54: 54 Dihedral angle restraints: 46395 sinusoidal: 34520 harmonic: 11875 Sorted by residual: dihedral pdb=" CA SER K 76 " pdb=" C SER K 76 " pdb=" N PRO K 77 " pdb=" CA PRO K 77 " ideal model delta harmonic sigma weight residual -180.00 -128.59 -51.41 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" O4' C A1702 " pdb=" C1' C A1702 " pdb=" N1 C A1702 " pdb=" C2 C A1702 " ideal model delta sinusoidal sigma weight residual 200.00 22.80 177.20 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1069 " pdb=" C1' C A1069 " pdb=" N1 C A1069 " pdb=" C2 C A1069 " ideal model delta sinusoidal sigma weight residual 200.00 24.67 175.33 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 46392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 11543 0.160 - 0.319: 1806 0.319 - 0.479: 70 0.479 - 0.639: 11 0.639 - 0.798: 4 Chirality restraints: 13434 Sorted by residual: chirality pdb=" C3' U A2053 " pdb=" C4' U A2053 " pdb=" O3' U A2053 " pdb=" C2' U A2053 " both_signs ideal model delta sigma weight residual False -2.74 -1.95 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" C3' U A1386 " pdb=" C4' U A1386 " pdb=" O3' U A1386 " pdb=" C2' U A1386 " both_signs ideal model delta sigma weight residual False -2.74 -2.06 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C3' A A 105 " pdb=" C4' A A 105 " pdb=" O3' A A 105 " pdb=" C2' A A 105 " both_signs ideal model delta sigma weight residual False -2.74 -2.06 -0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 13431 not shown) Planarity restraints: 7296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 76 " -0.101 5.00e-02 4.00e+02 1.53e-01 3.77e+01 pdb=" N PRO K 77 " 0.265 5.00e-02 4.00e+02 pdb=" CA PRO K 77 " -0.092 5.00e-02 4.00e+02 pdb=" CD PRO K 77 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A 427 " 0.060 2.00e-02 2.50e+03 2.71e-02 2.02e+01 pdb=" N9 A A 427 " -0.062 2.00e-02 2.50e+03 pdb=" C8 A A 427 " -0.007 2.00e-02 2.50e+03 pdb=" N7 A A 427 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A 427 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A 427 " 0.013 2.00e-02 2.50e+03 pdb=" N6 A A 427 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A 427 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 427 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A A 427 " -0.008 2.00e-02 2.50e+03 pdb=" C4 A A 427 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1209 " -0.063 2.00e-02 2.50e+03 2.51e-02 1.90e+01 pdb=" N9 G A1209 " 0.047 2.00e-02 2.50e+03 pdb=" C8 G A1209 " 0.013 2.00e-02 2.50e+03 pdb=" N7 G A1209 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G A1209 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G A1209 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G A1209 " -0.019 2.00e-02 2.50e+03 pdb=" N1 G A1209 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A1209 " 0.009 2.00e-02 2.50e+03 pdb=" N2 G A1209 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G A1209 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G A1209 " 0.017 2.00e-02 2.50e+03 ... (remaining 7293 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 94 2.35 - 2.99: 32162 2.99 - 3.63: 117008 3.63 - 4.26: 192117 4.26 - 4.90: 271627 Nonbonded interactions: 613008 Sorted by model distance: nonbonded pdb=" OP1 A A 169 " pdb="MG MG A2155 " model vdw 1.715 2.170 nonbonded pdb=" O ILE S 35 " pdb=" CG1 ILE S 38 " model vdw 1.757 3.440 nonbonded pdb=" OP2 A A 998 " pdb="MG MG A2140 " model vdw 1.822 2.170 nonbonded pdb=" O2 C A 759 " pdb=" C2 A A 788 " model vdw 1.841 3.340 nonbonded pdb=" O2' A A1447 " pdb=" OP2 U A1448 " model vdw 1.847 2.440 ... (remaining 613003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.950 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: 0.070 Extract box with map and model: 12.450 Check model and map are aligned: 0.760 Set scattering table: 0.520 Process input model: 196.790 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5417 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 : 0.008 0.127 73565 Z= 0.495 Angle : 1.394 17.070 107238 Z= 0.941 Chirality : 0.103 0.798 13434 Planarity : 0.007 0.153 7296 Dihedral : 24.278 179.539 38712 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 4.16 % Allowed : 10.46 % Favored : 85.38 % Rotamer: Outliers : 15.41 % Allowed : 15.77 % Favored : 68.83 % Cbeta Deviations : 1.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.18 % 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: -2.49 (0.12), residues: 4014 helix: 1.04 (0.11), residues: 1421 sheet: -2.97 (0.17), residues: 597 loop : -3.42 (0.12), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP O 72 HIS 0.015 0.002 HIS K 101 PHE 0.038 0.003 PHE L 65 TYR 0.032 0.003 TYR G 234 ARG 0.012 0.001 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1645 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 556 poor density : 1089 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 LEU cc_start: 0.6384 (tt) cc_final: 0.6084 (tt) REVERT: B 51 THR cc_start: 0.4861 (m) cc_final: 0.4268 (m) REVERT: B 129 THR cc_start: 0.3581 (OUTLIER) cc_final: 0.3205 (m) REVERT: B 130 LEU cc_start: 0.4932 (mt) cc_final: 0.4640 (mm) REVERT: B 137 MET cc_start: 0.4079 (mmt) cc_final: 0.3488 (mmt) REVERT: B 169 VAL cc_start: 0.4410 (t) cc_final: 0.4190 (t) REVERT: C 20 CYS cc_start: 0.4991 (OUTLIER) cc_final: 0.4782 (t) REVERT: C 28 ASN cc_start: 0.2206 (m-40) cc_final: 0.1575 (m-40) REVERT: C 40 ARG cc_start: 0.4220 (OUTLIER) cc_final: 0.4003 (ttm170) REVERT: C 199 ASP cc_start: 0.5619 (m-30) cc_final: 0.5278 (m-30) REVERT: C 200 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5465 (mmt) REVERT: D 11 PHE cc_start: 0.4930 (m-80) cc_final: 0.4729 (m-80) REVERT: D 22 ASN cc_start: 0.5265 (OUTLIER) cc_final: 0.4346 (m-40) REVERT: D 23 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6654 (mt-10) REVERT: D 27 ARG cc_start: 0.3673 (mmt-90) cc_final: 0.3293 (tpp-160) REVERT: D 129 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5467 (tt0) REVERT: D 167 ARG cc_start: 0.5149 (mtt90) cc_final: 0.4175 (mmt90) REVERT: D 191 LEU cc_start: 0.3248 (mp) cc_final: 0.2993 (tt) REVERT: E 6 ARG cc_start: 0.7557 (ttt90) cc_final: 0.7351 (tpp-160) REVERT: E 41 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7986 (mt-10) REVERT: E 42 ILE cc_start: 0.7391 (mm) cc_final: 0.7126 (mm) REVERT: E 80 MET cc_start: 0.6322 (mmp) cc_final: 0.6098 (mmp) REVERT: E 124 HIS cc_start: 0.7366 (t-170) cc_final: 0.7149 (t70) REVERT: E 153 GLU cc_start: 0.7362 (tt0) cc_final: 0.7065 (pt0) REVERT: E 158 PHE cc_start: 0.5437 (m-80) cc_final: 0.5172 (m-80) REVERT: E 177 LEU cc_start: 0.5122 (OUTLIER) cc_final: 0.4553 (tt) REVERT: F 50 ASN cc_start: 0.7625 (m110) cc_final: 0.7327 (m-40) REVERT: F 73 ASP cc_start: 0.7902 (m-30) cc_final: 0.7637 (m-30) REVERT: F 87 MET cc_start: 0.6846 (tpp) cc_final: 0.6540 (tpp) REVERT: F 116 ASN cc_start: 0.8057 (m110) cc_final: 0.7608 (p0) REVERT: F 117 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7145 (pm20) REVERT: F 151 HIS cc_start: 0.6640 (t70) cc_final: 0.6052 (t-90) REVERT: F 153 ASP cc_start: 0.6746 (m-30) cc_final: 0.6529 (m-30) REVERT: F 156 VAL cc_start: 0.6833 (OUTLIER) cc_final: 0.6578 (t) REVERT: F 161 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6857 (ttm-80) REVERT: F 168 LYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5646 (mtmm) REVERT: F 192 VAL cc_start: 0.6943 (t) cc_final: 0.6613 (t) REVERT: F 211 LYS cc_start: 0.7439 (ttpt) cc_final: 0.6798 (mmmm) REVERT: F 220 THR cc_start: 0.6293 (OUTLIER) cc_final: 0.5958 (m) REVERT: G 86 HIS cc_start: 0.6344 (m-70) cc_final: 0.6100 (m-70) REVERT: G 98 VAL cc_start: 0.4584 (OUTLIER) cc_final: 0.4364 (t) REVERT: H 31 ARG cc_start: 0.7023 (mtt90) cc_final: 0.6533 (mtp-110) REVERT: H 74 ARG cc_start: 0.6709 (mtt-85) cc_final: 0.6485 (mmm160) REVERT: H 85 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7531 (ttt180) REVERT: H 107 SER cc_start: 0.6185 (m) cc_final: 0.5879 (p) REVERT: H 137 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7648 (ttp-170) REVERT: H 143 LYS cc_start: 0.6972 (tmtt) cc_final: 0.6681 (tttt) REVERT: H 154 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.6856 (mtp180) REVERT: H 170 PHE cc_start: 0.6054 (m-80) cc_final: 0.5678 (m-10) REVERT: H 171 ILE cc_start: 0.7943 (mt) cc_final: 0.7630 (pt) REVERT: H 196 LYS cc_start: 0.6523 (mttt) cc_final: 0.5899 (tttt) REVERT: H 199 LEU cc_start: 0.7376 (mt) cc_final: 0.7147 (tp) REVERT: H 206 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7789 (tppt) REVERT: I 35 LYS cc_start: 0.5402 (OUTLIER) cc_final: 0.4660 (mmtt) REVERT: I 109 LYS cc_start: 0.2915 (OUTLIER) cc_final: 0.1797 (tmtt) REVERT: I 134 PRO cc_start: 0.4803 (Cg_endo) cc_final: 0.4583 (Cg_exo) REVERT: I 147 THR cc_start: 0.4816 (p) cc_final: 0.4152 (p) REVERT: I 160 ILE cc_start: 0.4860 (tp) cc_final: 0.4079 (mm) REVERT: I 183 LYS cc_start: 0.3494 (ttmt) cc_final: 0.3158 (mtpt) REVERT: J 20 ILE cc_start: 0.6441 (mt) cc_final: 0.6019 (mt) REVERT: J 31 SER cc_start: 0.0828 (OUTLIER) cc_final: 0.0436 (t) REVERT: J 68 ILE cc_start: 0.7728 (mm) cc_final: 0.7464 (mm) REVERT: K 2 VAL cc_start: 0.4692 (OUTLIER) cc_final: 0.4332 (t) REVERT: K 80 ASP cc_start: 0.7487 (p0) cc_final: 0.7272 (p0) REVERT: K 89 ILE cc_start: 0.6271 (mm) cc_final: 0.5931 (mm) REVERT: K 115 GLU cc_start: 0.5181 (OUTLIER) cc_final: 0.4684 (mm-30) REVERT: K 120 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6258 (m90) REVERT: K 125 VAL cc_start: 0.3834 (OUTLIER) cc_final: 0.3626 (p) REVERT: L 52 ASN cc_start: 0.7426 (m110) cc_final: 0.7189 (m110) REVERT: L 59 LYS cc_start: 0.6521 (OUTLIER) cc_final: 0.6165 (mtmt) REVERT: L 92 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6302 (tpt170) REVERT: L 98 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7551 (tmtt) REVERT: L 167 ASN cc_start: 0.2942 (m110) cc_final: 0.2604 (t0) REVERT: L 177 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6811 (tttt) REVERT: L 180 ARG cc_start: 0.5535 (mtp180) cc_final: 0.4819 (mtt-85) REVERT: M 103 LYS cc_start: 0.5134 (ttpp) cc_final: 0.4435 (ptpt) REVERT: N 28 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5724 (tt) REVERT: N 66 LYS cc_start: 0.6436 (mttt) cc_final: 0.6112 (mttp) REVERT: N 99 GLN cc_start: 0.3905 (OUTLIER) cc_final: 0.3537 (mm110) REVERT: O 36 LYS cc_start: 0.5966 (OUTLIER) cc_final: 0.5697 (tptp) REVERT: O 42 ARG cc_start: 0.4863 (OUTLIER) cc_final: 0.4155 (mtt180) REVERT: O 69 LYS cc_start: 0.4485 (OUTLIER) cc_final: 0.4141 (ptpp) REVERT: O 72 TRP cc_start: 0.3617 (OUTLIER) cc_final: 0.2491 (p-90) REVERT: O 73 LYS cc_start: 0.5438 (OUTLIER) cc_final: 0.4688 (mtmm) REVERT: P 75 MET cc_start: 0.5362 (ttp) cc_final: 0.4818 (mmm) REVERT: Q 84 THR cc_start: 0.6419 (OUTLIER) cc_final: 0.5684 (p) REVERT: R 85 MET cc_start: 0.4060 (mmm) cc_final: 0.3850 (tpt) REVERT: S 41 ARG cc_start: 0.2656 (OUTLIER) cc_final: 0.1176 (tpt-90) REVERT: S 84 TRP cc_start: 0.4919 (p-90) cc_final: 0.3705 (p-90) REVERT: S 85 PHE cc_start: 0.5223 (t80) cc_final: 0.5022 (t80) REVERT: S 96 LYS cc_start: 0.5766 (mmtt) cc_final: 0.5452 (mtmt) REVERT: S 98 ILE cc_start: 0.1084 (OUTLIER) cc_final: 0.0285 (mm) REVERT: T 17 ARG cc_start: 0.4904 (OUTLIER) cc_final: 0.3977 (ptt-90) REVERT: T 35 ASN cc_start: 0.4659 (m-40) cc_final: 0.4143 (m-40) REVERT: T 43 GLU cc_start: 0.5569 (mt-10) cc_final: 0.5253 (mt-10) REVERT: U 72 LEU cc_start: 0.4086 (OUTLIER) cc_final: 0.3813 (mm) REVERT: V 52 LYS cc_start: 0.6810 (mtpp) cc_final: 0.6285 (mtmm) REVERT: V 130 GLN cc_start: 0.6728 (OUTLIER) cc_final: 0.6419 (tp40) REVERT: W 78 ARG cc_start: 0.5492 (OUTLIER) cc_final: 0.5026 (tpt170) REVERT: W 97 TYR cc_start: 0.4999 (m-80) cc_final: 0.4447 (t80) REVERT: X 38 LYS cc_start: 0.4958 (pttt) cc_final: 0.4686 (mttt) REVERT: X 43 ARG cc_start: 0.4938 (ttt-90) cc_final: 0.3680 (tmm-80) REVERT: X 46 GLN cc_start: 0.2723 (OUTLIER) cc_final: 0.2246 (tt0) REVERT: X 72 LYS cc_start: 0.1016 (OUTLIER) cc_final: 0.0768 (mtmt) REVERT: X 89 MET cc_start: 0.2611 (mtm) cc_final: 0.2396 (mtm) REVERT: X 108 LYS cc_start: 0.1417 (OUTLIER) cc_final: 0.1172 (mmtt) REVERT: Y 38 ILE cc_start: 0.4776 (mt) cc_final: 0.3529 (mt) REVERT: Y 135 TYR cc_start: 0.4700 (m-80) cc_final: 0.3907 (m-10) REVERT: Y 160 ARG cc_start: 0.0444 (OUTLIER) cc_final: 0.0215 (ttm110) REVERT: Z 12 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.4618 (p90) REVERT: Z 38 MET cc_start: 0.3221 (mmp) cc_final: 0.2553 (mmp) REVERT: Z 76 LYS cc_start: 0.3390 (OUTLIER) cc_final: 0.2944 (ptmt) REVERT: 1 4 GLN cc_start: 0.7408 (mm110) cc_final: 0.7116 (tm-30) REVERT: 1 19 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.5676 (mpp80) REVERT: 1 27 ILE cc_start: 0.7678 (mp) cc_final: 0.7419 (mp) REVERT: 1 42 GLU cc_start: 0.7314 (tt0) cc_final: 0.6939 (pp20) REVERT: 1 61 PHE cc_start: 0.7379 (m-10) cc_final: 0.7071 (m-10) REVERT: 1 63 THR cc_start: 0.6968 (p) cc_final: 0.6613 (t) REVERT: 1 98 ILE cc_start: 0.7011 (OUTLIER) cc_final: 0.6796 (pt) REVERT: 1 112 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.6573 (mt) REVERT: 1 113 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7523 (tppt) REVERT: 3 64 LEU cc_start: 0.1700 (OUTLIER) cc_final: 0.1280 (mt) REVERT: 3 88 SER cc_start: 0.6984 (OUTLIER) cc_final: 0.6568 (p) REVERT: 6 27 LYS cc_start: 0.6113 (mttt) cc_final: 0.5828 (mtpt) outliers start: 556 outliers final: 109 residues processed: 1451 average time/residue: 0.8231 time to fit residues: 1920.8755 Evaluate side-chains 835 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 675 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 111 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 9 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 161 ARG Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 137 ARG Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 72 ARG Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain J residue 74 ARG Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 181 ARG Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 120 HIS Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 130 PHE Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 98 LYS Chi-restraints excluded: chain L residue 177 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 35 CYS Chi-restraints excluded: chain N residue 40 LYS Chi-restraints excluded: chain N residue 54 ARG Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain O residue 73 LYS Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 93 ILE Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 89 ARG Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain U residue 3 ARG Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 74 ILE Chi-restraints excluded: chain U residue 91 LEU Chi-restraints excluded: chain U residue 106 LYS Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 130 GLN Chi-restraints excluded: chain V residue 141 ASN Chi-restraints excluded: chain V residue 142 VAL Chi-restraints excluded: chain V residue 147 LYS Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain X residue 46 GLN Chi-restraints excluded: chain X residue 72 LYS Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 108 LYS Chi-restraints excluded: chain Y residue 50 LYS Chi-restraints excluded: chain Y residue 101 GLN Chi-restraints excluded: chain Y residue 160 ARG Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 48 LYS Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain Z residue 78 LEU Chi-restraints excluded: chain 1 residue 19 ARG Chi-restraints excluded: chain 1 residue 81 ASP Chi-restraints excluded: chain 1 residue 98 ILE Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 3 residue 26 CYS Chi-restraints excluded: chain 3 residue 50 GLN Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 3 residue 88 SER Chi-restraints excluded: chain 4 residue 41 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 473 optimal weight: 9.9990 chunk 425 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 286 optimal weight: 9.9990 chunk 227 optimal weight: 7.9990 chunk 439 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 267 optimal weight: 0.0670 chunk 327 optimal weight: 5.9990 chunk 509 optimal weight: 8.9990 overall best weight: 3.