Starting phenix.real_space_refine on Sat Sep 28 20:57:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/09_2024/7mei_23789.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/09_2024/7mei_23789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/09_2024/7mei_23789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/09_2024/7mei_23789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/09_2024/7mei_23789.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mei_23789/09_2024/7mei_23789.cif" } resolution = 3.54 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1453 atoms to isotropic. 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 16 6.06 5 P 179 5.49 5 Mg 4 5.21 5 S 374 5.16 5 C 43090 2.51 5 N 12103 2.21 5 O 13515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 252 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 69281 Number of models: 1 Model: "" Number of chains: 43 Chain: "N" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1519 Classifications: {'DNA': 74} Link IDs: {'rna3p': 73} Chain: "O" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1524 Classifications: {'DNA': 74} Link IDs: {'rna3p': 73} Chain: "a" Number of atoms: 11189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 11189 Classifications: {'peptide': 1425} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 65, 'TRANS': 1355} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "b" Number of atoms: 9197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1160, 9197 Classifications: {'peptide': 1160} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 5} Link IDs: {'CIS': 12, 'PCIS': 2, 'PTRANS': 49, 'TRANS': 1096} Chain breaks: 8 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "c" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "d" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1331 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "f" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "g" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1339 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 8, 'TRANS': 162} Chain: "h" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Chain: "i" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "j" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "k" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "l" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "r" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'RNA': 16} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna2p': 4, 'rna3p': 11} Chain: "A" Number of atoms: 11167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 11167 Classifications: {'peptide': 1425} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 65, 'TRANS': 1354} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 9227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9227 Classifications: {'peptide': 1166} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 8} Link IDs: {'CIS': 11, 'PCIS': 1, 'PTRANS': 50, 'TRANS': 1103} Chain breaks: 7 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "D" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1331 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "G" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1335 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 2 Chain: "I" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 927 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 540 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 924 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "R" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 312 Classifications: {'RNA': 15} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "Q" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1619 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 204} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 247 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 110 Chain: "M" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1106 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "a" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3883 SG CYS a 110 143.101 89.974 132.080 1.00216.77 S ATOM 4188 SG CYS a 148 142.917 87.744 135.027 1.00265.00 S ATOM 4326 SG CYS a 167 143.261 91.067 134.548 1.00271.97 S ATOM 3554 SG CYS a 67 126.247 103.790 87.332 1.00242.80 S ATOM 3576 SG CYS a 70 127.947 104.231 86.113 1.00263.01 S ATOM 22954 SG CYS b1163 137.626 92.328 93.875 1.00771.81 S ATOM 22972 SG CYS b1166 136.101 94.287 96.768 1.00731.01 S ATOM 23097 SG CYS b1182 136.790 96.157 94.092 1.00879.94 S ATOM 23116 SG CYS b1185 138.927 94.473 97.078 1.00908.11 S ATOM 24076 SG CYS c 86 69.945 95.490 48.384 1.00652.87 S ATOM 24093 SG CYS c 88 71.597 98.265 50.169 1.00684.17 S ATOM 24126 SG CYS c 92 68.379 99.019 48.302 1.00633.55 S ATOM 24149 SG CYS c 95 68.698 97.094 51.719 1.00603.63 S ATOM 31775 SG CYS i 7 84.985 86.318 174.627 1.00606.34 S ATOM 31800 SG CYS i 10 86.706 88.767 172.133 1.00604.81 S ATOM 31966 SG CYS i 29 88.421 85.538 173.195 1.00592.83 S ATOM 31990 SG CYS i 32 87.811 88.226 175.798 1.00615.85 S ATOM 32317 SG CYS i 75 51.236 62.644 149.736 1.00999.99 S ATOM 32339 SG CYS i 78 49.640 64.668 151.653 1.00999.99 S ATOM 32555 SG CYS i 103 51.158 66.265 148.410 1.00999.99 S ATOM 32575 SG CYS i 106 53.415 65.413 151.439 1.00999.99 S ATOM 32703 SG CYS j 7 56.135 83.273 78.168 1.00416.77 S ATOM 32726 SG CYS j 10 54.938 82.468 74.776 1.00474.02 S ATOM 33006 SG CYS j 45 53.978 79.817 77.351 1.00511.53 S ATOM 33012 SG CYS j 46 52.452 83.105 76.612 1.00497.40 S ATOM 34156 SG CYS l 31 68.846 125.062 87.865 1.00283.35 S ATOM 34176 SG CYS l 34 65.722 126.606 87.732 1.00331.71 S ATOM 34280 SG CYS l 48 68.957 128.719 87.723 1.00280.24 S ATOM 34303 SG CYS l 51 67.076 127.079 90.872 1.00298.71 S ATOM 35614 SG CYS A 107 76.826 149.319 80.882 1.00250.70 S ATOM 35638 SG CYS A 110 74.863 149.330 80.371 1.00242.09 S ATOM 35943 SG CYS A 148 76.337 147.863 84.023 1.00294.76 S ATOM 36081 SG CYS A 167 75.422 146.045 80.155 1.00293.62 S ATOM 35309 SG CYS A 67 65.025 188.014 48.670 1.00231.64 S ATOM 35331 SG CYS A 70 62.878 187.237 50.949 1.00224.65 S ATOM 35384 SG CYS A 77 66.695 187.084 51.740 1.00202.98 S ATOM 54717 SG CYS B1163 57.914 181.039 64.831 1.00222.04 S ATOM 54735 SG CYS B1166 60.848 178.403 64.277 1.00229.02 S ATOM 54860 SG CYS B1182 59.730 179.977 60.924 1.00232.64 S ATOM 55839 SG CYS C 86 89.925 250.669 37.699 1.00323.13 S ATOM 55856 SG CYS C 88 90.001 247.301 35.931 1.00317.15 S ATOM 55889 SG CYS C 92 91.956 250.068 34.597 1.00296.54 S ATOM 55912 SG CYS C 95 93.131 248.452 37.800 1.00293.39 S ATOM 63534 SG CYS I 7 147.346 148.717 91.140 1.00276.12 S ATOM 63559 SG CYS I 10 144.878 149.094 88.041 1.00275.03 S ATOM 63725 SG CYS I 29 143.487 148.672 91.406 1.00273.60 S ATOM 63749 SG CYS I 32 145.614 145.848 89.918 1.00262.01 S ATOM 64076 SG CYS I 75 159.167 193.215 99.029 1.00273.06 S ATOM 64098 SG CYS I 78 160.746 193.033 97.924 1.00266.82 S ATOM 64334 SG CYS I 106 158.673 190.496 97.735 1.00279.11 S ATOM 64462 SG CYS J 7 117.432 239.389 57.241 1.00192.03 S ATOM 64485 SG CYS J 10 116.542 242.927 57.477 1.00191.68 S ATOM 64765 SG CYS J 45 118.172 241.609 60.548 1.00197.06 S ATOM 64771 SG CYS J 46 119.576 242.878 57.272 1.00203.76 S ATOM 65915 SG CYS L 31 113.628 210.553 21.511 1.00302.20 S ATOM 66039 SG CYS L 48 115.276 207.336 21.312 1.00309.77 S ATOM 66062 SG CYS L 51 118.041 209.737 21.576 1.00 30.00 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="ZN ZN a1801 " occ=0.95 residue: pdb="ZN ZN A1801 " occ=0.95 Time building chain proxies: 29.82, per 1000 atoms: 0.43 Number of scatterers: 69281 At special positions: 0 Unit cell: (195.48, 282.96, 193.32, 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 16 29.99 S 374 16.00 P 179 15.00 Mg 4 11.99 O 13515 8.00 N 12103 7.00 C 43090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 13.81 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 31 " pdb=" ZN a1801 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 167 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 148 " pdb="ZN ZN a1801 " - pdb=" SG CYS a 110 " pdb=" ZN a1802 " pdb="ZN ZN a1802 " - pdb=" SG CYS a 67 " pdb="ZN ZN a1802 " - pdb=" NE2 HIS a 80 " pdb="ZN ZN a1802 " - pdb=" SG CYS a 70 " pdb=" ZN b1301 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1166 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1185 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1182 " pdb="ZN ZN b1301 " - pdb=" SG CYS b1163 " pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 88 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 95 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 92 " pdb="ZN ZN c 401 " - pdb=" SG CYS c 86 " pdb=" ZN i 201 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 32 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 29 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 7 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 10 " pdb=" ZN i 202 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 78 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 75 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 106 " pdb="ZN ZN i 202 " - pdb=" SG CYS i 103 