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN C 131 GLN D 13 ASN D 180 GLN E 38 ASN E 110 GLN F 13 ASN F 74 ASN F 116 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS H 11 ASN I 74 ASN I 101 GLN I 194 ASN J 107 ASN K 39 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN M 75 GLN N 27 ASN R 87 GLN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN U 69 ASN U 101 HIS U 105 ASN V 16 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 109 ASN V 130 GLN W 31 ASN W 48 ASN W 62 GLN Y 48 HIS Y 168 ASN 1 15 ASN 1 52 ASN 2 81 HIS 3 14 ASN 4 7 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 73565 Z= 0.328 Angle : 0.903 13.282 107238 Z= 0.451 Chirality : 0.047 0.459 13434 Planarity : 0.007 0.147 7296 Dihedral : 23.653 179.726 30459 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 1.57 % Allowed : 8.59 % Favored : 89.84 % Rotamer: Outliers : 8.89 % Allowed : 20.95 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.08 % 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: -1.66 (0.13), residues: 4014 helix: 1.54 (0.13), residues: 1406 sheet: -2.23 (0.19), residues: 576 loop : -2.84 (0.12), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP F 18 HIS 0.030 0.002 HIS I 42 PHE 0.024 0.003 PHE V 21 TYR 0.033 0.003 TYR Y 76 ARG 0.037 0.001 ARG T 17 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 875 time to evaluate : 3.960 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: B 129 THR cc_start: 0.5117 (OUTLIER) cc_final: 0.4832 (m) REVERT: B 164 ILE cc_start: 0.6560 (mt) cc_final: 0.6209 (mt) REVERT: B 168 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6291 (ptm) REVERT: C 34 LYS cc_start: 0.7280 (mmmt) cc_final: 0.6665 (mtmt) REVERT: C 49 ASN cc_start: 0.7548 (m-40) cc_final: 0.7230 (m110) REVERT: C 102 TRP cc_start: 0.6710 (t-100) cc_final: 0.6449 (t-100) REVERT: C 200 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5496 (tpt) REVERT: D 22 ASN cc_start: 0.6153 (t0) cc_final: 0.4694 (m-40) REVERT: D 151 MET cc_start: 0.4902 (mtm) cc_final: 0.3755 (ptt) REVERT: D 167 ARG cc_start: 0.5007 (mtt90) cc_final: 0.3860 (mtt180) REVERT: D 190 MET cc_start: 0.6255 (mtp) cc_final: 0.6006 (mtp) REVERT: E 6 ARG cc_start: 0.8225 (ttt90) cc_final: 0.7996 (tpp-160) REVERT: E 53 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7406 (mtm110) REVERT: E 64 GLU cc_start: 0.5903 (mm-30) cc_final: 0.5641 (pt0) REVERT: E 80 MET cc_start: 0.7021 (mmp) cc_final: 0.6511 (mmp) REVERT: E 138 LYS cc_start: 0.6965 (mttp) cc_final: 0.6311 (tttp) REVERT: E 145 SER cc_start: 0.9128 (OUTLIER) cc_final: 0.8817 (m) REVERT: E 177 LEU cc_start: 0.5070 (OUTLIER) cc_final: 0.4780 (tt) REVERT: F 23 MET cc_start: 0.7717 (mmp) cc_final: 0.7361 (mmp) REVERT: F 40 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7773 (mt-10) REVERT: F 54 TYR cc_start: 0.7861 (m-80) cc_final: 0.7626 (m-10) REVERT: F 151 HIS cc_start: 0.6741 (t70) cc_final: 0.6348 (t-170) REVERT: F 153 ASP cc_start: 0.7244 (m-30) cc_final: 0.6995 (m-30) REVERT: F 155 LYS cc_start: 0.6484 (mmtt) cc_final: 0.6239 (mptt) REVERT: F 176 GLN cc_start: 0.6160 (OUTLIER) cc_final: 0.5943 (mm110) REVERT: F 205 TYR cc_start: 0.8127 (m-80) cc_final: 0.7533 (m-80) REVERT: F 211 LYS cc_start: 0.7904 (ttpt) cc_final: 0.7672 (ttmm) REVERT: F 232 THR cc_start: 0.6675 (p) cc_final: 0.6379 (m) REVERT: F 247 ASP cc_start: 0.6553 (m-30) cc_final: 0.6352 (t70) REVERT: F 255 ARG cc_start: 0.7181 (tpt90) cc_final: 0.6803 (ttt180) REVERT: G 89 LYS cc_start: 0.7221 (tptt) cc_final: 0.6900 (ttmm) REVERT: G 95 ILE cc_start: 0.7426 (OUTLIER) cc_final: 0.7152 (mm) REVERT: G 99 GLN cc_start: 0.7343 (mt0) cc_final: 0.7141 (mt0) REVERT: G 107 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7044 (ptm-80) REVERT: G 123 CYS cc_start: 0.6851 (OUTLIER) cc_final: 0.5982 (t) REVERT: G 147 SER cc_start: 0.7660 (t) cc_final: 0.7090 (p) REVERT: G 180 ARG cc_start: 0.7342 (mtm180) cc_final: 0.6962 (mtm180) REVERT: G 199 MET cc_start: 0.6642 (mmp) cc_final: 0.6113 (tpt) REVERT: H 5 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7671 (mp) REVERT: H 29 GLU cc_start: 0.7471 (tt0) cc_final: 0.6934 (tm-30) REVERT: H 57 ASP cc_start: 0.7527 (p0) cc_final: 0.7039 (t0) REVERT: H 83 CYS cc_start: 0.7520 (m) cc_final: 0.7207 (t) REVERT: H 106 LEU cc_start: 0.7165 (pp) cc_final: 0.6938 (pp) REVERT: H 143 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6782 (ttmm) REVERT: H 154 ARG cc_start: 0.6789 (mtm-85) cc_final: 0.6390 (mtp180) REVERT: H 170 PHE cc_start: 0.5617 (m-80) cc_final: 0.5395 (m-10) REVERT: H 171 ILE cc_start: 0.8213 (mt) cc_final: 0.7884 (pt) REVERT: H 196 LYS cc_start: 0.6754 (mttt) cc_final: 0.6043 (ptmt) REVERT: H 197 ARG cc_start: 0.6552 (tpp-160) cc_final: 0.5698 (tpp80) REVERT: H 200 GLU cc_start: 0.7419 (tt0) cc_final: 0.7211 (pt0) REVERT: H 206 LYS cc_start: 0.8332 (tttt) cc_final: 0.7934 (tppt) REVERT: H 207 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7925 (mm-30) REVERT: I 35 LYS cc_start: 0.5158 (OUTLIER) cc_final: 0.4416 (mmtt) REVERT: I 59 ILE cc_start: 0.5090 (tt) cc_final: 0.4658 (pt) REVERT: I 66 SER cc_start: 0.7081 (t) cc_final: 0.6801 (p) REVERT: I 69 MET cc_start: 0.1021 (tpp) cc_final: 0.0734 (tpp) REVERT: J 6 LYS cc_start: 0.2990 (tmmt) cc_final: 0.2544 (pttp) REVERT: J 7 ARG cc_start: 0.6288 (ptm-80) cc_final: 0.6087 (ptm-80) REVERT: J 177 LYS cc_start: 0.5957 (tmtt) cc_final: 0.5750 (tppt) REVERT: K 46 TYR cc_start: 0.7268 (m-80) cc_final: 0.6963 (m-80) REVERT: K 89 ILE cc_start: 0.7076 (mm) cc_final: 0.6845 (mm) REVERT: K 106 THR cc_start: 0.8801 (m) cc_final: 0.8249 (p) REVERT: K 112 ASP cc_start: 0.6033 (OUTLIER) cc_final: 0.5749 (p0) REVERT: K 115 GLU cc_start: 0.6186 (mm-30) cc_final: 0.5281 (mm-30) REVERT: L 52 ASN cc_start: 0.7062 (m110) cc_final: 0.6446 (m-40) REVERT: L 86 SER cc_start: 0.8328 (t) cc_final: 0.7971 (p) REVERT: L 92 ARG cc_start: 0.7346 (ttm-80) cc_final: 0.6374 (tpt170) REVERT: L 101 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.7836 (mp) REVERT: L 111 THR cc_start: 0.7338 (m) cc_final: 0.7058 (p) REVERT: L 166 LYS cc_start: 0.4758 (OUTLIER) cc_final: 0.4554 (mttm) REVERT: L 168 ILE cc_start: 0.5309 (OUTLIER) cc_final: 0.5031 (tt) REVERT: L 180 ARG cc_start: 0.6098 (mtp180) cc_final: 0.5792 (mtt-85) REVERT: L 212 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6585 (mtm) REVERT: M 76 THR cc_start: 0.2078 (p) cc_final: 0.1671 (m) REVERT: M 103 LYS cc_start: 0.4714 (ttpp) cc_final: 0.4000 (ptpt) REVERT: M 136 ARG cc_start: 0.5861 (mtm-85) cc_final: 0.5608 (mtm-85) REVERT: N 31 ILE cc_start: 0.4925 (tt) cc_final: 0.4650 (tp) REVERT: N 39 MET cc_start: 0.4620 (ptp) cc_final: 0.4378 (ptm) REVERT: N 66 LYS cc_start: 0.7390 (mttt) cc_final: 0.7187 (mttp) REVERT: N 99 GLN cc_start: 0.4587 (OUTLIER) cc_final: 0.3986 (mm110) REVERT: N 112 GLU cc_start: 0.4112 (OUTLIER) cc_final: 0.3806 (mp0) REVERT: O 42 ARG cc_start: 0.5274 (OUTLIER) cc_final: 0.4224 (mtt180) REVERT: O 69 LYS cc_start: 0.4320 (OUTLIER) cc_final: 0.3995 (pptt) REVERT: O 72 TRP cc_start: 0.3478 (OUTLIER) cc_final: 0.3204 (p-90) REVERT: P 75 MET cc_start: 0.5603 (ttp) cc_final: 0.5305 (tmm) REVERT: P 147 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6554 (ptm160) REVERT: Q 66 SER cc_start: 0.5906 (m) cc_final: 0.5318 (p) REVERT: Q 75 GLN cc_start: 0.7424 (mt0) cc_final: 0.7135 (pt0) REVERT: Q 81 LYS cc_start: 0.6104 (mmtp) cc_final: 0.5392 (tppt) REVERT: S 32 LEU cc_start: 0.7328 (mt) cc_final: 0.7032 (mt) REVERT: S 41 ARG cc_start: 0.3265 (OUTLIER) cc_final: 0.2456 (mtp-110) REVERT: S 84 TRP cc_start: 0.4709 (p-90) cc_final: 0.3759 (p-90) REVERT: S 89 ARG cc_start: 0.2138 (OUTLIER) cc_final: 0.1896 (mtm180) REVERT: S 96 LYS cc_start: 0.6063 (mmtt) cc_final: 0.5575 (mtmt) REVERT: S 107 SER cc_start: 0.2938 (t) cc_final: 0.2362 (m) REVERT: T 43 GLU cc_start: 0.5349 (mt-10) cc_final: 0.4839 (mt-10) REVERT: U 105 ASN cc_start: 0.4646 (OUTLIER) cc_final: 0.3936 (m-40) REVERT: V 37 TYR cc_start: 0.8230 (t80) cc_final: 0.8016 (t80) REVERT: V 81 ASN cc_start: 0.7079 (OUTLIER) cc_final: 0.6870 (m110) REVERT: V 82 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7622 (tttt) REVERT: V 94 LEU cc_start: 0.8595 (mt) cc_final: 0.8378 (mm) REVERT: V 108 LYS cc_start: 0.7559 (tppt) cc_final: 0.7300 (ttmt) REVERT: W 78 ARG cc_start: 0.5439 (OUTLIER) cc_final: 0.4826 (tpt-90) REVERT: X 43 ARG cc_start: 0.4452 (ttt-90) cc_final: 0.3289 (tmt170) REVERT: X 46 GLN cc_start: 0.3434 (OUTLIER) cc_final: 0.2874 (tt0) REVERT: X 49 ILE cc_start: 0.1670 (OUTLIER) cc_final: 0.1434 (mm) REVERT: X 72 LYS cc_start: 0.1611 (OUTLIER) cc_final: 0.1326 (mtmt) REVERT: X 80 LEU cc_start: 0.2885 (OUTLIER) cc_final: 0.2431 (mp) REVERT: Y 20 VAL cc_start: 0.2762 (m) cc_final: 0.1955 (m) REVERT: Y 73 GLU cc_start: 0.7037 (tp30) cc_final: 0.6563 (tt0) REVERT: Y 76 TYR cc_start: 0.2415 (t80) cc_final: 0.2099 (m-80) REVERT: Y 135 TYR cc_start: 0.5357 (m-80) cc_final: 0.4576 (m-10) REVERT: Y 150 LYS cc_start: 0.3968 (OUTLIER) cc_final: 0.3600 (tppt) REVERT: Z 23 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6573 (tp) REVERT: Z 76 LYS cc_start: 0.4001 (OUTLIER) cc_final: 0.3101 (ptmt) REVERT: 1 21 LYS cc_start: 0.8389 (mmtt) cc_final: 0.8092 (mmtp) REVERT: 1 46 LYS cc_start: 0.7541 (tttp) cc_final: 0.7242 (mttt) REVERT: 1 47 MET cc_start: 0.6701 (ttm) cc_final: 0.6188 (mtp) REVERT: 1 113 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7314 (tppt) REVERT: 1 117 LYS cc_start: 0.5368 (OUTLIER) cc_final: 0.4036 (tppt) REVERT: 2 41 PHE cc_start: 0.0951 (OUTLIER) cc_final: -0.0321 (p90) REVERT: 3 6 ARG cc_start: 0.6825 (ptm160) cc_final: 0.6538 (ttt180) REVERT: 4 22 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7437 (tt) REVERT: 4 44 LEU cc_start: 0.3704 (OUTLIER) cc_final: 0.3090 (tp) REVERT: 6 20 LYS cc_start: 0.7724 (ttmt) cc_final: 0.6942 (tptp) outliers start: 321 outliers final: 139 residues processed: 1080 average time/residue: 0.7361 time to fit residues: 1306.6173 Evaluate side-chains 855 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 676 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 168 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain G residue 132 GLU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 129 ILE Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 89 ARG Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 22 CYS Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain T residue 50 PHE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 105 ASN Chi-restraints excluded: chain U residue 111 CYS Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 82 LYS Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 109 ASN Chi-restraints excluded: chain V residue 127 THR Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 146 GLU Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 101 ASP Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 46 GLN Chi-restraints excluded: chain X residue 49 ILE Chi-restraints excluded: chain X residue 72 LYS Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 57 VAL Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 2 residue 60 THR Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 3 residue 26 CYS Chi-restraints excluded: chain 3 residue 50 GLN Chi-restraints excluded: chain 3 residue 74 CYS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 4 residue 44 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 283 optimal weight: 30.0000 chunk 158 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 346 optimal weight: 6.9990 chunk 140 optimal weight: 40.0000 chunk 510 optimal weight: 6.9990 chunk 551 optimal weight: 10.0000 chunk 454 optimal weight: 4.9990 chunk 506 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 409 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS C 91 GLN C 110 GLN F 13 ASN F 50 ASN F 157 ASN F 231 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 HIS ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 ASN M 78 GLN ** P 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 GLN S 137 HIS T 24 ASN ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 31 ASN X 82 ASN Y 128 GLN 2 81 HIS 3 71 GLN 4 7 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.8376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.160 73565 Z= 0.373 Angle : 0.829 15.046 107238 Z= 0.423 Chirality : 0.046 0.528 13434 Planarity : 0.007 0.153 7296 Dihedral : 23.605 179.789 30263 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 1.52 % Allowed : 10.31 % Favored : 88.17 % Rotamer: Outliers : 9.03 % Allowed : 23.00 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.08 % 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 (0.13), residues: 4014 helix: 0.78 (0.13), residues: 1400 sheet: -2.01 (0.19), residues: 598 loop : -2.74 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP G 255 HIS 0.010 0.002 HIS O 74 PHE 0.024 0.003 PHE F 226 TYR 0.032 0.003 TYR B 118 ARG 0.047 0.001 ARG Y 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 900 time to evaluate : 3.915 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: B 37 MET cc_start: 0.5921 (mpp) cc_final: 0.5398 (mpp) REVERT: B 104 SER cc_start: 0.7893 (OUTLIER) cc_final: 0.7589 (p) REVERT: B 223 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.4778 (tp) REVERT: C 81 PHE cc_start: 0.4382 (OUTLIER) cc_final: 0.3986 (p90) REVERT: C 106 MET cc_start: 0.6418 (mtp) cc_final: 0.5993 (mtp) REVERT: C 127 ARG cc_start: 0.7377 (tpm170) cc_final: 0.7091 (mmm160) REVERT: C 154 GLU cc_start: 0.8097 (mp0) cc_final: 0.7503 (pm20) REVERT: C 169 SER cc_start: 0.6594 (OUTLIER) cc_final: 0.6348 (m) REVERT: C 203 TRP cc_start: 0.3934 (t60) cc_final: 0.3668 (t60) REVERT: D 22 ASN cc_start: 0.6292 (OUTLIER) cc_final: 0.5029 (m-40) REVERT: D 151 MET cc_start: 0.5297 (mtm) cc_final: 0.4440 (ptt) REVERT: D 167 ARG cc_start: 0.5781 (mtt90) cc_final: 0.4661 (ttt180) REVERT: E 11 THR cc_start: 0.9134 (t) cc_final: 0.8874 (t) REVERT: E 33 GLU cc_start: 0.8260 (tp30) cc_final: 0.7542 (tm-30) REVERT: E 74 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: E 106 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7695 (mt-10) REVERT: E 177 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.5504 (tt) REVERT: F 50 ASN cc_start: 0.8297 (m-40) cc_final: 0.7992 (m110) REVERT: F 73 ASP cc_start: 0.7987 (m-30) cc_final: 0.7759 (m-30) REVERT: F 143 ASP cc_start: 0.7643 (t70) cc_final: 0.7301 (t70) REVERT: F 163 ASP cc_start: 0.6675 (m-30) cc_final: 0.6185 (m-30) REVERT: F 176 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.6087 (mm110) REVERT: F 211 LYS cc_start: 0.7665 (ttpt) cc_final: 0.7456 (ttmm) REVERT: F 230 ASP cc_start: 0.6203 (t0) cc_final: 0.5949 (t0) REVERT: F 255 ARG cc_start: 0.7322 (tpt90) cc_final: 0.6627 (ttt180) REVERT: G 82 ASN cc_start: 0.7058 (OUTLIER) cc_final: 0.6552 (p0) REVERT: G 89 LYS cc_start: 0.7654 (tptt) cc_final: 0.7274 (ttmm) REVERT: G 99 GLN cc_start: 0.8341 (mt0) cc_final: 0.7787 (mt0) REVERT: G 107 ARG cc_start: 0.8552 (mtp85) cc_final: 0.7250 (ptm-80) REVERT: G 120 ASN cc_start: 0.8134 (t0) cc_final: 0.7251 (p0) REVERT: G 122 HIS cc_start: 0.8485 (m90) cc_final: 0.8083 (m-70) REVERT: G 123 CYS cc_start: 0.8382 (p) cc_final: 0.8055 (t) REVERT: G 142 ILE cc_start: 0.8676 (mt) cc_final: 0.8459 (mt) REVERT: G 147 SER cc_start: 0.7740 (t) cc_final: 0.7049 (p) REVERT: G 168 MET cc_start: 0.8716 (pmm) cc_final: 0.8315 (pmm) REVERT: G 178 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7914 (ptp-170) REVERT: G 199 MET cc_start: 0.7604 (mmp) cc_final: 0.6749 (tpt) REVERT: G 236 TYR cc_start: 0.8196 (t80) cc_final: 0.7368 (t80) REVERT: G 244 VAL cc_start: 0.4736 (OUTLIER) cc_final: 0.4372 (p) REVERT: H 57 ASP cc_start: 0.7737 (p0) cc_final: 0.7186 (t0) REVERT: H 89 LYS cc_start: 0.8377 (mmmt) cc_final: 0.8074 (tptt) REVERT: H 143 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6804 (tttt) REVERT: H 154 ARG cc_start: 0.6863 (mtm-85) cc_final: 0.6336 (mtp180) REVERT: H 171 ILE cc_start: 0.8149 (mt) cc_final: 0.7765 (pt) REVERT: H 174 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.6686 (mttm) REVERT: H 182 LYS cc_start: 0.7093 (ptpt) cc_final: 0.6825 (ptpt) REVERT: H 196 LYS cc_start: 0.6840 (mttt) cc_final: 0.6188 (ptmt) REVERT: H 200 GLU cc_start: 0.7584 (tt0) cc_final: 0.7303 (pt0) REVERT: H 206 LYS cc_start: 0.8161 (tttt) cc_final: 0.7596 (tptt) REVERT: I 35 LYS cc_start: 0.5358 (OUTLIER) cc_final: 0.4629 (mmtt) REVERT: I 49 LYS cc_start: 0.5219 (mttm) cc_final: 0.4555 (tttm) REVERT: J 6 LYS