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 10 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 46 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 45 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 7 " pdb=" ZN l 101 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 34 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 31 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 48 " pdb="ZN ZN l 101 " - pdb=" SG CYS l 51 " Number of angles added : 63 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15566 Finding SS restraints... Secondary structure from input PDB file: 280 helices and 82 sheets defined 37.0% alpha, 15.6% beta 60 base pairs and 120 stacking pairs defined. Time for finding SS restraints: 20.02 Creating SS restraints... Processing helix chain 'a' and resid 23 through 31 Processing helix chain 'a' and resid 92 through 95 Processing helix chain 'a' and resid 96 through 105 Processing helix chain 'a' and resid 120 through 128 Processing helix chain 'a' and resid 132 through 142 Processing helix chain 'a' and resid 191 through 195 Processing helix chain 'a' and resid 203 through 214 Processing helix chain 'a' and resid 215 through 222 removed outlier: 3.715A pdb=" N PHE a 219 " --> pdb=" O SER a 215 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR a 220 " --> pdb=" O VAL a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 235 removed outlier: 3.581A pdb=" N ILE a 235 " --> pdb=" O GLU a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 243 through 247 removed outlier: 3.551A pdb=" N VAL a 246 " --> pdb=" O PRO a 243 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 282 removed outlier: 3.529A pdb=" N PHE a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 288 through 305 Processing helix chain 'a' and resid 324 through 330 Processing helix chain 'a' and resid 368 through 374 Processing helix chain 'a' and resid 384 through 395 Processing helix chain 'a' and resid 471 through 473 No H-bonds generated for 'chain 'a' and resid 471 through 473' Processing helix chain 'a' and resid 474 through 479 removed outlier: 3.634A pdb=" N TYR a 478 " --> pdb=" O VAL a 474 " (cutoff:3.500A) Processing helix chain 'a' and resid 494 through 502 Processing helix chain 'a' and resid 506 through 510 Processing helix chain 'a' and resid 524 through 535 Processing helix chain 'a' and resid 542 through 553 Processing helix chain 'a' and resid 573 through 581 removed outlier: 3.929A pdb=" N VAL a 580 " --> pdb=" O GLN a 576 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA a 581 " --> pdb=" O ILE a 577 " (cutoff:3.500A) Processing helix chain 'a' and resid 618 through 623 Processing helix chain 'a' and resid 628 through 637 Processing helix chain 'a' and resid 640 through 661 removed outlier: 3.933A pdb=" N LYS a 644 " --> pdb=" O GLN a 640 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE a 655 " --> pdb=" O LYS a 651 " (cutoff:3.500A) Processing helix chain 'a' and resid 665 through 669 Processing helix chain 'a' and resid 672 through 699 Processing helix chain 'a' and resid 709 through 737 Processing helix chain 'a' and resid 741 through 749 removed outlier: 3.902A pdb=" N GLN a 745 " --> pdb=" O ASN a 741 " (cutoff:3.500A) Processing helix chain 'a' and resid 754 through 763 Processing helix chain 'a' and resid 809 through 843 removed outlier: 4.724A pdb=" N ALA a 832 " --> pdb=" O ALA a 828 " (cutoff:3.500A) Processing helix chain 'a' and resid 867 through 871 Processing helix chain 'a' and resid 889 through 898 Processing helix chain 'a' and resid 909 through 913 Processing helix chain 'a' and resid 922 through 947 Processing helix chain 'a' and resid 960 through 970 Processing helix chain 'a' and resid 982 through 997 removed outlier: 4.200A pdb=" N LYS a 991 " --> pdb=" O VAL a 987 " (cutoff:3.500A) Processing helix chain 'a' and resid 1004 through 1015 removed outlier: 3.627A pdb=" N GLN a1008 " --> pdb=" O ASN a1004 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL a1015 " --> pdb=" O GLN a1011 " (cutoff:3.500A) Processing helix chain 'a' and resid 1015 through 1026 Processing helix chain 'a' and resid 1027 through 1034 Processing helix chain 'a' and resid 1038 through 1056 Processing helix chain 'a' and resid 1063 through 1078 Proline residue: a1075 - end of helix removed outlier: 3.903A pdb=" N GLN a1078 " --> pdb=" O GLU a1074 " (cutoff:3.500A) Processing helix chain 'a' and resid 1096 through 1106 Processing helix chain 'a' and resid 1127 through 1139 Processing helix chain 'a' and resid 1142 through 1146 removed outlier: 3.568A