cc_start: 0.3675 (tmmt) cc_final: 0.3312 (pttp) REVERT: J 51 GLU cc_start: 0.4765 (OUTLIER) cc_final: 0.4519 (tm-30) REVERT: J 128 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7152 (tm-30) REVERT: J 177 LYS cc_start: 0.6951 (tmtt) cc_final: 0.6638 (tppt) REVERT: K 89 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7389 (mm) REVERT: K 112 ASP cc_start: 0.8290 (p0) cc_final: 0.7931 (p0) REVERT: K 115 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6386 (mm-30) REVERT: K 120 HIS cc_start: 0.7982 (t70) cc_final: 0.7498 (t70) REVERT: L 42 GLN cc_start: 0.7659 (tt0) cc_final: 0.7411 (tt0) REVERT: L 52 ASN cc_start: 0.7141 (m110) cc_final: 0.6876 (m110) REVERT: L 86 SER cc_start: 0.8142 (t) cc_final: 0.7732 (p) REVERT: L 92 ARG cc_start: 0.7344 (ttm-80) cc_final: 0.6227 (tpt170) REVERT: L 175 GLN cc_start: 0.7766 (tt0) cc_final: 0.7458 (tt0) REVERT: L 180 ARG cc_start: 0.6728 (mtp180) cc_final: 0.6005 (mtt90) REVERT: L 198 TYR cc_start: 0.8553 (p90) cc_final: 0.7956 (p90) REVERT: L 210 ARG cc_start: 0.7386 (ttp-110) cc_final: 0.6942 (tpt170) REVERT: L 212 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6829 (mtm) REVERT: M 31 LYS cc_start: 0.3734 (mttt) cc_final: 0.3061 (tttt) REVERT: M 79 ILE cc_start: 0.3391 (mt) cc_final: 0.3022 (mm) REVERT: M 107 LYS cc_start: 0.4331 (mttt) cc_final: 0.4077 (mtpt) REVERT: M 133 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.4754 (tmtt) REVERT: N 39 MET cc_start: 0.4886 (ptp) cc_final: 0.4601 (ptm) REVERT: N 66 LYS cc_start: 0.7005 (mttt) cc_final: 0.6601 (mttp) REVERT: N 112 GLU cc_start: 0.4819 (OUTLIER) cc_final: 0.4484 (pm20) REVERT: O 42 ARG cc_start: 0.5176 (OUTLIER) cc_final: 0.3634 (mtm110) REVERT: O 72 TRP cc_start: 0.3727 (OUTLIER) cc_final: 0.3189 (p-90) REVERT: P 38 ASN cc_start: 0.6861 (OUTLIER) cc_final: 0.6218 (t0) REVERT: P 56 ILE cc_start: 0.8078 (mm) cc_final: 0.7199 (mt) REVERT: P 60 MET cc_start: 0.6547 (mtt) cc_final: 0.6305 (mtt) REVERT: P 75 MET cc_start: 0.7336 (ttp) cc_final: 0.7016 (tmm) REVERT: P 76 MET cc_start: 0.6108 (tpt) cc_final: 0.5856 (tpt) REVERT: P 79 GLN cc_start: 0.5256 (mt0) cc_final: 0.4857 (mm110) REVERT: Q 63 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6620 (tp-100) REVERT: Q 66 SER cc_start: 0.7706 (m) cc_final: 0.6868 (p) REVERT: Q 75 GLN cc_start: 0.7625 (mt0) cc_final: 0.7074 (pt0) REVERT: Q 79 ASN cc_start: 0.7696 (t0) cc_final: 0.7182 (t0) REVERT: Q 81 LYS cc_start: 0.6625 (mmtp) cc_final: 0.5751 (tppt) REVERT: Q 99 ASN cc_start: 0.7689 (t0) cc_final: 0.7183 (m-40) REVERT: Q 136 PHE cc_start: 0.8355 (t80) cc_final: 0.8132 (t80) REVERT: Q 144 ARG cc_start: 0.8380 (ttt180) cc_final: 0.7836 (mmt90) REVERT: S 96 LYS cc_start: 0.6302 (mmtt) cc_final: 0.5813 (ttmt) REVERT: T 17 ARG cc_start: 0.4452 (OUTLIER) cc_final: 0.2821 (tpt90) REVERT: T 24 ASN cc_start: 0.3669 (OUTLIER) cc_final: 0.3459 (t0) REVERT: T 35 ASN cc_start: 0.6748 (m-40) cc_final: 0.5701 (t0) REVERT: T 51 LYS cc_start: 0.5910 (mptt) cc_final: 0.5693 (mmtt) REVERT: U 76 ARG cc_start: 0.7075 (mmt90) cc_final: 0.6363 (mmm-85) REVERT: U 78 GLN cc_start: 0.7560 (tm-30) cc_final: 0.7121 (mm-40) REVERT: U 128 TYR cc_start: 0.9209 (t80) cc_final: 0.8898 (t80) REVERT: U 135 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7904 (mp) REVERT: V 8 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7396 (mm-40) REVERT: V 9 HIS cc_start: 0.7443 (m-70) cc_final: 0.7181 (m-70) REVERT: V 81 ASN cc_start: 0.6852 (OUTLIER) cc_final: 0.5915 (m110) REVERT: V 90 ARG cc_start: 0.8733 (mtp-110) cc_final: 0.8526 (ptm160) REVERT: V 139 ARG cc_start: 0.8007 (mmt90) cc_final: 0.7653 (mmt-90) REVERT: W 78 ARG cc_start: 0.5403 (OUTLIER) cc_final: 0.4871 (tpt-90) REVERT: X 43 ARG cc_start: 0.4530 (ttt-90) cc_final: 0.3023 (tmt170) REVERT: X 65 LYS cc_start: 0.3498 (OUTLIER) cc_final: 0.2657 (ptmt) REVERT: X 80 LEU cc_start: 0.2739 (OUTLIER) cc_final: 0.2119 (mt) REVERT: Y 67 LYS cc_start: 0.5646 (tptt) cc_final: 0.5428 (mtpt) REVERT: Y 73 GLU cc_start: 0.6646 (tp30) cc_final: 0.6409 (tt0) REVERT: Y 85 ARG cc_start: 0.5402 (ttp80) cc_final: 0.5108 (ttp80) REVERT: Y 150 LYS cc_start: 0.3514 (OUTLIER) cc_final: 0.3052 (tppt) REVERT: Z 60 GLN cc_start: 0.7727 (tp40) cc_final: 0.7218 (mm-40) REVERT: Z 61 ASN cc_start: 0.7258 (m-40) cc_final: 0.6878 (m110) REVERT: Z 76 LYS cc_start: 0.5561 (OUTLIER) cc_final: 0.4550 (ptmt) REVERT: 1 21 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7980 (mmtp) REVERT: 1 42 GLU cc_start: 0.7554 (tt0) cc_final: 0.7313 (pp20) REVERT: 1 47 MET cc_start: 0.7572 (ttm) cc_final: 0.7161 (mtp) REVERT: 1 50 LEU cc_start: 0.7745 (mt) cc_final: 0.7498 (mp) REVERT: 1 113 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7653 (tppt) REVERT: 1 117 LYS cc_start: 0.5490 (OUTLIER) cc_final: 0.5086 (tppt) REVERT: 2 37 ASN cc_start: 0.4998 (p0) cc_final: 0.4786 (p0) REVERT: 2 41 PHE cc_start: 0.1318 (OUTLIER) cc_final: 0.0048 (p90) REVERT: 2 64 ILE cc_start: 0.4893 (mm) cc_final: 0.4537 (pt) REVERT: 3 66 LYS cc_start: 0.5965 (mttt) cc_final: 0.5448 (mmmt) REVERT: 3 91 GLN cc_start: 0.7245 (tp40) cc_final: 0.6939 (tp40) REVERT: 4 22 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.6969 (tt) REVERT: 4 59 ILE cc_start: 0.6757 (tp) cc_final: 0.6349 (pt) REVERT: 4 82 GLU cc_start: 0.4991 (OUTLIER) cc_final: 0.4331 (pm20) REVERT: 6 27 LYS cc_start: 0.7027 (mtmm) cc_final: 0.6264 (mmmt) outliers start: 326 outliers final: 160 residues processed: 1104 average time/residue: 0.7287 time to fit residues: 1324.3259 Evaluate side-chains 931 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 734 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 81 PHE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 51 GLU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 72 CYS Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 38 ASN Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 81 ILE Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 72 LEU Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 81 ASN Chi-restraints excluded: chain V residue 108 LYS Chi-restraints excluded: chain V residue 117 CYS Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 142 VAL Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 54 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 101 ASP Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 65 LYS Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 22 PHE Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 67 CYS Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 81 ASP Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 2 residue 60 THR Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 26 CYS Chi-restraints excluded: chain 3 residue 50 GLN Chi-restraints excluded: chain 3 residue 64 LEU Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 4 residue 9 ASP Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain 4 residue 82 GLU Chi-restraints excluded: chain 5 residue 28 GLN Chi-restraints excluded: chain 6 residue 31 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 504 optimal weight: 20.0000 chunk 383 optimal weight: 30.0000 chunk 264 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 342 optimal weight: 3.9990 chunk 512 optimal weight: 0.6980 chunk 542 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 chunk 485 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS B 200 GLN C 155 HIS E 139 GLN F 112 HIS F 151 HIS F 201 ASN F 231 ASN ** F 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN K 56 HIS ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN ** O 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 HIS Q 112 HIS ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN T 33 ASN U 45 GLN U 105 ASN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 66 ASN 2 81 HIS 3 71 GLN 4 7 ASN 4 49 GLN 4 58 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.9463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 73565 Z= 0.270 Angle : 0.700 11.379 107238 Z= 0.356 Chirality : 0.040 0.385 13434 Planarity : 0.006 0.145 7296 Dihedral : 23.447 179.690 30218 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 1.42 % Allowed : 8.00 % Favored : 90.58 % Rotamer: Outliers : 8.17 % Allowed : 24.88 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -1.86 (0.13), residues: 4014 helix: 0.73 (0.13), residues: 1391 sheet: -1.73 (0.19), residues: 617 loop : -2.61 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP G 255 HIS 0.010 0.002 HIS I 42 PHE 0.018 0.002 PHE Z 80 TYR 0.032 0.002 TYR Z 73 ARG 0.015 0.001 ARG S 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 847 time to evaluate : 3.970 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: B 24 PHE cc_start: 0.6825 (m-10) cc_final: 0.5481 (t80) REVERT: B 157 GLN cc_start: 0.7487 (mt0) cc_final: 0.6691 (mp10) REVERT: B 161 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7344 (mt) REVERT: C 33 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.6115 (mmm) REVERT: C 106 MET cc_start: 0.6907 (mtp) cc_final: 0.6436 (mtp) REVERT: C 150 ASP cc_start: 0.7184 (t0) cc_final: 0.6765 (t70) REVERT: C 154 GLU cc_start: 0.8187 (mp0) cc_final: 0.7562 (pm20) REVERT: C 197 MET cc_start: 0.7870 (mtp) cc_final: 0.6657 (tmm) REVERT: C 201 PHE cc_start: 0.8255 (m-80) cc_final: 0.7979 (m-80) REVERT: D 22 ASN cc_start: 0.6413 (t0) cc_final: 0.5214 (m-40) REVERT: D 129 GLU cc_start: 0.5262 (OUTLIER) cc_final: 0.4999 (tp30) REVERT: D 151 MET cc_start: 0.5381 (mtm) cc_final: 0.4546 (ptt) REVERT: D 159 ILE cc_start: 0.7134 (tt) cc_final: 0.6655 (mp) REVERT: D 167 ARG cc_start: 0.5213 (mtt90) cc_final: 0.4042 (ttt180) REVERT: E 11 THR cc_start: 0.9139 (t) cc_final: 0.8931 (t) REVERT: E 16 LYS cc_start: 0.7234 (tptt) cc_final: 0.6460 (mptt) REVERT: E 33 GLU cc_start: 0.8462 (tp30) cc_final: 0.7890 (tm-30) REVERT: E 47 TYR cc_start: 0.8624 (t80) cc_final: 0.8368 (t80) REVERT: E 74 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7609 (tp30) REVERT: E 106 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7760 (mt-10) REVERT: E 153 GLU cc_start: 0.7941 (tp30) cc_final: 0.7648 (tp30) REVERT: E 177 LEU cc_start: 0.6100 (OUTLIER) cc_final: 0.5580 (tt) REVERT: F 50 ASN cc_start: 0.8296 (m-40) cc_final: 0.8085 (m110) REVERT: F 102 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7399 (mm) REVERT: F 117 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7428 (pm20) REVERT: F 118 GLU cc_start: 0.7757 (pm20) cc_final: 0.7314 (pm20) REVERT: F 143 ASP cc_start: 0.7738 (t70) cc_final: 0.7433 (t70) REVERT: F 163 ASP cc_start: 0.6270 (m-30) cc_final: 0.5978 (m-30) REVERT: F 168 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.5502 (tppt) REVERT: F 176 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.6319 (mm110) REVERT: F 206 ASP cc_start: 0.8457 (m-30) cc_final: 0.8037 (m-30) REVERT: F 255 ARG cc_start: 0.7209 (tpt90) cc_final: 0.6528 (ttt180) REVERT: G 45 THR cc_start: 0.7315 (t) cc_final: 0.6977 (p) REVERT: G 89 LYS cc_start: 0.7689 (tptt) cc_final: 0.7327 (ttmm) REVERT: G 99 GLN cc_start: 0.8305 (mt0) cc_final: 0.7703 (mt0) REVERT: G 107 ARG cc_start: 0.8468 (mtp85) cc_final: 0.7249 (ptm-80) REVERT: G 120 ASN cc_start: 0.7993 (t0) cc_final: 0.7348 (p0) REVERT: G 122 HIS cc_start: 0.8491 (m90) cc_final: 0.8119 (m-70) REVERT: G 168 MET cc_start: 0.8626 (pmm) cc_final: 0.8258 (pmm) REVERT: G 180 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7486 (mtp85) REVERT: G 199 MET cc_start: 0.7741 (mmp) cc_final: 0.6777 (tpt) REVERT: G 244 VAL cc_start: 0.5048 (OUTLIER) cc_final: 0.4813 (p) REVERT: H 57 ASP cc_start: 0.7651 (p0) cc_final: 0.6943 (t0) REVERT: H 89 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8206 (tptt) REVERT: H 143 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6820 (tttt) REVERT: H 154 ARG cc_start: 0.6859 (mtm-85) cc_final: 0.6515 (mtp180) REVERT: H 171 ILE cc_start: 0.8130 (mt) cc_final: 0.7730 (pt) REVERT: H 182 LYS cc_start: 0.7042 (ptpt) cc_final: 0.6737 (ptpt) REVERT: H 196 LYS cc_start: 0.6938 (mttt) cc_final: 0.6355 (ptmt) REVERT: H 206 LYS cc_start: 0.8016 (tttt) cc_final: 0.7580 (ttmt) REVERT: I 35 LYS cc_start: 0.5383 (OUTLIER) cc_final: 0.4803 (mmtt) REVERT: I 49 LYS cc_start: 0.5208 (mttm) cc_final: 0.4881 (tttm) REVERT: I 144 LEU cc_start: 0.2814 (OUTLIER) cc_final: 0.2596 (mm) REVERT: J 44 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7172 (pp) REVERT: J 84 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6921 (mm) REVERT: J 143 MET cc_start: 0.7731 (mmm) cc_final: 0.7416 (mtp) REVERT: J 177 LYS cc_start: 0.7396 (tmtt) cc_final: 0.7071 (tppt) REVERT: K 89 ILE cc_start: 0.7656 (mm) cc_final: 0.7421 (mm) REVERT: K 112 ASP cc_start: 0.8423 (p0) cc_final: 0.8111 (p0) REVERT: K 120 HIS cc_start: 0.8084 (t70) cc_final: 0.7563 (t70) REVERT: L 86 SER cc_start: 0.8136 (t) cc_final: 0.7859 (p) REVERT: L 92 ARG cc_start: 0.7608 (ttm-80) cc_final: 0.6342 (tpt170) REVERT: L 93 THR cc_start: 0.7474 (m) cc_final: 0.7051 (p) REVERT: L 180 ARG cc_start: 0.7234 (mtp180) cc_final: 0.6527 (mpt180) REVERT: L 198 TYR cc_start: 0.8584 (p90) cc_final: 0.8157 (p90) REVERT: L 210 ARG cc_start: 0.7454 (ttp-110) cc_final: 0.6932 (tpt170) REVERT: L 212 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6755 (mtm) REVERT: M 31 LYS cc_start: 0.4534 (mttt) cc_final: 0.3816 (tttt) REVERT: M 95 GLN cc_start: 0.6398 (OUTLIER) cc_final: 0.6130 (pt0) REVERT: M 133 LYS cc_start: 0.7164 (mtmm) cc_final: 0.5817 (tmtt) REVERT: N 39 MET cc_start: 0.4781 (ptp) cc_final: 0.4482 (ptm) REVERT: N 62 ILE cc_start: 0.6618 (mm) cc_final: 0.6359 (tp) REVERT: N 83 ILE cc_start: 0.4015 (pt) cc_final: 0.3635 (tt) REVERT: N 112 GLU cc_start: 0.5329 (OUTLIER) cc_final: 0.4623 (pm20) REVERT: O 21 LEU cc_start: 0.2211 (OUTLIER) cc_final: 0.1934 (pp) REVERT: O 42 ARG cc_start: 0.5051 (OUTLIER) cc_final: 0.3519 (mtm110) REVERT: O 72 TRP cc_start: 0.4189 (OUTLIER) cc_final: 0.3174 (p-90) REVERT: P 56 ILE cc_start: 0.8198 (mm) cc_final: 0.7351 (mt) REVERT: P 75 MET cc_start: 0.7503 (ttp) cc_final: 0.7115 (ppp) REVERT: P 76 MET cc_start: 0.6368 (tpt) cc_final: 0.6051 (tpt) REVERT: P 79 GLN cc_start: 0.5855 (mt0) cc_final: 0.5393 (mm110) REVERT: P 88 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5714 (tt) REVERT: P 126 ILE cc_start: 0.7668 (mm) cc_final: 0.7459 (mp) REVERT: Q 63 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6616 (tp-100) REVERT: Q 66 SER cc_start: 0.7842 (m) cc_final: 0.6940 (p) REVERT: Q 75 GLN cc_start: 0.7449 (mt0) cc_final: 0.7083 (mm-40) REVERT: Q 79 ASN cc_start: 0.7830 (t0) cc_final: 0.7567 (t0) REVERT: Q 81 LYS cc_start: 0.6113 (mmtp) cc_final: 0.5584 (tppt) REVERT: Q 98 GLU cc_start: 0.6919 (tp30) cc_final: 0.6515 (tp30) REVERT: Q 99 ASN cc_start: 0.7801 (t0) cc_final: 0.7210 (m-40) REVERT: Q 136 PHE cc_start: 0.8408 (t80) cc_final: 0.8150 (t80) REVERT: Q 144 ARG cc_start: 0.8366 (ttt180) cc_final: 0.7863 (mmt90) REVERT: R 95 HIS cc_start: 0.2799 (OUTLIER) cc_final: 0.2499 (m90) REVERT: S 26 GLU cc_start: 0.2867 (OUTLIER) cc_final: 0.2465 (pm20) REVERT: S 96 LYS cc_start: 0.6275 (mmtt) cc_final: 0.5816 (ttpt) REVERT: S 137 HIS cc_start: 0.3812 (OUTLIER) cc_final: 0.3510 (m90) REVERT: T 12 TYR cc_start: 0.4495 (OUTLIER) cc_final: 0.4000 (t80) REVERT: T 17 ARG cc_start: 0.4444 (OUTLIER) cc_final: 0.2997 (tpt90) REVERT: T 24 ASN cc_start: 0.3350 (OUTLIER) cc_final: 0.3137 (t0) REVERT: T 35 ASN cc_start: 0.6923 (m-40) cc_final: 0.5718 (t0) REVERT: T 51 LYS cc_start: 0.5887 (mptt) cc_final: 0.5676 (mmtt) REVERT: U 53 THR cc_start: 0.7908 (m) cc_final: 0.7690 (p) REVERT: U 78 GLN cc_start: 0.7591 (tm-30) cc_final: 0.7214 (mm-40) REVERT: U 98 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7021 (mtp) REVERT: U 105 ASN cc_start: 0.6347 (OUTLIER) cc_final: 0.5923 (t0) REVERT: U 108 ASP cc_start: 0.7697 (t0) cc_final: 0.7477 (t0) REVERT: U 110 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6409 (m-30) REVERT: V 9 HIS cc_start: 0.7606 (m-70) cc_final: 0.7389 (m-70) REVERT: V 17 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8361 (tt0) REVERT: V 58 ASP cc_start: 0.9226 (t0) cc_final: 0.8990 (t0) REVERT: V 108 LYS cc_start: 0.8203 (tppt) cc_final: 0.7993 (ttmt) REVERT: V 139 ARG cc_start: 0.7878 (mmt90) cc_final: 0.7568 (mmt-90) REVERT: W 3 ARG cc_start: 0.3037 (ttm-80) cc_final: 0.2733 (tmm-80) REVERT: W 45 ARG cc_start: 0.6143 (ttp80) cc_final: 0.5555 (ttp-170) REVERT: W 46 MET cc_start: 0.6793 (tpt) cc_final: 0.6571 (mmp) REVERT: W 78 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5118 (tpt-90) REVERT: X 43 ARG cc_start: 0.4789 (ttt-90) cc_final: 0.2692 (tmt170) REVERT: X 80 LEU cc_start: 0.2622 (OUTLIER) cc_final: 0.1997 (mt) REVERT: Y 85 ARG cc_start: 0.5630 (ttp80) cc_final: 0.5375 (ttm-80) REVERT: Y 114 HIS cc_start: 0.5446 (m90) cc_final: 0.5123 (m-70) REVERT: Y 150 LYS cc_start: 0.3940 (OUTLIER) cc_final: 0.3508 (tppt) REVERT: Y 164 LYS cc_start: 0.3961 (mtpt) cc_final: 0.3653 (mttp) REVERT: Z 18 SER cc_start: 0.6859 (OUTLIER) cc_final: 0.6374 (p) REVERT: Z 57 HIS cc_start: 0.7990 (t70) cc_final: 0.7782 (t70) REVERT: Z 60 GLN cc_start: 0.7839 (tp40) cc_final: 0.7552 (mm-40) REVERT: Z 76 LYS cc_start: 0.6121 (OUTLIER) cc_final: 0.5101 (pttt) REVERT: 1 21 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8088 (mmtp) REVERT: 1 25 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8245 (tp) REVERT: 1 32 LYS cc_start: 0.7212 (pttt) cc_final: 0.6498 (tttm) REVERT: 1 47 MET cc_start: 0.7530 (ttm) cc_final: 0.7257 (mtp) REVERT: 1 99 ASP cc_start: 0.6147 (t0) cc_final: 0.5912 (t0) REVERT: 1 113 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7672 (tppt) REVERT: 1 117 LYS cc_start: 0.5604 (OUTLIER) cc_final: 0.5197 (tppt) REVERT: 1 119 VAL cc_start: 0.2447 (OUTLIER) cc_final: 0.2039 (t) REVERT: 2 37 ASN cc_start: 0.5186 (p0) cc_final: 0.4902 (p0) REVERT: 2 41 PHE cc_start: 0.0797 (OUTLIER) cc_final: -0.0297 (p90) REVERT: 2 64 ILE cc_start: 0.5409 (mm) cc_final: 0.5082 (pt) REVERT: 3 43 ASN cc_start: 0.7704 (m-40) cc_final: 0.7457 (t0) REVERT: 3 66 LYS cc_start: 0.6728 (mttt) cc_final: 0.6367 (mtpt) REVERT: 3 82 ARG cc_start: 0.7627 (mmt90) cc_final: 0.7218 (mmt90) REVERT: 4 22 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7367 (tm) REVERT: 4 23 ILE cc_start: 0.8052 (mt) cc_final: 0.7741 (mm) REVERT: 4 49 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: 4 50 ASN cc_start: 0.6293 (p0) cc_final: 0.6091 (p0) REVERT: 4 52 VAL cc_start: 0.7844 (m) cc_final: 0.7546 (m) REVERT: 4 82 GLU cc_start: 0.5103 (OUTLIER) cc_final: 0.4576 (pm20) REVERT: 5 42 ARG cc_start: 0.4154 (tpp80) cc_final: 0.3923 (mmm-85) REVERT: 5 64 ARG cc_start: 0.2659 (OUTLIER) cc_final: 0.1717 (ptt-90) REVERT: 6 27 LYS cc_start: 0.7214 (mtmm) cc_final: 0.6423 (mmmt) outliers start: 295 outliers final: 167 residues processed: 1048 average time/residue: 0.7117 time to fit residues: 1242.2757 Evaluate side-chains 953 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 740 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 20 CYS Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 33 MET Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 244 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 95 GLN Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain S residue 137 HIS Chi-restraints excluded: chain T residue 12 TYR Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain T residue 28 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 98 MET Chi-restraints excluded: chain U residue 105 ASN Chi-restraints excluded: chain U residue 110 ASP Chi-restraints excluded: chain U residue 147 SER Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 101 ASP Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 25 LEU Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 81 ASP Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 117 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 2 residue 60 THR Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 50 GLN Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 4 residue 11 VAL Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 41 ILE Chi-restraints excluded: chain 4 residue 49 GLN Chi-restraints excluded: chain 4 residue 65 THR Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain 4 residue 82 GLU Chi-restraints excluded: chain 5 residue 64 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 451 optimal weight: 6.9990 chunk 307 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 403 optimal weight: 10.0000 chunk 223 optimal weight: 0.8980 chunk 462 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 276 optimal weight: 0.7980 chunk 486 optimal weight: 4.9990 chunk 136 optimal weight: 40.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** I 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN U 105 ASN V 16 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 HIS Y 128 GLN 2 81 HIS ** 3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 1.0111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 73565 Z= 0.222 Angle : 0.654 11.328 107238 Z= 0.333 Chirality : 0.038 0.388 13434 Planarity : 0.005 0.144 7296 Dihedral : 23.310 178.414 30206 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 1.40 % Allowed : 8.42 % Favored : 90.18 % Rotamer: Outliers : 8.06 % Allowed : 25.35 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -1.77 (0.13), residues: 4014 helix: 0.78 (0.14), residues: 1401 sheet: -1.62 (0.19), residues: 612 loop : -2.56 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP O 72 HIS 0.009 0.001 HIS K 101 PHE 0.018 0.002 PHE 4 77 TYR 0.031 0.002 TYR Z 73 ARG 0.013 0.001 ARG N 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 826 time to evaluate : 3.907 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: B 161 ILE cc_start: 0.7807 (pt) cc_final: 0.7507 (mt) REVERT: C 84 ARG cc_start: 0.6373 (mmm-85) cc_final: 0.6105 (mmm-85) REVERT: C 106 MET cc_start: 0.7290 (mtp) cc_final: 0.6813 (mtp) REVERT: C 125 ASP cc_start: 0.7642 (t0) cc_final: 0.7435 (t0) REVERT: C 144 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7718 (mm) REVERT: C 150 ASP cc_start: 0.6951 (t0) cc_final: 0.6737 (t70) REVERT: C 154 GLU cc_start: 0.8441 (mp0) cc_final: 0.7689 (pm20) REVERT: C 197 MET cc_start: 0.7884 (mtp) cc_final: 0.6913 (tmm) REVERT: D 22 ASN cc_start: 0.6415 (t0) cc_final: 0.6192 (t0) REVERT: D 23 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6024 (tp30) REVERT: D 151 MET cc_start: 0.5784 (mtm) cc_final: 0.4703 (ptt) REVERT: D 167 ARG cc_start: 0.5642 (mtt90) cc_final: 0.4610 (ttt180) REVERT: E 16 LYS cc_start: 0.7103 (tptt) cc_final: 0.6396 (mptt) REVERT: E 33 GLU cc_start: 0.8680 (tp30) cc_final: 0.8102 (tm-30) REVERT: E 106 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7728 (mt-10) REVERT: E 114 PHE cc_start: 0.7356 (t80) cc_final: 0.6997 (t80) REVERT: E 177 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5624 (tt) REVERT: F 6 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7318 (mtpp) REVERT: F 50 ASN cc_start: 0.8332 (m-40) cc_final: 0.8081 (m110) REVERT: F 52 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8183 (mt) REVERT: F 60 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8170 (mt-10) REVERT: F 114 ILE cc_start: 0.5970 (OUTLIER) cc_final: 0.5768 (mm) REVERT: F 117 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7632 (pm20) REVERT: F 118 GLU cc_start: 0.7736 (pm20) cc_final: 0.7253 (pm20) REVERT: F 176 GLN cc_start: 0.6670 (OUTLIER) cc_final: 0.6277 (mm110) REVERT: F 228 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7679 (pt) REVERT: F 255 ARG cc_start: 0.7203 (tpt90) cc_final: 0.6513 (ttt180) REVERT: G 45 THR cc_start: 0.7043 (t) cc_final: 0.6835 (p) REVERT: G 89 LYS cc_start: 0.7748 (tptt) cc_final: 0.7453 (ttmm) REVERT: G 90 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7638 (t0) REVERT: G 93 VAL cc_start: 0.8717 (p) cc_final: 0.8313 (m) REVERT: G 99 GLN cc_start: 0.8296 (mt0) cc_final: 0.7648 (mt0) REVERT: G 120 ASN cc_start: 0.7884 (t0) cc_final: 0.7395 (p0) REVERT: G 168 MET cc_start: 0.8674 (pmm) cc_final: 0.8080 (pmm) REVERT: G 180 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7187 (mtt180) REVERT: G 199 MET cc_start: 0.7678 (mmp) cc_final: 0.6915 (tpt) REVERT: G 216 THR cc_start: 0.8980 (p) cc_final: 0.8515 (p) REVERT: G 232 LYS cc_start: 0.8296 (ttmm) cc_final: 0.7997 (ttmt) REVERT: H 57 ASP cc_start: 0.7623 (p0) cc_final: 0.7000 (t0) REVERT: H 89 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8132 (tptt) REVERT: H 143 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.6800 (tttt) REVERT: H 154 ARG cc_start: 0.6917 (mtm-85) cc_final: 0.6463 (mtp180) REVERT: H 182 LYS cc_start: 0.7091 (ptpt) cc_final: 0.6742 (ptpt) REVERT: H 197 ARG cc_start: 0.7290 (tpp-160) cc_final: 0.7041 (tpp-160) REVERT: H 206 LYS cc_start: 0.8157 (tttt) cc_final: 0.7476 (tptt) REVERT: H 207 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8052 (mm-30) REVERT: I 35 LYS cc_start: 0.5432 (OUTLIER) cc_final: 0.4749 (mmtt) REVERT: I 49 LYS cc_start: 0.5513 (mttm) cc_final: 0.5153 (tttm) REVERT: I 59 ILE cc_start: 0.4413 (tt) cc_final: 0.4140 (pt) REVERT: J 77 GLN cc_start: 0.7129 (pm20) cc_final: 0.6312 (tp40) REVERT: J 85 GLU cc_start: 0.6199 (tp30) cc_final: 0.5940 (tm-30) REVERT: J 143 MET cc_start: 0.7503 (mmm) cc_final: 0.7122 (mtp) REVERT: J 162 ARG cc_start: 0.4682 (OUTLIER) cc_final: 0.4251 (mmm160) REVERT: J 177 LYS cc_start: 0.7452 (tmtt) cc_final: 0.7133 (tppt) REVERT: K 89 ILE cc_start: 0.7759 (mm) cc_final: 0.7535 (mm) REVERT: K 112 ASP cc_start: 0.8435 (p0) cc_final: 0.8048 (p0) REVERT: K 120 HIS cc_start: 0.8036 (t70) cc_final: 0.7505 (t70) REVERT: L 28 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: L 44 HIS cc_start: 0.7852 (m-70) cc_final: 0.7406 (m170) REVERT: L 59 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6663 (mttt) REVERT: L 86 SER cc_start: 0.8151 (t) cc_final: 0.7850 (p) REVERT: L 92 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.6293 (tpt170) REVERT: L 166 LYS cc_start: 0.4136 (OUTLIER) cc_final: 0.3565 (mmmt) REVERT: L 180 ARG cc_start: 0.7091 (mtp180) cc_final: 0.6396 (mmt180) REVERT: L 210 ARG cc_start: 0.7447 (ttp-110) cc_final: 0.6838 (tpt170) REVERT: L 212 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6910 (mtm) REVERT: M 31 LYS cc_start: 0.4384 (mttt) cc_final: 0.3625 (tttt) REVERT: M 71 LYS cc_start: 0.3721 (tttt) cc_final: 0.3484 (ttpp) REVERT: M 133 LYS cc_start: 0.7381 (mtmm) cc_final: 0.6216 (tmtt) REVERT: N 39 MET cc_start: 0.4431 (ptp) cc_final: 0.4054 (ptm) REVERT: N 62 ILE cc_start: 0.6675 (mm) cc_final: 0.6344 (tp) REVERT: N 77 ASP cc_start: 0.7299 (p0) cc_final: 0.7066 (p0) REVERT: N 112 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.4718 (pm20) REVERT: O 21 LEU cc_start: 0.2170 (OUTLIER) cc_final: 0.1866 (pp) REVERT: O 42 ARG cc_start: 0.5452 (OUTLIER) cc_final: 0.3638 (mtm110) REVERT: O 72 TRP cc_start: 0.4355 (OUTLIER) cc_final: 0.3707 (p-90) REVERT: P 56 ILE cc_start: 0.7647 (mm) cc_final: 0.7409 (mp) REVERT: P 63 LYS cc_start: 0.4977 (tppt) cc_final: 0.4724 (ptpp) REVERT: P 75 MET cc_start: 0.7577 (ttp) cc_final: 0.7284 (ppp) REVERT: P 76 MET cc_start: 0.6626 (tpt) cc_final: 0.5777 (tpt) REVERT: P 142 LYS cc_start: 0.8439 (tttm) cc_final: 0.8211 (ttmt) REVERT: P 146 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8072 (ptm-80) REVERT: Q 26 ASP cc_start: 0.8711 (t0) cc_final: 0.8446 (t70) REVERT: Q 37 ARG cc_start: 0.8040 (ttt180) cc_final: 0.7453 (tmm-80) REVERT: Q 63 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6965 (tp40) REVERT: Q 66 SER cc_start: 0.7761 (m) cc_final: 0.6863 (p) REVERT: Q 75 GLN cc_start: 0.7591 (mt0) cc_final: 0.6945 (pt0) REVERT: Q 81 LYS cc_start: 0.6066 (mmtp) cc_final: 0.5576 (tppt) REVERT: Q 99 ASN cc_start: 0.7893 (t0) cc_final: 0.7287 (m-40) REVERT: Q 136 PHE cc_start: 0.8426 (t80) cc_final: 0.8195 (t80) REVERT: Q 144 ARG cc_start: 0.8251 (ttt180) cc_final: 0.7854 (mmt90) REVERT: R 95 HIS cc_start: 0.2761 (OUTLIER) cc_final: 0.2466 (m90) REVERT: S 26 GLU cc_start: 0.2766 (OUTLIER) cc_final: 0.2443 (pm20) REVERT: S 96 LYS cc_start: 0.6352 (mmtt) cc_final: 0.6138 (ttmt) REVERT: T 17 ARG cc_start: 0.4924 (OUTLIER) cc_final: 0.3472 (tpt90) REVERT: T 24 ASN cc_start: 0.4202 (OUTLIER) cc_final: 0.3560 (t0) REVERT: T 35 ASN cc_start: 0.6858 (m-40) cc_final: 0.5900 (t0) REVERT: T 51 LYS cc_start: 0.6115 (mptt) cc_final: 0.5898 (mmtt) REVERT: U 53 THR cc_start: 0.7998 (m) cc_final: 0.7726 (p) REVERT: U 76 ARG cc_start: 0.7001 (mmm-85) cc_final: 0.5996 (mmm-85) REVERT: U 105 ASN cc_start: 0.7384 (t0) cc_final: 0.7174 (t0) REVERT: U 135 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8080 (mp) REVERT: V 58 ASP cc_start: 0.9165 (t0) cc_final: 0.8925 (t0) REVERT: V 124 ASP cc_start: 0.8698 (m-30) cc_final: 0.8457 (m-30) REVERT: W 45 ARG cc_start: 0.6310 (ttp80) cc_final: 0.6034 (ttp-170) REVERT: W 46 MET cc_start: 0.6825 (tpt) cc_final: 0.6511 (mmp) REVERT: W 78 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5129 (tpt-90) REVERT: X 22 LEU cc_start: 0.2601 (OUTLIER) cc_final: 0.1871 (mt) REVERT: X 43 ARG cc_start: 0.4808 (ttt-90) cc_final: 0.3387 (tmt170) REVERT: X 65 LYS cc_start: 0.3898 (tmmt) cc_final: 0.3258 (ptmt) REVERT: X 80 LEU cc_start: 0.2655 (OUTLIER) cc_final: 0.1987 (mt) REVERT: Y 107 ARG cc_start: 0.5200 (OUTLIER) cc_final: 0.4410 (mtp-110) REVERT: Y 141 LYS cc_start: 0.5554 (OUTLIER) cc_final: 0.4664 (tmmt) REVERT: Y 150 LYS cc_start: 0.3589 (OUTLIER) cc_final: 0.3020 (tppt) REVERT: Y 164 LYS cc_start: 0.4049 (mtpt) cc_final: 0.3710 (mttp) REVERT: Z 18 SER cc_start: 0.7314 (OUTLIER) cc_final: 0.7025 (p) REVERT: Z 20 THR cc_start: 0.7293 (p) cc_final: 0.6841 (t) REVERT: Z 76 LYS cc_start: 0.5999 (OUTLIER) cc_final: 0.4749 (pttt) REVERT: 1 21 LYS cc_start: 0.8327 (mmtt) cc_final: 0.8121 (mmtp) REVERT: 1 32 LYS cc_start: 0.7252 (pttt) cc_final: 0.6483 (tttm) REVERT: 1 47 MET cc_start: 0.7699 (ttm) cc_final: 0.7432 (mtp) REVERT: 1 113 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7671 (tppt) REVERT: 1 119 VAL cc_start: 0.2261 (OUTLIER) cc_final: 0.1857 (t) REVERT: 2 41 PHE cc_start: 0.0347 (OUTLIER) cc_final: -0.0216 (p90) REVERT: 2 64 ILE cc_start: 0.5681 (mm) cc_final: 0.5366 (pt) REVERT: 3 43 ASN cc_start: 0.7627 (m-40) cc_final: 0.7165 (t0) REVERT: 3 63 GLN cc_start: 0.6683 (mm110) cc_final: 0.6048 (mm110) REVERT: 3 66 LYS cc_start: 0.6823 (mttt) cc_final: 0.6576 (mtpt) REVERT: 4 22 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7462 (tm) REVERT: 4 23 ILE cc_start: 0.8301 (mt) cc_final: 0.8051 (mm) REVERT: 4 49 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7383 (mm-40) REVERT: 4 63 GLN cc_start: 0.6784 (tp40) cc_final: 0.6377 (mt0) REVERT: 4 82 GLU cc_start: 0.5131 (OUTLIER) cc_final: 0.4640 (pm20) REVERT: 5 64 ARG cc_start: 0.2698 (OUTLIER) cc_final: 0.1748 (ptt-90) REVERT: 6 27 LYS cc_start: 0.7230 (mtmm) cc_final: 0.6402 (mmmt) outliers start: 291 outliers final: 177 residues processed: 1014 average time/residue: 0.7202 time to fit residues: 1213.6538 Evaluate side-chains 981 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 762 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 ARG Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 162 ARG Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain T residue 17 ARG Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 147 SER Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 101 ASP Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Y residue 150 LYS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 63 THR Chi-restraints excluded: chain 1 residue 81 ASP Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 11 VAL Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 49 GLN Chi-restraints excluded: chain 4 residue 59 ILE Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain 4 residue 82 GLU Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 6 residue 31 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 182 optimal weight: 20.0000 chunk 488 optimal weight: 40.0000 chunk 107 optimal weight: 40.0000 chunk 318 optimal weight: 8.9990 chunk 133 optimal weight: 40.0000 chunk 542 optimal weight: 8.9990 chunk 450 optimal weight: 7.9990 chunk 251 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 175 GLN ** M 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 HIS ** O 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 ASN Q 79 ASN T 8 HIS T 14 GLN T 24 ASN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 GLN 1 15 ASN ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS 3 13 HIS 3 71 GLN 4 7 ASN 4 40 GLN ** 4 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 1.