pdb=" N VAL a1146 " --> pdb=" O THR a1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1142 through 1146' Processing helix chain 'a' and resid 1167 through 1173 Processing helix chain 'a' and resid 1198 through 1205 Processing helix chain 'a' and resid 1208 through 1220 removed outlier: 3.746A pdb=" N PHE a1220 " --> pdb=" O ILE a1216 " (cutoff:3.500A) Processing helix chain 'a' and resid 1255 through 1269 removed outlier: 3.511A pdb=" N MET a1259 " --> pdb=" O GLU a1255 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU a1269 " --> pdb=" O ASN a1265 " (cutoff:3.500A) Processing helix chain 'a' and resid 1315 through 1319 Processing helix chain 'a' and resid 1331 through 1339 Processing helix chain 'a' and resid 1340 through 1358 Processing helix chain 'a' and resid 1364 through 1377 removed outlier: 4.115A pdb=" N MET a1368 " --> pdb=" O ASN a1364 " (cutoff:3.500A) Processing helix chain 'a' and resid 1395 through 1401 removed outlier: 3.823A pdb=" N ARG a1399 " --> pdb=" O GLY a1395 " (cutoff:3.500A) Processing helix chain 'a' and resid 1406 through 1416 Processing helix chain 'a' and resid 1423 through 1431 Processing helix chain 'a' and resid 1436 through 1441 removed outlier: 4.048A pdb=" N PHE a1441 " --> pdb=" O THR a1438 " (cutoff:3.500A) Processing helix chain 'a' and resid 1447 through 1453 Processing helix chain 'b' and resid 27 through 29 No H-bonds generated for 'chain 'b' and resid 27 through 29' Processing helix chain 'b' and resid 30 through 42 removed outlier: 3.872A pdb=" N ILE b 34 " --> pdb=" O SER b 30 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER b 35 " --> pdb=" O TRP b 31 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA b 36 " --> pdb=" O ALA b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 57 removed outlier: 3.629A pdb=" N PHE b 51 " --> pdb=" O GLN b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 66 removed outlier: 4.154A pdb=" N ASP b 66 " --> pdb=" O ILE b 62 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 121 Processing helix chain 'b' and resid 179 through 184 Processing helix chain 'b' and resid 185 through 192 Processing helix chain 'b' and resid 246 through 250 removed outlier: 3.515A pdb=" N PHE b 250 " --> pdb=" O GLY b 247 " (cutoff:3.500A) Processing helix chain 'b' and resid 282 through 290 Processing helix chain 'b' and resid 293 through 302 removed outlier: 3.627A pdb=" N ILE b 297 " --> pdb=" O PRO b 293 " (cutoff:3.500A) Processing helix chain 'b' and resid 308 through 321 Proline residue: b 316 - end of helix removed outlier: 3.583A pdb=" N GLY b 321 " --> pdb=" O CYS b 317 " (cutoff:3.500A) Processing helix chain 'b' and resid 322 through 324 No H-bonds generated for 'chain 'b' and resid 322 through 324' Processing helix chain 'b' and resid 326 through 333 Processing helix chain 'b' and resid 348 through 359 Processing helix chain 'b' and resid 370 through 390 Processing helix chain 'b' and resid 408 through 430 removed outlier: 3.900A pdb=" N LEU b 416 " --> pdb=" O LEU b 412 " (cutoff:3.500A) Processing helix chain 'b' and resid 444 through 464 removed outlier: 4.250A pdb=" N ILE b 448 " --> pdb=" O MET b 444 " (cutoff:3.500A) Processing helix chain 'b' and resid 487 through 496 removed outlier: 3.878A pdb=" N ARG b 496 " --> pdb=" O LEU b 492 " (cutoff:3.500A) Processing helix chain 'b' and resid 515 through 519 Processing helix chain 'b' and resid 551 through 561 removed outlier: 3.826A pdb=" N ILE b 555 " --> pdb=" O PRO b 551 " (cutoff:3.500A) Processing helix chain 'b' and resid 565 through 569 Processing helix chain 'b' and resid 592 through 606 removed outlier: 3.944A pdb=" N LEU b 596 " --> pdb=" O ASN b 592 " (cutoff:3.500A) Processing helix chain 'b' and resid 654 through 668 removed outlier: 3.629A pdb=" N ILE b 658 " --> pdb=" O ARG b 654 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP b 668 " --> pdb=" O THR b 664 " (cutoff:3.500A) Processing helix chain 'b' and resid 680 through 688 removed outlier: 3.524A pdb=" N GLY b 688 " --> pdb=" O LEU b 684 " (cutoff:3.500A) Processing helix chain 'b' and resid 695 through 699 removed outlier: 4.144A pdb=" N GLU b 699 " --> pdb=" O ALA b 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 695 through 699' Processing helix chain 'b' and resid 744 through 749 Processing helix chain 'b' and resid 750 through 756 removed outlier: 4.071A pdb=" N ILE b 755 " --> pdb=" O VAL b 751 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE b 756 " --> pdb=" O ALA b 752 " (cutoff:3.500A) Processing helix chain 'b' and resid 758 through 762 Processing helix chain 'b' and resid 763 through 775 removed outlier: 4.131A pdb=" N LYS b 775 " --> pdb=" O SER b 771 " (cutoff:3.500A) Processing helix chain 'b' and resid 807 through 812 Processing helix chain 'b' and resid 843 through 849 Processing helix chain 'b' and resid 889 through 893 removed outlier: 3.584A pdb=" N LYS b 892 " --> pdb=" O THR b 889 " (cutoff:3.500A) Processing helix chain 'b' and resid 995 through 999 Processing helix chain 'b' and resid 1014 through 1017 Processing helix chain 'b' and resid 1023 through 1039 Processing helix chain 'b' and resid 1051 through 1063 removed outlier: 3.516A pdb=" N ILE b1055 " --> pdb=" O THR b1051 " (cutoff:3.500A) Processing helix chain 'b' and resid 1099 through 1103 Processing helix chain 'b' and resid 1131 through 1142 Processing helix chain 'b' and resid 1143 through 1153 Processing helix chain 'b' and resid 1197 through 1210 Processing helix chain 'c' and resid 26 through 40 Processing helix chain 'c' and resid 59 through 68 Processing helix chain 'c' and resid 76 through 80 Processing helix chain 'c' and resid 92 through 96 removed outlier: 3.696A pdb=" N SER c 96 " --> pdb=" O ASP c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 114 through 118 removed outlier: 3.525A pdb=" N LEU c 118 " --> pdb=" O SER c 115 " (cutoff:3.500A) Processing helix chain 'c' and resid 167 through 171 Processing helix chain 'c' and resid 204 through 209 Processing helix chain 'c' and resid 239 through 266 Processing helix chain 'd' and resid 51 through 75 removed outlier: 3.582A pdb=" N ALA d 55 " --> pdb=" O ASN d 51 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG d 56 " --> pdb=" O LEU d 52 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU d 57 " --> pdb=" O SER d 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS d 75 " --> pdb=" O LYS d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 134 removed outlier: 4.145A pdb=" N THR d 133 " --> pdb=" O LEU d 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 138 through 152 removed outlier: 4.306A pdb=" N ASN d 150 " --> pdb=" O GLN d 146 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 171 removed outlier: 3.841A pdb=" N SER d 169 " --> pdb=" O GLN d 165 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR d 170 " --> pdb=" O LEU d 166 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 179 removed outlier: 4.059A pdb=" N VAL d 177 " --> pdb=" O HIS d 173 " (cutoff:3.500A) Processing helix chain 'd' and resid 180 through 183 removed outlier: 4.012A pdb=" N LEU d 183 " --> pdb=" O LEU d 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 180 through 183' Processing helix chain 'd' and resid 187 through 195 removed outlier: 4.166A pdb=" N ALA d 191 " --> pdb=" O THR d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 202 removed outlier: 4.044A pdb=" N ASN d 199 " --> pdb=" O ILE d 195 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE d 202 " --> pdb=" O LEU d 198 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 216 removed outlier: 4.587A pdb=" N GLU d 213 " --> pdb=" O ARG d 209 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU d 214 " --> pdb=" O ILE d 210 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN d 216 " --> pdb=" O LYS d 212 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 26 removed outlier: 4.389A pdb=" N ARG e 7 " --> pdb=" O GLN e 3 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 36 removed outlier: 3.540A pdb=" N VAL e 35 " --> pdb=" O THR e 31 " (cutoff:3.500A) Processing helix chain 'e' and resid 38 through 47 Processing helix chain 'e' and resid 65 through 72 Processing helix chain 'e' and resid 89 through 104 Processing helix chain 'e' and resid 117 through 122 Processing helix chain 'e' and resid 157 through 169 Processing helix chain 'e' and resid 182 through 189 Processing helix chain 'f' and resid 86 through 103 Processing helix chain 'f' and resid 116 through 128 Processing helix chain 'g' and resid 14 through 18 Processing helix chain 'g' and resid 21 through 35 Processing helix chain 'i' and resid 61 through 65 removed outlier: 3.710A pdb=" N ASP i 65 " --> pdb=" O ILE i 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 17 through 28 Processing helix chain 'j' and resid 31 through 40 Processing helix chain 'j' and resid 43 through 52 removed outlier: 3.813A pdb=" N ARG j 47 " --> pdb=" O ARG j 43 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N MET j 49 " --> pdb=" O CYS j 45 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE j 50 " --> pdb=" O CYS j 46 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 