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 73565 Z= 0.440 Angle : 0.865 16.459 107238 Z= 0.434 Chirality : 0.047 0.353 13434 Planarity : 0.007 0.148 7296 Dihedral : 23.731 179.918 30190 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 1.37 % Allowed : 9.49 % Favored : 89.14 % Rotamer: Outliers : 9.59 % Allowed : 24.72 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.05 % 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: -2.47 (0.12), residues: 4014 helix: -0.21 (0.13), residues: 1391 sheet: -1.87 (0.19), residues: 600 loop : -2.68 (0.12), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP S 129 HIS 0.013 0.002 HIS L 44 PHE 0.033 0.003 PHE Z 80 TYR 0.059 0.003 TYR T 12 ARG 0.020 0.001 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 810 time to evaluate : 3.843 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: B 24 PHE cc_start: 0.7240 (m-10) cc_final: 0.5894 (t80) REVERT: B 50 LYS cc_start: 0.7489 (ttmm) cc_final: 0.7186 (mmtt) REVERT: B 54 LYS cc_start: 0.4349 (pttt) cc_final: 0.3908 (mmtt) REVERT: B 70 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8690 (tt) REVERT: B 86 LEU cc_start: 0.7636 (mt) cc_final: 0.7395 (mt) REVERT: B 161 ILE cc_start: 0.8007 (pt) cc_final: 0.7597 (mt) REVERT: B 203 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.5371 (tptm) REVERT: B 223 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6206 (pt) REVERT: C 46 HIS cc_start: 0.7229 (m90) cc_final: 0.6652 (m90) REVERT: C 114 LYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6542 (mmtt) REVERT: C 125 ASP cc_start: 0.7515 (t0) cc_final: 0.7278 (t0) REVERT: C 150 ASP cc_start: 0.7201 (t0) cc_final: 0.6947 (t70) REVERT: C 197 MET cc_start: 0.7888 (mtp) cc_final: 0.6817 (tmm) REVERT: C 198 VAL cc_start: 0.6263 (OUTLIER) cc_final: 0.5962 (t) REVERT: D 34 TYR cc_start: 0.5208 (t80) cc_final: 0.4973 (t80) REVERT: D 78 PHE cc_start: 0.5152 (OUTLIER) cc_final: 0.4729 (m-80) REVERT: D 167 ARG cc_start: 0.5615 (mtt90) cc_final: 0.4829 (ttt180) REVERT: E 16 LYS cc_start: 0.7404 (tptt) cc_final: 0.6620 (mptt) REVERT: E 33 GLU cc_start: 0.8818 (tp30) cc_final: 0.8593 (tp30) REVERT: E 77 LEU cc_start: 0.8388 (mm) cc_final: 0.8169 (mt) REVERT: E 106 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7952 (mt-10) REVERT: E 114 PHE cc_start: 0.7538 (t80) cc_final: 0.7241 (t80) REVERT: E 177 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6094 (tt) REVERT: F 6 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7234 (mtpp) REVERT: F 50 ASN cc_start: 0.8350 (m-40) cc_final: 0.8049 (m110) REVERT: F 52 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8356 (mm) REVERT: F 117 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: F 118 GLU cc_start: 0.7704 (pm20) cc_final: 0.6712 (pm20) REVERT: F 153 ASP cc_start: 0.8823 (m-30) cc_final: 0.7952 (p0) REVERT: F 168 LYS cc_start: 0.6268 (mttp) cc_final: 0.5891 (tppt) REVERT: F 242 LYS cc_start: 0.7859 (mtmm) cc_final: 0.7176 (mmtm) REVERT: F 247 ASP cc_start: 0.7480 (t70) cc_final: 0.7177 (t0) REVERT: F 250 GLU cc_start: 0.7524 (mp0) cc_final: 0.7132 (mp0) REVERT: G 82 ASN cc_start: 0.6881 (OUTLIER) cc_final: 0.6468 (p0) REVERT: G 89 LYS cc_start: 0.7974 (tptt) cc_final: 0.7664 (ttmm) REVERT: G 90 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.7162 (t0) REVERT: G 93 VAL cc_start: 0.8972 (p) cc_final: 0.8647 (m) REVERT: G 99 GLN cc_start: 0.8358 (mt0) cc_final: 0.7687 (mt0) REVERT: G 120 ASN cc_start: 0.7960 (t0) cc_final: 0.7636 (t0) REVERT: G 168 MET cc_start: 0.8751 (pmm) cc_final: 0.8132 (pmm) REVERT: G 180 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7211 (mtt180) REVERT: G 199 MET cc_start: 0.7733 (mmp) cc_final: 0.6976 (tpt) REVERT: G 255 TRP cc_start: 0.7396 (m100) cc_final: 0.6925 (m100) REVERT: G 258 PHE cc_start: 0.6360 (t80) cc_final: 0.6133 (t80) REVERT: H 17 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6482 (mp0) REVERT: H 89 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8046 (tptt) REVERT: H 98 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6784 (tpt90) REVERT: H 111 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6754 (pp) REVERT: H 143 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6348 (tttt) REVERT: H 154 ARG cc_start: 0.6991 (mtm-85) cc_final: 0.6726 (mtp180) REVERT: H 174 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7490 (ttmm) REVERT: H 182 LYS cc_start: 0.6949 (ptpt) cc_final: 0.6700 (ptpt) REVERT: H 197 ARG cc_start: 0.7458 (tpp-160) cc_final: 0.7201 (tpp-160) REVERT: H 206 LYS cc_start: 0.7984 (tttt) cc_final: 0.7426 (tppt) REVERT: H 207 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8095 (mm-30) REVERT: I 35 LYS cc_start: 0.5369 (OUTLIER) cc_final: 0.4809 (mmtt) REVERT: I 49 LYS cc_start: 0.5745 (mttm) cc_final: 0.5416 (tttm) REVERT: I 69 MET cc_start: 0.6461 (tmm) cc_final: 0.5312 (tpp) REVERT: J 77 GLN cc_start: 0.7252 (pm20) cc_final: 0.6604 (tp40) REVERT: J 98 ARG cc_start: 0.6142 (mtm180) cc_final: 0.5860 (mtt-85) REVERT: J 128 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7292 (mm-30) REVERT: J 143 MET cc_start: 0.7892 (mmm) cc_final: 0.7521 (mtp) REVERT: J 164 ASN cc_start: 0.6226 (OUTLIER) cc_final: 0.5908 (m-40) REVERT: J 177 LYS cc_start: 0.7794 (tmtt) cc_final: 0.7548 (tptt) REVERT: J 183 ASP cc_start: 0.7097 (t70) cc_final: 0.6620 (m-30) REVERT: K 89 ILE cc_start: 0.7694 (mm) cc_final: 0.7376 (mm) REVERT: K 114 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7646 (pp20) REVERT: K 115 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7149 (mm-30) REVERT: K 120 HIS cc_start: 0.7862 (t70) cc_final: 0.7522 (t-170) REVERT: L 28 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7692 (mp0) REVERT: L 59 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6763 (mttt) REVERT: L 86 SER cc_start: 0.8162 (t) cc_final: 0.7808 (p) REVERT: L 92 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.6405 (tpt170) REVERT: L 166 LYS cc_start: 0.4370 (OUTLIER) cc_final: 0.3708 (mmmt) REVERT: L 180 ARG cc_start: 0.7279 (mtp180) cc_final: 0.6628 (mmt-90) REVERT: L 210 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.6776 (tpt170) REVERT: L 212 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7171 (mtm) REVERT: M 35 LYS cc_start: 0.3521 (OUTLIER) cc_final: 0.3268 (tttt) REVERT: M 133 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.6942 (tmtt) REVERT: M 141 LYS cc_start: 0.6105 (mtmt) cc_final: 0.5698 (ptmt) REVERT: N 39 MET cc_start: 0.4282 (ptp) cc_final: 0.4069 (ptm) REVERT: N 62 ILE cc_start: 0.6923 (mm) cc_final: 0.6661 (tp) REVERT: N 77 ASP cc_start: 0.7439 (p0) cc_final: 0.6867 (p0) REVERT: N 103 ILE cc_start: 0.2587 (OUTLIER) cc_final: 0.2377 (mp) REVERT: N 112 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.4775 (pm20) REVERT: O 21 LEU cc_start: 0.2452 (OUTLIER) cc_final: 0.2171 (pp) REVERT: O 42 ARG cc_start: 0.5589 (OUTLIER) cc_final: 0.3675 (mtm110) REVERT: P 39 ASP cc_start: 0.8703 (t70) cc_final: 0.8367 (t70) REVERT: P 56 ILE cc_start: 0.7359 (mm) cc_final: 0.6713 (mt) REVERT: P 60 MET cc_start: 0.8409 (mtt) cc_final: 0.8056 (mtp) REVERT: P 75 MET cc_start: 0.7368 (ttp) cc_final: 0.7099 (ttm) REVERT: P 106 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7205 (mmmm) REVERT: P 114 SER cc_start: 0.8226 (m) cc_final: 0.7907 (t) REVERT: P 142 LYS cc_start: 0.8542 (tttm) cc_final: 0.8243 (ttmt) REVERT: Q 37 ARG cc_start: 0.8014 (ttt180) cc_final: 0.7393 (tmm-80) REVERT: Q 63 GLN cc_start: 0.7234 (OUTLIER) cc_final: 0.6736 (tp-100) REVERT: Q 75 GLN cc_start: 0.7529 (mt0) cc_final: 0.7002 (tp40) REVERT: Q 81 LYS cc_start: 0.6461 (mmtp) cc_final: 0.6252 (tttt) REVERT: Q 99 ASN cc_start: 0.7542 (t0) cc_final: 0.7206 (m-40) REVERT: Q 144 ARG cc_start: 0.8039 (ttt180) cc_final: 0.7681 (mmt90) REVERT: R 95 HIS cc_start: 0.2867 (OUTLIER) cc_final: 0.2498 (m90) REVERT: S 26 GLU cc_start: 0.3121 (OUTLIER) cc_final: 0.2428 (pm20) REVERT: S 32 LEU cc_start: 0.7525 (mt) cc_final: 0.7311 (mt) REVERT: S 41 ARG cc_start: 0.5479 (OUTLIER) cc_final: 0.4456 (ptm160) REVERT: S 96 LYS cc_start: 0.6575 (mmtt) cc_final: 0.6254 (ttpt) REVERT: S 137 HIS cc_start: 0.3861 (m90) cc_final: 0.3551 (m90) REVERT: T 24 ASN cc_start: 0.4062 (OUTLIER) cc_final: 0.3501 (t0) REVERT: T 29 ILE cc_start: 0.7546 (mt) cc_final: 0.7153 (tt) REVERT: T 35 ASN cc_start: 0.7643 (m-40) cc_final: 0.6702 (t0) REVERT: T 42 ARG cc_start: 0.6843 (mtp85) cc_final: 0.6251 (ttm-80) REVERT: U 49 GLN cc_start: 0.7104 (mt0) cc_final: 0.6831 (mm-40) REVERT: V 9 HIS cc_start: 0.7098 (m-70) cc_final: 0.6778 (m-70) REVERT: V 134 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8921 (mp) REVERT: W 46 MET cc_start: 0.6932 (tpt) cc_final: 0.6606 (mmp) REVERT: W 78 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5641 (tpt170) REVERT: X 41 GLN cc_start: 0.5957 (mt0) cc_final: 0.5714 (mt0) REVERT: X 43 ARG cc_start: 0.5300 (ttt-90) cc_final: 0.3321 (ttp-110) REVERT: X 80 LEU cc_start: 0.2217 (OUTLIER) cc_final: 0.1627 (mt) REVERT: Y 100 ARG cc_start: 0.4672 (mtm-85) cc_final: 0.4290 (ptp-110) REVERT: Y 107 ARG cc_start: 0.5931 (OUTLIER) cc_final: 0.5265 (mtp-110) REVERT: Y 108 ARG cc_start: 0.3827 (tpm170) cc_final: 0.3410 (mtp-110) REVERT: Y 141 LYS cc_start: 0.5756 (OUTLIER) cc_final: 0.4967 (tmmt) REVERT: Z 18 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8270 (m) REVERT: Z 20 THR cc_start: 0.7944 (p) cc_final: 0.7416 (t) REVERT: Z 60 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7173 (mm-40) REVERT: Z 70 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6790 (ttp80) REVERT: Z 76 LYS cc_start: 0.6353 (OUTLIER) cc_final: 0.4901 (pttt) REVERT: 1 32 LYS cc_start: 0.7350 (pttt) cc_final: 0.6656 (tttm) REVERT: 1 47 MET cc_start: 0.7767 (ttm) cc_final: 0.7563 (mtp) REVERT: 1 113 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7804 (tppt) REVERT: 2 41 PHE cc_start: 0.0232 (OUTLIER) cc_final: -0.0663 (p90) REVERT: 2 64 ILE cc_start: 0.5390 (mm) cc_final: 0.5109 (pt) REVERT: 3 11 SER cc_start: 0.8596 (m) cc_final: 0.7912 (p) REVERT: 3 43 ASN cc_start: 0.7547 (m-40) cc_final: 0.7279 (t0) REVERT: 3 50 GLN cc_start: 0.5646 (mm110) cc_final: 0.5127 (mt0) REVERT: 3 63 GLN cc_start: 0.7675 (mm110) cc_final: 0.7256 (mm-40) REVERT: 4 22 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7586 (tm) REVERT: 4 40 GLN cc_start: 0.5715 (pt0) cc_final: 0.5358 (pt0) REVERT: 4 49 GLN cc_start: 0.7945 (mt0) cc_final: 0.7270 (mp10) REVERT: 4 61 LEU cc_start: 0.8444 (mt) cc_final: 0.8100 (mt) REVERT: 4 62 CYS cc_start: 0.8304 (p) cc_final: 0.8045 (p) REVERT: 5 64 ARG cc_start: 0.3545 (OUTLIER) cc_final: 0.2350 (ptt-90) REVERT: 6 27 LYS cc_start: 0.7275 (mtmm) cc_final: 0.6521 (mmmt) outliers start: 346 outliers final: 202 residues processed: 1040 average time/residue: 0.7303 time to fit residues: 1254.8380 Evaluate side-chains 989 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 738 time to evaluate : 3.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 78 PHE Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 82 ASN Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 41 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 66 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 27 ILE Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 136 ILE Chi-restraints excluded: chain J residue 162 ARG Chi-restraints excluded: chain J residue 164 ASN Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 180 THR Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 35 LYS Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 40 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 89 ARG Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain T residue 24 ASN Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 147 SER Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 134 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain V residue 142 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 107 ARG Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Y residue 145 ARG Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 70 ARG Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain Z residue 77 LEU Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 9 VAL Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 63 THR Chi-restraints excluded: chain 1 residue 81 ASP Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 2 residue 41 PHE Chi-restraints excluded: chain 2 residue 60 THR Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 79 ILE Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 6 residue 31 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 523 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 309 optimal weight: 5.9990 chunk 396 optimal weight: 6.9990 chunk 307 optimal weight: 7.9990 chunk 456 optimal weight: 0.8980 chunk 303 optimal weight: 0.3980 chunk 540 optimal weight: 3.9990 chunk 338 optimal weight: 9.9990 chunk 329 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN ** O 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 ASN Q 79 ASN U 22 GLN ** U 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS 4 7 ASN ** 4 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 1.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 73565 Z= 0.213 Angle : 0.665 11.287 107238 Z= 0.337 Chirality : 0.038 0.350 13434 Planarity : 0.005 0.143 7296 Dihedral : 23.427 177.853 30182 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 1.32 % Allowed : 7.95 % Favored : 90.73 % Rotamer: Outliers : 6.87 % Allowed : 28.26 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -2.15 (0.12), residues: 4014 helix: 0.15 (0.13), residues: 1405 sheet: -1.72 (0.19), residues: 603 loop : -2.57 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 72 HIS 0.011 0.001 HIS K 101 PHE 0.024 0.002 PHE 4 77 TYR 0.030 0.002 TYR T 12 ARG 0.012 0.001 ARG K 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 814 time to evaluate : 3.832 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: B 24 PHE cc_start: 0.7188 (m-80) cc_final: 0.5819 (t80) REVERT: B 50 LYS cc_start: 0.7320 (ttmm) cc_final: 0.7099 (mmtt) REVERT: B 86 LEU cc_start: 0.7535 (mt) cc_final: 0.7286 (mt) REVERT: B 95 ASP cc_start: 0.6214 (t0) cc_final: 0.5888 (t70) REVERT: B 148 ASN cc_start: 0.6410 (m-40) cc_final: 0.5753 (t0) REVERT: C 49 ASN cc_start: 0.7615 (t0) cc_final: 0.7414 (t0) REVERT: C 110 GLN cc_start: 0.8026 (pm20) cc_final: 0.7695 (pm20) REVERT: C 153 LEU cc_start: 0.7295 (mt) cc_final: 0.6839 (mp) REVERT: C 197 MET cc_start: 0.7832 (mtp) cc_final: 0.6372 (tmm) REVERT: C 198 VAL cc_start: 0.6215 (t) cc_final: 0.5394 (t) REVERT: D 23 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6078 (tp30) REVERT: D 151 MET cc_start: 0.5386 (mtm) cc_final: 0.4750 (ptt) REVERT: D 164 PRO cc_start: 0.6816 (Cg_exo) cc_final: 0.6500 (Cg_endo) REVERT: D 167 ARG cc_start: 0.5632 (mtt90) cc_final: 0.4867 (ttt180) REVERT: E 14 ASN cc_start: 0.8155 (m110) cc_final: 0.7910 (m-40) REVERT: E 16 LYS cc_start: 0.7314 (tptt) cc_final: 0.6525 (mptt) REVERT: E 33 GLU cc_start: 0.8813 (tp30) cc_final: 0.8234 (tm-30) REVERT: E 77 LEU cc_start: 0.8313 (mm) cc_final: 0.8089 (mt) REVERT: E 80 MET cc_start: 0.7425 (mmm) cc_final: 0.7175 (mmp) REVERT: E 106 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7708 (mt-10) REVERT: E 114 PHE cc_start: 0.7578 (t80) cc_final: 0.7275 (t80) REVERT: E 177 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6219 (tt) REVERT: F 6 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7222 (mtpp) REVERT: F 50 ASN cc_start: 0.8358 (m-40) cc_final: 0.8130 (m110) REVERT: F 60 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8062 (mt-10) REVERT: F 117 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7669 (pm20) REVERT: F 118 GLU cc_start: 0.8044 (pm20) cc_final: 0.7283 (pm20) REVERT: F 153 ASP cc_start: 0.8685 (m-30) cc_final: 0.7906 (p0) REVERT: F 168 LYS cc_start: 0.6403 (mttp) cc_final: 0.5861 (tppt) REVERT: F 252 ARG cc_start: 0.7921 (mmm160) cc_final: 0.7503 (mmm160) REVERT: G 89 LYS cc_start: 0.7735 (tptt) cc_final: 0.7423 (ttmm) REVERT: G 90 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7141 (t0) REVERT: G 93 VAL cc_start: 0.8788 (p) cc_final: 0.8551 (m) REVERT: G 99 GLN cc_start: 0.8245 (mt0) cc_final: 0.7603 (mt0) REVERT: G 180 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7328 (mtt180) REVERT: G 199 MET cc_start: 0.7686 (mmp) cc_final: 0.7034 (tpt) REVERT: H 57 ASP cc_start: 0.7668 (p0) cc_final: 0.7254 (t0) REVERT: H 59 GLN cc_start: 0.8223 (mp10) cc_final: 0.7917 (mp10) REVERT: H 89 LYS cc_start: 0.8515 (mmmt) cc_final: 0.7978 (tptt) REVERT: H 106 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7131 (mt) REVERT: H 143 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6656 (tttt) REVERT: H 154 ARG cc_start: 0.6996 (mtm-85) cc_final: 0.6700 (mtp180) REVERT: H 174 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.6762 (tttm) REVERT: H 197 ARG cc_start: 0.7406 (tpp-160) cc_final: 0.7107 (tpp-160) REVERT: H 206 LYS cc_start: 0.8127 (tttt) cc_final: 0.7521 (tppt) REVERT: H 207 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7973 (mm-30) REVERT: I 35 LYS cc_start: 0.5623 (OUTLIER) cc_final: 0.4868 (mmtt) REVERT: I 49 LYS cc_start: 0.5829 (mttm) cc_final: 0.5433 (tttm) REVERT: I 67 MET cc_start: 0.6674 (tpt) cc_final: 0.6190 (mmm) REVERT: I 69 MET cc_start: 0.6362 (tmm) cc_final: 0.5203 (tpp) REVERT: I 72 ARG cc_start: 0.2690 (ptm-80) cc_final: 0.2416 (ttp-170) REVERT: J 9 LEU cc_start: 0.4984 (OUTLIER) cc_final: 0.4751 (pp) REVERT: J 98 ARG cc_start: 0.6043 (mtm180) cc_final: 0.5636 (mtt-85) REVERT: J 128 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7385 (mm-30) REVERT: J 137 ILE cc_start: 0.7420 (OUTLIER) cc_final: 0.7209 (mt) REVERT: J 143 MET cc_start: 0.7557 (mmm) cc_final: 0.7244 (mtp) REVERT: J 162 ARG cc_start: 0.5236 (OUTLIER) cc_final: 0.4995 (tpp80) REVERT: J 177 LYS cc_start: 0.7788 (tmtt) cc_final: 0.7573 (tptt) REVERT: J 183 ASP cc_start: 0.7139 (t70) cc_final: 0.6804 (m-30) REVERT: K 89 ILE cc_start: 0.7818 (mm) cc_final: 0.7483 (mm) REVERT: K 114 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7603 (pp20) REVERT: K 118 ARG cc_start: 0.7039 (mtm110) cc_final: 0.6818 (mtm110) REVERT: K 120 HIS cc_start: 0.7909 (t70) cc_final: 0.7538 (t-170) REVERT: L 8 ARG cc_start: 0.5602 (OUTLIER) cc_final: 0.3220 (mtp180) REVERT: L 28 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7785 (mt-10) REVERT: L 59 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6642 (mtpt) REVERT: L 92 ARG cc_start: 0.7491 (ttm-80) cc_final: 0.6271 (tpt170) REVERT: L 105 ASP cc_start: 0.8301 (t70) cc_final: 0.7573 (p0) REVERT: L 166 LYS cc_start: 0.4313 (OUTLIER) cc_final: 0.3730 (mmmt) REVERT: L 173 LEU cc_start: 0.7662 (tp) cc_final: 0.7314 (mm) REVERT: L 180 ARG cc_start: 0.7118 (mtp180) cc_final: 0.6692 (mmt180) REVERT: L 203 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6778 (t70) REVERT: L 210 ARG cc_start: 0.7490 (ttp-110) cc_final: 0.6777 (tpt170) REVERT: L 212 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7072 (mtm) REVERT: M 112 ARG cc_start: 0.3721 (ptm-80) cc_final: 0.3433 (ptm160) REVERT: M 124 ARG cc_start: 0.5467 (OUTLIER) cc_final: 0.4730 (ttm110) REVERT: M 133 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7080 (tmtt) REVERT: M 141 LYS cc_start: 0.6479 (mtmt) cc_final: 0.5871 (ptmt) REVERT: N 39 MET cc_start: 0.4111 (ptp) cc_final: 0.3716 (ptm) REVERT: N 62 ILE cc_start: 0.6706 (mm) cc_final: 0.6460 (tt) REVERT: N 77 ASP cc_start: 0.7601 (p0) cc_final: 0.7375 (p0) REVERT: N 112 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.4778 (pm20) REVERT: O 21 LEU cc_start: 0.2068 (OUTLIER) cc_final: 0.1815 (pp) REVERT: O 42 ARG cc_start: 0.5260 (OUTLIER) cc_final: 0.3475 (mtm110) REVERT: O 73 LYS cc_start: 0.6566 (mmmt) cc_final: 0.6048 (mtmt) REVERT: P 37 PHE cc_start: 0.7136 (m-80) cc_final: 0.6807 (m-80) REVERT: P 39 ASP cc_start: 0.8424 (t70) cc_final: 0.7815 (t0) REVERT: P 61 LYS cc_start: 0.8665 (mmmt) cc_final: 0.7636 (mmmm) REVERT: P 63 LYS cc_start: 0.4873 (tppt) cc_final: 0.4603 (ptpp) REVERT: P 75 MET cc_start: 0.7488 (ttp) cc_final: 0.7135 (ttm) REVERT: P 76 MET cc_start: 0.7478 (mmm) cc_final: 0.7167 (mmp) REVERT: P 114 SER cc_start: 0.8276 (m) cc_final: 0.7987 (t) REVERT: P 142 LYS cc_start: 0.8420 (tttm) cc_final: 0.8171 (ttmt) REVERT: Q 9 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8339 (tt) REVERT: Q 26 ASP cc_start: 0.8738 (t0) cc_final: 0.8460 (t70) REVERT: Q 63 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6934 (tp40) REVERT: Q 75 GLN cc_start: 0.7644 (mt0) cc_final: 0.7083 (tp40) REVERT: Q 99 ASN cc_start: 0.7649 (t0) cc_final: 0.7216 (m-40) REVERT: Q 144 ARG cc_start: 0.8064 (ttt180) cc_final: 0.7689 (mpt180) REVERT: R 95 HIS cc_start: 0.3150 (OUTLIER) cc_final: 0.2780 (m90) REVERT: S 26 GLU cc_start: 0.3508 (OUTLIER) cc_final: 0.2754 (pm20) REVERT: S 32 LEU cc_start: 0.7636 (mt) cc_final: 0.7423 (mt) REVERT: S 41 ARG cc_start: 0.5290 (OUTLIER) cc_final: 0.4580 (ptm160) REVERT: S 96 LYS cc_start: 0.6447 (mmtt) cc_final: 0.6199 (ttpt) REVERT: S 101 ILE cc_start: 0.4530 (mm) cc_final: 0.4126 (mt) REVERT: S 137 HIS cc_start: 0.3744 (m90) cc_final: 0.3434 (m90) REVERT: T 35 ASN cc_start: 0.7640 (m-40) cc_final: 0.6766 (t0) REVERT: T 42 ARG cc_start: 0.6794 (mtp85) cc_final: 0.6128 (ttm-80) REVERT: V 8 GLN cc_start: 0.7453 (mm-40) cc_final: 0.7150 (mm-40) REVERT: V 9 HIS cc_start: 0.7034 (m-70) cc_final: 0.6739 (m-70) REVERT: V 134 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8834 (mp) REVERT: V 157 GLN cc_start: 0.7497 (mp10) cc_final: 0.6226 (mp10) REVERT: W 78 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5619 (tpt-90) REVERT: X 43 ARG cc_start: 0.4964 (ttt-90) cc_final: 0.3194 (ttp-110) REVERT: Y 59 PHE cc_start: 0.4609 (p90) cc_final: 0.4389 (p90) REVERT: Y 100 ARG cc_start: 0.4964 (mtm-85) cc_final: 0.4612 (ptp-170) REVERT: Y 108 ARG cc_start: 0.3878 (tpm170) cc_final: 0.3604 (mtp-110) REVERT: Y 164 LYS cc_start: 0.4017 (mtpt) cc_final: 0.3739 (mttp) REVERT: Z 18 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.7974 (m) REVERT: Z 20 THR cc_start: 0.7917 (p) cc_final: 0.7350 (t) REVERT: Z 70 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6800 (ttm110) REVERT: Z 76 LYS cc_start: 0.6058 (OUTLIER) cc_final: 0.4826 (pttt) REVERT: 1 32 LYS cc_start: 0.7298 (pttt) cc_final: 0.6559 (tttm) REVERT: 1 47 MET cc_start: 0.7777 (ttm) cc_final: 0.7503 (mtp) REVERT: 1 113 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7682 (mmmt) REVERT: 2 64 ILE cc_start: 0.5547 (mm) cc_final: 0.5306 (pt) REVERT: 3 11 SER cc_start: 0.8410 (m) cc_final: 0.8047 (p) REVERT: 3 36 ILE cc_start: 0.8438 (mt) cc_final: 0.8206 (mt) REVERT: 3 63 GLN cc_start: 0.7723 (mm110) cc_final: 0.7333 (mm-40) REVERT: 4 22 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7833 (tp) REVERT: 4 49 GLN cc_start: 0.7769 (mt0) cc_final: 0.7559 (mp10) REVERT: 4 61 LEU cc_start: 0.8285 (mt) cc_final: 0.7926 (mt) REVERT: 4 78 ARG cc_start: 0.6618 (mtm-85) cc_final: 0.6352 (mpt180) REVERT: 5 22 VAL cc_start: 0.5054 (OUTLIER) cc_final: 0.4747 (p) REVERT: 5 64 ARG cc_start: 0.3567 (OUTLIER) cc_final: 0.2409 (ptt-90) REVERT: 6 27 LYS cc_start: 0.7066 (mtmm) cc_final: 0.6282 (mmmt) outliers start: 248 outliers final: 164 residues processed: 966 average time/residue: 0.7189 time to fit residues: 1148.8015 Evaluate side-chains 952 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 752 time to evaluate : 3.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 162 ARG Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 184 CYS Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 206 LEU Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 124 ARG Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 79 ASN Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 95 PHE Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 26 GLU Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 89 ARG Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 147 SER Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 134 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 70 ARG Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 63 THR Chi-restraints excluded: chain 1 residue 81 ASP Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 2 residue 60 THR Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 6 residue 31 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 334 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 322 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 106 optimal weight: 40.0000 chunk 104 optimal weight: 30.0000 chunk 343 optimal weight: 7.9990 chunk 368 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 425 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN C 113 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS ** I 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 HIS ** O 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN U 22 GLN ** U 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 HIS ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS 4 40 GLN ** 4 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 1.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 73565 Z= 0.371 Angle : 0.786 11.488 107238 Z= 0.395 Chirality : 0.044 0.549 13434 Planarity : 0.006 0.145 7296 Dihedral : 23.553 179.313 30176 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 1.22 % Allowed : 9.67 % Favored : 89.11 % Rotamer: Outliers : 7.95 % Allowed : 28.04 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -2.40 (0.12), residues: 4014 helix: -0.15 (0.13), residues: 1407 sheet: -1.83 (0.19), residues: 606 loop : -2.66 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 29 HIS 0.012 0.002 HIS F 36 PHE 0.026 0.002 PHE Z 80 TYR 0.034 0.003 TYR T 12 ARG 0.010 0.001 ARG S 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 760 time to evaluate : 4.322 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: B 50 LYS cc_start: 0.7028 (ttmm) cc_final: 0.6716 (mmtt) REVERT: B 70 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8709 (tt) REVERT: B 95 ASP cc_start: 0.6010 (t0) cc_final: 0.5682 (t70) REVERT: B 148 ASN cc_start: 0.6418 (m-40) cc_final: 0.5894 (t0) REVERT: B 223 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6650 (pt) REVERT: C 49 ASN cc_start: 0.7560 (t0) cc_final: 0.7359 (t0) REVERT: C 56 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7658 (mttt) REVERT: C 110 GLN cc_start: 0.8093 (pm20) cc_final: 0.7696 (pm20) REVERT: C 165 LYS cc_start: 0.7168 (mppt) cc_final: 0.6802 (mtpp) REVERT: C 197 MET cc_start: 0.7776 (mtp) cc_final: 0.6638 (tmm) REVERT: C 198 VAL cc_start: 0.5732 (OUTLIER) cc_final: 0.5096 (t) REVERT: D 23 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6562 (mm-30) REVERT: D 128 MET cc_start: 0.7492 (mmm) cc_final: 0.6174 (tpt) REVERT: D 164 PRO cc_start: 0.7328 (Cg_exo) cc_final: 0.7085 (Cg_endo) REVERT: D 167 ARG cc_start: 0.5688 (mtt90) cc_final: 0.4894 (ttt180) REVERT: E 16 LYS cc_start: 0.7351 (tptt) cc_final: 0.6567 (mptt) REVERT: E 33 GLU cc_start: 0.8837 (tp30) cc_final: 0.8616 (tp30) REVERT: E 77 LEU cc_start: 0.8394 (mm) cc_final: 0.8163 (mt) REVERT: E 80 MET cc_start: 0.7475 (mmm) cc_final: 0.7252 (mmp) REVERT: E 106 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7685 (mt-10) REVERT: E 114 PHE cc_start: 0.7532 (t80) cc_final: 0.7214 (t80) REVERT: F 6 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7216 (mtpp) REVERT: F 50 ASN cc_start: 0.8515 (m-40) cc_final: 0.8169 (m110) REVERT: F 60 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8120 (mt-10) REVERT: F 117 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7741 (pm20) REVERT: F 168 LYS cc_start: 0.6542 (mttp) cc_final: 0.5983 (tppt) REVERT: F 250 GLU cc_start: 0.7291 (mp0) cc_final: 0.6704 (mp0) REVERT: F 255 ARG cc_start: 0.6976 (tpt90) cc_final: 0.6256 (ttt180) REVERT: G 89 LYS cc_start: 0.7860 (tptt) cc_final: 0.7556 (ttmm) REVERT: G 90 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7126 (t0) REVERT: G 93 VAL cc_start: 0.8758 (p) cc_final: 0.8544 (m) REVERT: G 99 GLN cc_start: 0.8341 (mt0) cc_final: 0.7711 (mt0) REVERT: G 168 MET cc_start: 0.8565 (pmm) cc_final: 0.8191 (pmm) REVERT: G 180 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7236 (mtt180) REVERT: G 199 MET cc_start: 0.7570 (mmp) cc_final: 0.6920 (tpt) REVERT: G 236 TYR cc_start: 0.8171 (t80) cc_final: 0.7277 (t80) REVERT: G 246 ASN cc_start: 0.7845 (m-40) cc_final: 0.7452 (t0) REVERT: H 57 ASP cc_start: 0.8049 (p0) cc_final: 0.7524 (t0) REVERT: H 89 LYS cc_start: 0.8548 (mmmt) cc_final: 0.8021 (tptt) REVERT: H 111 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6595 (pp) REVERT: H 143 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6423 (mttt) REVERT: H 154 ARG cc_start: 0.6986 (mtm-85) cc_final: 0.6691 (mtp180) REVERT: H 174 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7025 (tttm) REVERT: H 177 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6677 (mtt-85) REVERT: H 197 ARG cc_start: 0.7447 (tpp-160) cc_final: 0.7149 (tpp-160) REVERT: H 206 LYS cc_start: 0.8125 (tttt) cc_final: 0.7518 (tppt) REVERT: H 207 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7975 (mm-30) REVERT: I 35 LYS cc_start: 0.5640 (OUTLIER) cc_final: 0.5003 (mmtt) REVERT: I 49 LYS cc_start: 0.5838 (mttm) cc_final: 0.5423 (tttm) REVERT: I 67 MET cc_start: 0.6788 (tpt) cc_final: 0.6270 (mmm) REVERT: I 72 ARG cc_start: 0.2792 (ptm-80) cc_final: 0.2540 (ttp-170) REVERT: J 9 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5426 (pp) REVERT: J 98 ARG cc_start: 0.6534 (mtm180) cc_final: 0.6116 (mtt-85) REVERT: J 119 LEU cc_start: 0.8009 (tp) cc_final: 0.7777 (tt) REVERT: J 128 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7413 (mm-30) REVERT: J 143 MET cc_start: 0.7791 (mmm) cc_final: 0.7400 (mtp) REVERT: J 183 ASP cc_start: 0.7552 (t70) cc_final: 0.7147 (m-30) REVERT: K 89 ILE cc_start: 0.7785 (mm) cc_final: 0.7446 (mm) REVERT: K 114 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7648 (pp20) REVERT: K 120 HIS cc_start: 0.7919 (t70) cc_final: 0.7281 (t70) REVERT: L 28 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: L 44 HIS cc_start: 0.7742 (m-70) cc_final: 0.7304 (m170) REVERT: L 59 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6576 (mtpt) REVERT: L 92 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.6206 (tpt170) REVERT: L 166 LYS cc_start: 0.4302 (OUTLIER) cc_final: 0.3757 (mmmt) REVERT: L 180 ARG cc_start: 0.7324 (mtp180) cc_final: 0.6788 (mmt-90) REVERT: L 210 ARG cc_start: 0.7492 (ttp-110) cc_final: 0.6774 (tpt170) REVERT: L 212 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7176 (mtm) REVERT: M 35 LYS cc_start: 0.3882 (OUTLIER) cc_final: 0.3606 (ttpp) REVERT: M 112 ARG cc_start: 0.3621 (ptm-80) cc_final: 0.3060 (ptm-80) REVERT: M 124 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.5081 (ttm110) REVERT: M 141 LYS cc_start: 0.5900 (mtmt) cc_final: 0.5606 (ptmt) REVERT: N 54 ARG cc_start: 0.2408 (mtm-85) cc_final: 0.2172 (mtm-85) REVERT: N 62 ILE cc_start: 0.7027 (mm) cc_final: 0.6555 (tp) REVERT: N 77 ASP cc_start: 0.7709 (p0) cc_final: 0.7281 (p0) REVERT: N 81 LEU cc_start: 0.5745 (tp) cc_final: 0.5484 (tt) REVERT: N 112 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.4983 (pm20) REVERT: O 21 LEU cc_start: 0.2631 (OUTLIER) cc_final: 0.2275 (pp) REVERT: O 42 ARG cc_start: 0.4865 (OUTLIER) cc_final: 0.3266 (mtm110) REVERT: O 72 TRP cc_start: 0.5547 (OUTLIER) cc_final: 0.5257 (p-90) REVERT: O 73 LYS cc_start: 0.6632 (mmmt) cc_final: 0.6076 (mtmt) REVERT: P 37 PHE cc_start: 0.8066 (m-80) cc_final: 0.7728 (m-80) REVERT: P 56 ILE cc_start: 0.7567 (mm) cc_final: 0.7318 (mt) REVERT: P 61 LYS cc_start: 0.8724 (mmmt) cc_final: 0.8193 (mmmm) REVERT: P 63 LYS cc_start: 0.5112 (tppt) cc_final: 0.4599 (ptpp) REVERT: P 69 SER cc_start: 0.8237 (p) cc_final: 0.7444 (m) REVERT: P 75 MET cc_start: 0.7439 (ttp) cc_final: 0.7058 (ttm) REVERT: P 106 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7336 (mmmm) REVERT: P 114 SER cc_start: 0.8144 (m) cc_final: 0.7924 (t) REVERT: P 142 LYS cc_start: 0.8489 (tttm) cc_final: 0.8225 (ttmt) REVERT: P 146 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8005 (ptm-80) REVERT: Q 63 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6938 (tp40) REVERT: Q 75 GLN cc_start: 0.7707 (mt0) cc_final: 0.7089 (tm-30) REVERT: Q 81 LYS cc_start: 0.6487 (mmtp) cc_final: 0.6200 (tttt) REVERT: Q 144 ARG cc_start: 0.8009 (ttt180) cc_final: 0.7689 (mmt90) REVERT: R 95 HIS cc_start: 0.2886 (OUTLIER) cc_final: 0.2512 (m90) REVERT: S 96 LYS cc_start: 0.6565 (mmtt) cc_final: 0.6265 (ttpt) REVERT: S 137 HIS cc_start: 0.3728 (m90) cc_final: 0.3375 (m90) REVERT: T 17 ARG cc_start: 0.6234 (pmt170) cc_final: 0.5189 (tpt90) REVERT: T 42 ARG cc_start: 0.6927 (mtp85) cc_final: 0.6305 (ttm-80) REVERT: V 124 ASP cc_start: 0.8739 (m-30) cc_final: 0.8406 (m-30) REVERT: V 134 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8886 (mp) REVERT: W 60 ARG cc_start: 0.5416 (mmp80) cc_final: 0.4398 (ttm110) REVERT: W 78 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6159 (tpt-90) REVERT: W 81 ARG cc_start: 0.5429 (OUTLIER) cc_final: 0.4974 (mmm-85) REVERT: X 43 ARG cc_start: 0.5051 (ttt-90) cc_final: 0.4134 (tpt-90) REVERT: X 78 THR cc_start: 0.3688 (OUTLIER) cc_final: 0.3459 (t) REVERT: Y 100 ARG cc_start: 0.5137 (mtm-85) cc_final: 0.4810 (ptp-110) REVERT: Y 105 LYS cc_start: 0.5955 (mtmm) cc_final: 0.5385 (ttmt) REVERT: Z 18 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.7886 (m) REVERT: Z 20 THR cc_start: 0.7949 (p) cc_final: 0.7346 (t) REVERT: Z 35 ASN cc_start: 0.7756 (m-40) cc_final: 0.7430 (m110) REVERT: Z 60 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7122 (mm-40) REVERT: Z 76 LYS cc_start: 0.6569 (OUTLIER) cc_final: 0.5067 (pttt) REVERT: 1 32 LYS cc_start: 0.7367 (pttt) cc_final: 0.6648 (tttm) REVERT: 1 47 MET cc_start: 0.7844 (ttm) cc_final: 0.7531 (mtp) REVERT: 1 50 LEU cc_start: 0.7696 (mt) cc_final: 0.7487 (mt) REVERT: 1 71 LYS cc_start: 0.8022 (mptt) cc_final: 0.7777 (mmtt) REVERT: 1 113 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7823 (tppt) REVERT: 2 64 ILE cc_start: 0.5550 (mm) cc_final: 0.5325 (pt) REVERT: 2 99 LYS cc_start: 0.2201 (tttp) cc_final: 0.1517 (tttp) REVERT: 3 11 SER cc_start: 0.8404 (m) cc_final: 0.8040 (p) REVERT: 3 36 ILE cc_start: 0.8541 (mt) cc_final: 0.8335 (mt) REVERT: 3 63 GLN cc_start: 0.7774 (mm110) cc_final: 0.7362 (mm-40) REVERT: 4 22 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7787 (tp) REVERT: 4 61 LEU cc_start: 0.8110 (mt) cc_final: 0.7718 (mt) REVERT: 4 78 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.6913 (mpt180) REVERT: 5 26 ARG cc_start: 0.4561 (ttm170) cc_final: 0.4141 (tpt-90) REVERT: 5 64 ARG cc_start: 0.3672 (OUTLIER) cc_final: 0.2468 (ptt-90) REVERT: 6 27 LYS cc_start: 0.7065 (mtmm) cc_final: 0.6338 (mmmt) outliers start: 287 outliers final: 200 residues processed: 944 average time/residue: 0.7449 time to fit residues: 1153.2591 Evaluate side-chains 960 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 724 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 18 TRP Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 159 LYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 180 ARG Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 256 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 35 LYS Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain I residue 154 PHE Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 162 ARG Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 184 CYS Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain L residue 212 MET Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 35 LYS Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 124 ARG Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 91 THR Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain P residue 119 LEU Chi-restraints excluded: chain P residue 137 THR Chi-restraints excluded: chain P residue 146 ARG Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 41 ARG Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 70 VAL Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 31 SER Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 134 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 24 LEU Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain W residue 101 ASP Chi-restraints excluded: chain W residue 102 THR Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 92 SER Chi-restraints excluded: chain X residue 114 TYR Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Y residue 145 ARG Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 18 SER Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 1 residue 63 THR Chi-restraints excluded: chain 1 residue 81 ASP Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 2 residue 74 VAL Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 79 ILE Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 4 residue 40 GLN Chi-restraints excluded: chain 4 residue 72 THR Chi-restraints excluded: chain 4 residue 73 GLU Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 64 ARG Chi-restraints excluded: chain 6 residue 31 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 491 optimal weight: 0.6980 chunk 518 optimal weight: 9.9990 chunk 472 optimal weight: 7.9990 chunk 503 optimal weight: 2.9990 chunk 517 optimal weight: 2.9990 chunk 303 optimal weight: 50.0000 chunk 219 optimal weight: 2.9990 chunk 395 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 455 optimal weight: 6.9990 chunk 476 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN ** I 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 GLN ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN O 43 HIS O 50 ASN ** O 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 14 GLN T 24 ASN U 22 GLN U 78 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 ASN ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 81 HIS 4 7 ASN ** 4 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 1.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 73565 Z= 0.186 Angle : 0.642 14.134 107238 Z= 0.324 Chirality : 0.037 0.338 13434 Planarity : 0.005 0.141 7296 Dihedral : 23.293 179.503 30174 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 1.22 % Allowed : 7.62 % Favored : 91.16 % Rotamer: Outliers : 5.62 % Allowed : 30.31 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -2.10 (0.13), residues: 4014 helix: 0.17 (0.13), residues: 1409 sheet: -1.70 (0.19), residues: 604 loop : -2.52 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 29 HIS 0.008 0.001 HIS I 42 PHE 0.023 0.002 PHE 3 39 TYR 0.023 0.002 TYR G 155 ARG 0.014 0.001 ARG K 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 798 time to evaluate : 3.982 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: B 24 PHE cc_start: 0.7121 (m-80) cc_final: 0.5724 (t80) REVERT: B 50 LYS cc_start: 0.6915 (ttmm) cc_final: 0.6545 (mmtp) REVERT: B 95 ASP cc_start: 0.6238 (t0) cc_final: 0.5839 (t70) REVERT: B 137 MET cc_start: 0.8425 (mmt) cc_final: 0.8207 (mmm) REVERT: B 148 ASN cc_start: 0.6061 (m-40) cc_final: 0.5762 (t0) REVERT: B 223 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6595 (pp) REVERT: B 229 MET cc_start: 0.6460 (mmp) cc_final: 0.5593 (ptm) REVERT: C 34 LYS cc_start: 0.7764 (mtpp) cc_final: 0.7121 (ptmt) REVERT: C 110 GLN cc_start: 0.8087 (pm20) cc_final: 0.7664 (pm20) REVERT: C 153 LEU cc_start: 0.7113 (mt) cc_final: 0.6639 (mp) REVERT: C 165 LYS cc_start: 0.7497 (mppt) cc_final: 0.7235 (mtpp) REVERT: C 197 MET cc_start: 0.7635 (mtp) cc_final: 0.6542 (tmm) REVERT: D 23 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6602 (mm-30) REVERT: D 27 ARG cc_start: 0.2281 (ptt90) cc_final: 0.2020 (ppt170) REVERT: D 151 MET cc_start: 0.5855 (mtm) cc_final: 0.4986 (ptt) REVERT: D 164 PRO cc_start: 0.7358 (Cg_exo) cc_final: 0.7059 (Cg_endo) REVERT: D 167 ARG cc_start: 0.5614 (mtt90) cc_final: 0.4564 (tpt170) REVERT: E 14 ASN cc_start: 0.8025 (m110) cc_final: 0.7743 (m-40) REVERT: E 16 LYS cc_start: 0.7390 (tptt) cc_final: 0.6629 (mptt) REVERT: E 33 GLU cc_start: 0.8810 (tp30) cc_final: 0.8249 (tm-30) REVERT: E 77 LEU cc_start: 0.8296 (mm) cc_final: 0.8078 (mt) REVERT: E 106 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7586 (mt-10) REVERT: E 114 PHE cc_start: 0.7565 (t80) cc_final: 0.7269 (t80) REVERT: F 6 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7241 (mtpp) REVERT: F 50 ASN cc_start: 0.8416 (m110) cc_final: 0.8088 (m-40) REVERT: F 60 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8079 (mt-10) REVERT: F 117 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: F 119 SER cc_start: 0.8637 (OUTLIER) cc_final: 0.7990 (p) REVERT: F 168 LYS cc_start: 0.6637 (mttp) cc_final: 0.6029 (tppt) REVERT: F 252 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7623 (mmm160) REVERT: F 255 ARG cc_start: 0.7051 (tpt90) cc_final: 0.6253 (ttt180) REVERT: G 53 GLU cc_start: 0.7731 (mp0) cc_final: 0.7227 (mt-10) REVERT: G 89 LYS cc_start: 0.7934 (tptt) cc_final: 0.7704 (ttmm) REVERT: G 90 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.7086 (t0) REVERT: G 99 GLN cc_start: 0.8213 (mt0) cc_final: 0.7974 (mt0) REVERT: G 155 TYR cc_start: 0.8358 (m-10) cc_final: 0.8093 (m-10) REVERT: G 168 MET cc_start: 0.8612 (pmm) cc_final: 0.8089 (pmm) REVERT: G 199 MET cc_start: 0.7775 (mmp) cc_final: 0.7195 (tpt) REVERT: H 57 ASP cc_start: 0.8010 (p0) cc_final: 0.7440 (t0) REVERT: H 89 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8142 (tptt) REVERT: H 143 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6401 (mttt) REVERT: H 154 ARG cc_start: 0.6976 (mtm-85) cc_final: 0.6672 (mtp180) REVERT: H 177 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6615 (mtt-85) REVERT: H 197 ARG cc_start: 0.7429 (tpp-160) cc_final: 0.7164 (tpp-160) REVERT: H 206 LYS cc_start: 0.8277 (tttt) cc_final: 0.7508 (tppt) REVERT: H 207 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7977 (mm-30) REVERT: I 49 LYS cc_start: 0.5487 (mttm) cc_final: 0.5145 (tttm) REVERT: I 67 MET cc_start: 0.7142 (tpt) cc_final: 0.6720 (mmm) REVERT: I 69 MET cc_start: 0.6409 (tmm) cc_final: 0.5376 (tpp) REVERT: I 109 LYS cc_start: 0.2383 (OUTLIER) cc_final: 0.2050 (tttm) REVERT: J 9 LEU cc_start: 0.5425 (OUTLIER) cc_final: 0.5182 (pp) REVERT: J 98 ARG cc_start: 0.6356 (mtm180) cc_final: 0.5811 (mtt-85) REVERT: J 123 TYR cc_start: 0.7562 (m-10) cc_final: 0.7085 (m-80) REVERT: J 128 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7462 (mm-30) REVERT: J 143 MET cc_start: 0.7501 (mmm) cc_final: 0.7291 (mtp) REVERT: J 162 ARG cc_start: 0.5284 (OUTLIER) cc_final: 0.4787 (mmm160) REVERT: K 64 ASN cc_start: 0.8149 (m110) cc_final: 0.7893 (m110) REVERT: K 89 ILE cc_start: 0.7745 (mm) cc_final: 0.7368 (mm) REVERT: K 114 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7244 (pp20) REVERT: L 28 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7490 (mp0) REVERT: L 35 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7619 (p0) REVERT: L 44 HIS cc_start: 0.7765 (m-70) cc_final: 0.7310 (m-70) REVERT: L 59 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6636 (mtpt) REVERT: L 92 ARG cc_start: 0.7434 (ttm-80) cc_final: 0.6234 (tpt170) REVERT: L 101 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8087 (pt) REVERT: L 105 ASP cc_start: 0.8224 (t70) cc_final: 0.7744 (p0) REVERT: L 110 THR cc_start: 0.7725 (m) cc_final: 0.7331 (p) REVERT: L 166 LYS cc_start: 0.4224 (OUTLIER) cc_final: 0.3716 (mmmt) REVERT: L 180 ARG cc_start: 0.7260 (mtp180) cc_final: 0.6821 (mmt180) REVERT: L 203 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6833 (t70) REVERT: L 210 ARG cc_start: 0.7465 (ttp-110) cc_final: 0.6745 (tpt170) REVERT: L 211 LYS cc_start: 0.7691 (mptt) cc_final: 0.7383 (mmmt) REVERT: M 124 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.5489 (ttm110) REVERT: M 133 LYS cc_start: 0.6834 (pttt) cc_final: 0.6401 (mtpt) REVERT: M 141 LYS cc_start: 0.5919 (mtmt) cc_final: 0.5416 (ptmt) REVERT: N 77 ASP cc_start: 0.7778 (p0) cc_final: 0.7444 (p0) REVERT: N 112 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.4821 (pm20) REVERT: O 21 LEU cc_start: 0.2217 (OUTLIER) cc_final: 0.1848 (pp) REVERT: O 42 ARG cc_start: 0.4654 (OUTLIER) cc_final: 0.2996 (mtm110) REVERT: O 72 TRP cc_start: 0.5461 (OUTLIER) cc_final: 0.5185 (p-90) REVERT: O 73 LYS cc_start: 0.6450 (mmmt) cc_final: 0.5971 (mtmt) REVERT: P 37 PHE cc_start: 0.7977 (m-80) cc_final: 0.7631 (m-80) REVERT: P 39 ASP cc_start: 0.8293 (t70) cc_final: 0.7899 (t0) REVERT: P 51 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8145 (mm-30) REVERT: P 61 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8121 (mmmm) REVERT: P 63 LYS cc_start: 0.4819 (tppt) cc_final: 0.4203 (ptpp) REVERT: P 75 MET cc_start: 0.7452 (ttp) cc_final: 0.7219 (ttm) REVERT: P 95 ILE cc_start: 0.7464 (pt) cc_final: 0.7249 (pt) REVERT: P 114 SER cc_start: 0.8176 (m) cc_final: 0.7921 (t) REVERT: Q 9 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8317 (tt) REVERT: Q 33 HIS cc_start: 0.8670 (m170) cc_final: 0.8200 (m170) REVERT: Q 63 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6776 (tp40) REVERT: Q 75 GLN cc_start: 0.7691 (mt0) cc_final: 0.7097 (tm-30) REVERT: Q 81 LYS cc_start: 0.6491 (mmtp) cc_final: 0.6246 (tppt) REVERT: Q 144 ARG cc_start: 0.7848 (ttt180) cc_final: 0.7614 (mmt90) REVERT: R 95 HIS cc_start: 0.2783 (OUTLIER) cc_final: 0.2126 (m90) REVERT: S 86 LEU cc_start: 0.5721 (mp) cc_final: 0.5471 (pp) REVERT: S 96 LYS cc_start: 0.6513 (mmtt) cc_final: 0.6221 (ttpt) REVERT: S 98 ILE cc_start: 0.6305 (OUTLIER) cc_final: 0.5968 (tt) REVERT: T 17 ARG cc_start: 0.5838 (pmt170) cc_final: 0.5188 (tpt90) REVERT: T 29 ILE cc_start: 0.7372 (mt) cc_final: 0.7101 (tt) REVERT: T 42 ARG cc_start: 0.6699 (mtp85) cc_final: 0.6257 (ttm-80) REVERT: T 51 LYS cc_start: 0.6542 (mtmt) cc_final: 0.5568 (mmtt) REVERT: U 71 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.7092 (mt) REVERT: U 107 LYS cc_start: 0.7093 (mmmm) cc_final: 0.6101 (ttpp) REVERT: U 149 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7356 (mt) REVERT: V 9 HIS cc_start: 0.7046 (m-70) cc_final: 0.6843 (m-70) REVERT: V 157 GLN cc_start: 0.7100 (mp10) cc_final: 0.5934 (mp10) REVERT: W 5 ARG cc_start: 0.6072 (mpt180) cc_final: 0.5713 (mpt-90) REVERT: W 46 MET cc_start: 0.6563 (mmm) cc_final: 0.6355 (tpt) REVERT: W 78 ARG cc_start: 0.6853 (OUTLIER) cc_final: 0.6116 (tpt-90) REVERT: W 81 ARG cc_start: 0.5440 (OUTLIER) cc_final: 0.4952 (mmm-85) REVERT: X 22 LEU cc_start: 0.3045 (OUTLIER) cc_final: 0.2590 (mp) REVERT: X 43 ARG cc_start: 0.5088 (ttt-90) cc_final: 0.4162 (tpt-90) REVERT: X 78 THR cc_start: 0.3821 (OUTLIER) cc_final: 0.3583 (t) REVERT: Y 67 LYS cc_start: 0.5297 (pttt) cc_final: 0.4837 (mtpt) REVERT: Y 100 ARG cc_start: 0.4945 (mtm-85) cc_final: 0.4629 (ptp-170) REVERT: Z 18 SER cc_start: 0.8544 (t) cc_final: 0.7822 (m) REVERT: Z 35 ASN cc_start: 0.7702 (m-40) cc_final: 0.7456 (m110) REVERT: Z 76 LYS cc_start: 0.6173 (OUTLIER) cc_final: 0.4784 (pttt) REVERT: 1 32 LYS cc_start: 0.7267 (pttt) cc_final: 0.6543 (tttm) REVERT: 1 47 MET cc_start: 0.7692 (ttm) cc_final: 0.7438 (mtp) REVERT: 1 90 TYR cc_start: 0.8057 (p90) cc_final: 0.7730 (p90) REVERT: 1 113 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7548 (tppt) REVERT: 2 99 LYS cc_start: 0.1650 (tttp) cc_final: 0.1134 (tttm) REVERT: 3 11 SER cc_start: 0.8298 (m) cc_final: 0.7837 (p) REVERT: 3 63 GLN cc_start: 0.7764 (mm110) cc_final: 0.7356 (mm-40) REVERT: 4 22 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7763 (tp) REVERT: 4 49 GLN cc_start: 0.7893 (mt0) cc_final: 0.7173 (mp10) REVERT: 4 61 LEU cc_start: 0.7940 (mt) cc_final: 0.7544 (mt) REVERT: 5 26 ARG cc_start: 0.4561 (ttm170) cc_final: 0.4246 (mmm-85) REVERT: 5 64 ARG cc_start: 0.3938 (OUTLIER) cc_final: 0.3012 (mtm110) REVERT: 6 27 LYS cc_start: 0.7028 (mtmm) cc_final: 0.6201 (mmmt) outliers start: 203 outliers final: 139 residues processed: 930 average time/residue: 0.7304 time to fit residues: 1121.1260 Evaluate side-chains 913 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 739 time to evaluate : 3.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 177 ARG Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 162 ARG Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 184 CYS Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain L residue 206 LEU Chi-restraints excluded: chain M residue 124 ARG Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain O residue 72 TRP Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain Q residue 95 PHE Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 131 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 114 TYR Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 63 THR Chi-restraints excluded: chain 1 residue 81 ASP Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 2 residue 74 VAL Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 66 LYS Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 79 ILE Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 64 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 502 optimal weight: 8.9990 chunk 330 optimal weight: 2.9990 chunk 532 optimal weight: 10.0000 chunk 325 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 chunk 370 optimal weight: 0.9980 chunk 558 optimal weight: 40.0000 chunk 514 optimal weight: 8.9990 chunk 445 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 343 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN D 13 ASN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 HIS ** O 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 GLN U 45 GLN U 78 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 35 ASN ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 7 ASN 4 40 GLN 4 50 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 1.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 73565 Z= 0.251 Angle : 0.675 11.312 107238 Z= 0.341 Chirality : 0.038 0.303 13434 Planarity : 0.006 0.141 7296 Dihedral : 23.285 179.034 30169 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.87 % Favored : 89.89 % Rotamer: Outliers : 5.62 % Allowed : 30.37 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -2.11 (0.12), residues: 4014 helix: 0.15 (0.13), residues: 1405 sheet: -1.71 (0.19), residues: 605 loop : -2.51 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP S 84 HIS 0.008 0.001 HIS I 42 PHE 0.033 0.002 PHE Y 59 TYR 0.022 0.002 TYR V 13 ARG 0.017 0.001 ARG K 118 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8028 Ramachandran restraints generated. 4014 Oldfield, 0 Emsley, 4014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 744 time to evaluate : 3.923 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: B 50 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6642 (mmtp) REVERT: B 95 ASP cc_start: 0.6207 (t0) cc_final: 0.5821 (t70) REVERT: B 137 MET cc_start: 0.8473 (mmt) cc_final: 0.7898 (mmm) REVERT: B 148 ASN cc_start: 0.5872 (m-40) cc_final: 0.5433 (t0) REVERT: B 223 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6555 (pp) REVERT: B 229 MET cc_start: 0.6338 (mmp) cc_final: 0.5759 (ptm) REVERT: C 34 LYS cc_start: 0.7730 (mtpp) cc_final: 0.7127 (ptmt) REVERT: C 165 LYS cc_start: 0.7272 (mppt) cc_final: 0.6929 (mtpp) REVERT: C 197 MET cc_start: 0.7676 (mtp) cc_final: 0.6590 (tmm) REVERT: C 198 VAL cc_start: 0.5693 (OUTLIER) cc_final: 0.4995 (t) REVERT: D 23 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6568 (mm-30) REVERT: D 108 TYR cc_start: 0.4440 (t80) cc_final: 0.4188 (t80) REVERT: D 128 MET cc_start: 0.7459 (mmm) cc_final: 0.6337 (tpt) REVERT: D 151 MET cc_start: 0.6041 (mtm) cc_final: 0.5238 (ptt) REVERT: D 167 ARG cc_start: 0.5572 (mtt90) cc_final: 0.4543 (tpt170) REVERT: E 14 ASN cc_start: 0.8073 (m110) cc_final: 0.7762 (m-40) REVERT: E 16 LYS cc_start: 0.7354 (tptt) cc_final: 0.6591 (mptt) REVERT: E 77 LEU cc_start: 0.8341 (mm) cc_final: 0.8125 (mt) REVERT: E 92 LYS cc_start: 0.7468 (ttmt) cc_final: 0.6665 (mptt) REVERT: E 106 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7621 (mt-10) REVERT: E 114 PHE cc_start: 0.7523 (t80) cc_final: 0.7229 (t80) REVERT: E 152 SER cc_start: 0.7810 (m) cc_final: 0.7534 (t) REVERT: F 6 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7220 (mtpp) REVERT: F 50 ASN cc_start: 0.8423 (m110) cc_final: 0.8034 (m110) REVERT: F 119 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.7959 (p) REVERT: F 168 LYS cc_start: 0.6634 (mttp) cc_final: 0.6031 (tppt) REVERT: F 252 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7479 (mmm160) REVERT: F 255 ARG cc_start: 0.7050 (tpt90) cc_final: 0.6243 (ttt180) REVERT: G 53 GLU cc_start: 0.7824 (mp0) cc_final: 0.7245 (mt-10) REVERT: G 89 LYS cc_start: 0.7937 (tptt) cc_final: 0.7702 (ttmm) REVERT: G 90 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7108 (t0) REVERT: G 99 GLN cc_start: 0.8208 (mt0) cc_final: 0.7958 (mt0) REVERT: G 107 ARG cc_start: 0.8470 (mtp85) cc_final: 0.7634 (mmm160) REVERT: G 168 MET cc_start: 0.8619 (pmm) cc_final: 0.8107 (pmm) REVERT: G 199 MET cc_start: 0.7799 (mmp) cc_final: 0.7005 (tpt) REVERT: H 57 ASP cc_start: 0.7965 (p0) cc_final: 0.7407 (t0) REVERT: H 89 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8146 (tptt) REVERT: H 143 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6485 (tttt) REVERT: H 154 ARG cc_start: 0.7149 (mtm-85) cc_final: 0.6831 (mtp180) REVERT: H 174 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.6922 (mttm) REVERT: H 197 ARG cc_start: 0.7472 (tpp-160) cc_final: 0.7188 (tpp-160) REVERT: H 206 LYS cc_start: 0.8152 (tttt) cc_final: 0.7397 (tppt) REVERT: H 207 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8071 (mm-30) REVERT: I 49 LYS cc_start: 0.5498 (mttm) cc_final: 0.5152 (tttm) REVERT: I 67 MET cc_start: 0.6918 (tpt) cc_final: 0.6436 (mmm) REVERT: J 9 LEU cc_start: 0.5590 (OUTLIER) cc_final: 0.5326 (pp) REVERT: J 98 ARG cc_start: 0.6264 (mtm180) cc_final: 0.5931 (mtt-85) REVERT: J 104 LYS cc_start: 0.5701 (tmmt) cc_final: 0.5335 (pttp) REVERT: J 128 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7442 (mm-30) REVERT: J 143 MET cc_start: 0.7573 (mmm) cc_final: 0.7313 (mtp) REVERT: J 162 ARG cc_start: 0.5216 (OUTLIER) cc_final: 0.4679 (mmm160) REVERT: J 168 LYS cc_start: 0.6192 (mmtt) cc_final: 0.5837 (mtmt) REVERT: K 64 ASN cc_start: 0.8191 (m110) cc_final: 0.7926 (m110) REVERT: K 89 ILE cc_start: 0.7711 (mm) cc_final: 0.7350 (mm) REVERT: K 111 MET cc_start: 0.8284 (pmm) cc_final: 0.8064 (pmm) REVERT: K 114 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7210 (pp20) REVERT: L 28 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: L 35 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7855 (p0) REVERT: L 44 HIS cc_start: 0.7801 (m-70) cc_final: 0.7354 (m170) REVERT: L 59 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6649 (mttt) REVERT: L 92 ARG cc_start: 0.7456 (ttm-80) cc_final: 0.6245 (tpt170) REVERT: L 166 LYS cc_start: 0.4136 (OUTLIER) cc_final: 0.3740 (mmmt) REVERT: L 180 ARG cc_start: 0.7250 (mtp180) cc_final: 0.6646 (mmt-90) REVERT: L 203 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6991 (t70) REVERT: L 210 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.6756 (tpt170) REVERT: L 211 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7388 (mmmt) REVERT: M 51 GLU cc_start: 0.5526 (OUTLIER) cc_final: 0.4260 (tt0) REVERT: M 124 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.5461 (ttm110) REVERT: M 133 LYS cc_start: 0.7118 (pttt) cc_final: 0.6688 (mtpt) REVERT: M 141 LYS cc_start: 0.5775 (mtmt) cc_final: 0.5465 (ptmt) REVERT: N 62 ILE cc_start: 0.7008 (tp) cc_final: 0.6623 (tt) REVERT: N 77 ASP cc_start: 0.7821 (p0) cc_final: 0.7487 (p0) REVERT: N 81 LEU cc_start: 0.6267 (tt) cc_final: 0.5999 (tt) REVERT: N 103 ILE cc_start: 0.3332 (OUTLIER) cc_final: 0.3124 (mp) REVERT: N 112 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.4803 (pm20) REVERT: O 21 LEU cc_start: 0.2224 (OUTLIER) cc_final: 0.1860 (pp) REVERT: O 42 ARG cc_start: 0.4676 (OUTLIER) cc_final: 0.2989 (mtm110) REVERT: O 73 LYS cc_start: 0.6431 (mmmt) cc_final: 0.5962 (mtmt) REVERT: P 37 PHE cc_start: 0.8017 (m-80) cc_final: 0.7657 (m-80) REVERT: P 39 ASP cc_start: 0.8408 (t70) cc_final: 0.7961 (t0) REVERT: P 61 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8241 (mmmm) REVERT: P 63 LYS cc_start: 0.4859 (tppt) cc_final: 0.4188 (ptpp) REVERT: P 75 MET cc_start: 0.7311 (ttp) cc_final: 0.7107 (ttm) REVERT: P 114 SER cc_start: 0.8185 (m) cc_final: 0.7958 (t) REVERT: Q 9 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8364 (tt) REVERT: Q 26 ASP cc_start: 0.8874 (t0) cc_final: 0.8582 (t70) REVERT: Q 33 HIS cc_start: 0.8687 (m170) cc_final: 0.8112 (m170) REVERT: Q 37 ARG cc_start: 0.7210 (ttp-170) cc_final: 0.6889 (ttp-170) REVERT: Q 57 VAL cc_start: 0.7959 (t) cc_final: 0.7603 (m) REVERT: Q 63 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6768 (tp40) REVERT: Q 75 GLN cc_start: 0.7701 (mt0) cc_final: 0.7103 (tm-30) REVERT: Q 81 LYS cc_start: 0.6579 (mmtp) cc_final: 0.6287 (tppt) REVERT: Q 144 ARG cc_start: 0.7811 (ttt180) cc_final: 0.7605 (mmt90) REVERT: R 95 HIS cc_start: 0.3111 (OUTLIER) cc_final: 0.2375 (m90) REVERT: S 86 LEU cc_start: 0.5392 (mp) cc_final: 0.5070 (pp) REVERT: S 96 LYS cc_start: 0.6593 (mmtt) cc_final: 0.6308 (ttpt) REVERT: S 98 ILE cc_start: 0.5963 (pt) cc_final: 0.5624 (tt) REVERT: T 17 ARG cc_start: 0.5752 (pmt170) cc_final: 0.5332 (tpt90) REVERT: T 42 ARG cc_start: 0.6798 (mtp85) cc_final: 0.6297 (ttm-80) REVERT: U 107 LYS cc_start: 0.7148 (mmmm) cc_final: 0.6792 (tppt) REVERT: V 124 ASP cc_start: 0.8664 (m-30) cc_final: 0.8317 (m-30) REVERT: V 134 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8829 (mp) REVERT: V 157 GLN cc_start: 0.6565 (mp10) cc_final: 0.6240 (mp10) REVERT: W 5 ARG cc_start: 0.5930 (mpt180) cc_final: 0.5383 (mpt-90) REVERT: W 46 MET cc_start: 0.6521 (mmm) cc_final: 0.6302 (tpt) REVERT: W 78 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6126 (tpt-90) REVERT: W 81 ARG cc_start: 0.5623 (OUTLIER) cc_final: 0.5136 (mmm-85) REVERT: X 22 LEU cc_start: 0.3065 (OUTLIER) cc_final: 0.2563 (mp) REVERT: X 43 ARG cc_start: 0.5070 (ttt-90) cc_final: 0.4138 (tpt-90) REVERT: X 78 THR cc_start: 0.3952 (OUTLIER) cc_final: 0.3731 (t) REVERT: X 80 LEU cc_start: 0.2543 (OUTLIER) cc_final: 0.2251 (mp) REVERT: Y 67 LYS cc_start: 0.5279 (pttt) cc_final: 0.4800 (mtpt) REVERT: Y 135 TYR cc_start: 0.5164 (m-80) cc_final: 0.4945 (m-10) REVERT: Z 18 SER cc_start: 0.8636 (t) cc_final: 0.7885 (m) REVERT: Z 35 ASN cc_start: 0.7608 (m110) cc_final: 0.7315 (m110) REVERT: Z 60 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7249 (mm-40) REVERT: Z 76 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.5193 (pttt) REVERT: 1 32 LYS cc_start: 0.7290 (pttt) cc_final: 0.6589 (tttt) REVERT: 1 47 MET cc_start: 0.7673 (ttm) cc_final: 0.7424 (mtp) REVERT: 1 50 LEU cc_start: 0.7683 (mt) cc_final: 0.7471 (mt) REVERT: 1 90 TYR cc_start: 0.8107 (p90) cc_final: 0.7794 (p90) REVERT: 1 113 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7620 (tppt) REVERT: 3 11 SER cc_start: 0.8384 (m) cc_final: 0.8054 (p) REVERT: 3 63 GLN cc_start: 0.7804 (mm110) cc_final: 0.7391 (mm-40) REVERT: 4 22 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7624 (tp) REVERT: 4 61 LEU cc_start: 0.8097 (mt) cc_final: 0.7672 (mt) REVERT: 5 26 ARG cc_start: 0.5038 (ttm170) cc_final: 0.4323 (tpt-90) REVERT: 5 64 ARG cc_start: 0.4107 (OUTLIER) cc_final: 0.2760 (ptt-90) REVERT: 6 27 LYS cc_start: 0.7026 (mtmm) cc_final: 0.6210 (mmmt) outliers start: 203 outliers final: 152 residues processed: 878 average time/residue: 0.7228 time to fit residues: 1053.8839 Evaluate side-chains 921 residues out of total 3617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 735 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 28 ASN Chi-restraints excluded: chain C residue 40 ARG Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 135 CYS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 36 HIS Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 235 TYR Chi-restraints excluded: chain G residue 41 TRP Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 21 GLU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 143 LYS Chi-restraints excluded: chain H residue 174 LYS Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain I residue 109 LYS Chi-restraints excluded: chain J residue 4 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 12 ASN Chi-restraints excluded: chain J residue 68 ILE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 162 ARG Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 76 SER Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 GLU Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 59 LYS Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 CYS Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 184 CYS Chi-restraints excluded: chain L residue 203 ASP Chi-restraints excluded: chain L residue 204 GLU Chi-restraints excluded: chain L residue 206 LEU Chi-restraints excluded: chain L residue 211 LYS Chi-restraints excluded: chain M residue 51 GLU Chi-restraints excluded: chain M residue 124 ARG Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 99 GLN Chi-restraints excluded: chain N residue 103 ILE Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 34 VAL Chi-restraints excluded: chain O residue 42 ARG Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 107 THR Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 36 THR Chi-restraints excluded: chain Q residue 63 GLN Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 84 THR Chi-restraints excluded: chain Q residue 94 ASN Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 107 PHE Chi-restraints excluded: chain Q residue 132 LEU Chi-restraints excluded: chain R residue 95 HIS Chi-restraints excluded: chain S residue 19 ASN Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 55 THR Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 37 ILE Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain U residue 60 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 83 THR Chi-restraints excluded: chain U residue 144 SER Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 7 VAL Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 53 GLU Chi-restraints excluded: chain V residue 68 SER Chi-restraints excluded: chain V residue 74 LEU Chi-restraints excluded: chain V residue 87 ILE Chi-restraints excluded: chain V residue 128 VAL Chi-restraints excluded: chain V residue 134 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 98 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 78 THR Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 114 TYR Chi-restraints excluded: chain Y residue 56 TRP Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 90 HIS Chi-restraints excluded: chain Z residue 12 TYR Chi-restraints excluded: chain Z residue 44 VAL Chi-restraints excluded: chain Z residue 76 LYS Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 63 THR Chi-restraints excluded: chain 1 residue 81 ASP Chi-restraints excluded: chain 1 residue 113 LYS Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 122 THR Chi-restraints excluded: chain 2 residue 70 VAL Chi-restraints excluded: chain 2 residue 74 VAL Chi-restraints excluded: chain 3 residue 18 VAL Chi-restraints excluded: chain 3 residue 69 ILE Chi-restraints excluded: chain 3 residue 79 ILE Chi-restraints excluded: chain 4 residue 7 ASN Chi-restraints excluded: chain 4 residue 17 HIS Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 5 residue 48 VAL Chi-restraints excluded: chain 5 residue 64 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 561 random chunks: chunk 272 optimal weight: 5.9990 chunk 353 optimal weight: 6.9990 chunk 474 optimal weight: 10.0000 chunk 136 optimal weight: 40.0000 chunk 410 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 445 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 457 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 12 ASN ** J 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 HIS O 50 ASN ** O 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS ** T 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 GLN U 78 GLN ** V 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 7 ASN 4 40 GLN ** 4 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 50 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.171490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.143132 restraints weight = 120816.369| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.23 r_work: 0.3605 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 1.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 73565 Z= 0.300 Angle : 0.720 11.385 107238 Z= 0.364 Chirality : 0.041 0.353 13434 Planarity : 0.006 0.142 7296 Dihedral : 23.376 179.865 30163 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 1.25 % Allowed : 9.19 % Favored : 89.56 % Rotamer: Outliers : 6.01 % Allowed : 29.95 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -2.23 (0.12), residues: 4014 helix: -0.04 (0.13), residues: 1407 sheet: -1.72 (0.20), residues: 599 loop : -2.53 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP S 84 HIS 0.010 0.002 HIS K 101 PHE 0.029 0.002 PHE Y 59 TYR 0.027 0.002 TYR T 12 ARG 0.015 0.001 ARG K 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18546.11 seconds wall clock time: 326 minutes 31.24 seconds (19591.24 seconds total)