62 Processing helix chain 'k' and resid 6 through 10 removed outlier: 3.549A pdb=" N LEU k 9 " --> pdb=" O ARG k 6 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 52 removed outlier: 3.684A pdb=" N GLY k 43 " --> pdb=" O ASP k 39 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU k 45 " --> pdb=" O THR k 41 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN k 52 " --> pdb=" O ALA k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 112 Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 105 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.593A pdb=" N ILE A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.541A pdb=" N PHE A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 287 through 305 removed outlier: 4.033A pdb=" N GLU A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.656A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.774A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.919A pdb=" N ARG A 498 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.629A pdb=" N LEU A 509 " --> pdb=" O ALA A 506 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE A 511 " --> pdb=" O PRO A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.712A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 4.073A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 640 through 661 removed outlier: 3.660A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 4.016A pdb=" N THR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.558A pdb=" N GLN A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 845 removed outlier: 4.637A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 913 through 917 removed outlier: 4.613A pdb=" N SER A 917 " --> pdb=" O GLU A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 947 Processing helix chain 'A' and resid 960 through 972 Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.919A pdb=" N LYS A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.509A pdb=" N GLN A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1035 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1075 through 1077 No H-bonds generated for 'chain 'A' and resid 1075 through 1077' Processing helix chain 'A' and resid 1096 through 1106 removed outlier: 3.526A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1142 through 1146 removed outlier: 3.734A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1142 through 1146' Processing helix chain 'A' and resid 1163 through 1166 Processing helix chain 'A' and resid 1167 through 1174 removed outlier: 3.610A pdb=" N GLN A1171 " --> pdb=" O GLU A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 removed outlier: 3.599A pdb=" N LYS A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1221 removed outlier: 3.645A pdb=" N VAL A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A1220 " --> pdb=" O ILE A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1271 removed outlier: 4.169A pdb=" N MET A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1339 removed outlier: 3.865A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 4.070A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1401 Processing helix chain 'A' and resid 1404 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 removed outlier: 3.526A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 42 removed outlier: 4.293A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 Processing helix chain 'B' and resid 59 through 66 removed outlier: 4.018A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.677A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.560A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 370 through 390 removed outlier: 3.588A pdb=" N CYS B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 430 Processing helix chain 'B' and resid 444 through 464 removed outlier: 3.853A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.503A pdb=" N LEU B 495 " --> pdb=" O THR B 491 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 606 removed outlier: 4.165A pdb=" N LEU B 596 " --> pdb=" O ASN B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 667 removed outlier: 3.673A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 4.562A pdb=" N GLU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.664A pdb=" N GLU B 699 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.941A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 removed outlier: 3.592A pdb=" N SER B 754 " --> pdb=" O GLY B 750 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 750 through 755' Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.713A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 4.332A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 4.307A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 4.341A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 889 through 893 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.405A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1039 Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.758A pdb=" N ILE B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1103 removed outlier: 3.752A pdb=" N LYS B1102 " --> pdb=" O MET B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1174 through 1178 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 68 Processing helix chain 'C' and resid 92 through 96 removed outlier: 3.740A pdb=" N SER C 96 " --> pdb=" O ASP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 76 removed outlier: 3.870A pdb=" N LYS D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.850A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 152 removed outlier: 3.593A pdb=" N PHE D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.672A pdb=" N VAL D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 195 through 202 removed outlier: 3.575A pdb=" N ILE D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 4.184A pdb=" N GLU D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 26 removed outlier: 4.413A pdb=" N ARG E 7 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.877A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 36' Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.549A pdb=" N MET E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 54 through 59' Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.553A pdb=" N ILE E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 138 through 141 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 17 through 25 removed outlier: 3.522A pdb=" N LEU J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 44 through 53 removed outlier: 4.209A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.739A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 removed outlier: 3.597A pdb=" N GLU K 8 " --> pdb=" O ASP K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 4.818A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 112 Processing helix chain 'Q' and resid 23 through 35 removed outlier: 3.657A pdb=" N MET Q 27 " --> pdb=" O LYS Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 112 removed outlier: 3.748A pdb=" N GLU Q 112 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 133 Processing helix chain 'Q' and resid 152 through 164 Processing helix chain 'Q' and resid 336 through 347 Processing helix chain 'Q' and resid 405 through 414 Processing helix chain 'Q' and resid 423 through 432 Processing helix chain 'Q' and resid 436 through 447 Processing helix chain 'M' and resid 61 through 65 removed outlier: 3.797A pdb=" N SER M 64 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN M 65 " --> pdb=" O GLU M 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 65' Processing helix chain 'M' and resid 74 through 82 removed outlier: 3.503A pdb=" N LYS M 80 " --> pdb=" O PHE M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 113 Processing helix chain 'M' and resid 234 through 243 removed outlier: 3.503A pdb=" N GLU M 238 " --> pdb=" O HIS M 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'a' and resid 82 through 83 removed outlier: 3.769A pdb=" N GLY a 82 " --> pdb=" O VAL a 241 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 106 through 107 Processing sheet with id=AA4, first strand: chain 'a' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'a' and resid 343 through 344 Processing sheet with id=AA6, first strand: chain 'a' and resid 455 through 458 removed outlier: 3.559A pdb=" N MET a 487 " --> pdb=" O THR a 351 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR a 351 " --> pdb=" O MET a 487 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA a 349 " --> pdb=" O LEU a 489 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N PHE a 468 " --> pdb=" O ARG a 350 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL a 352 " --> pdb=" O PHE a 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 455 through 458 removed outlier: 3.559A pdb=" N MET a 487 " --> pdb=" O THR a 351 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR a 351 " --> pdb=" O MET a 487 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA a 349 " --> pdb=" O LEU a 489 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 365 through 367 removed outlier: 5.628A pdb=" N VAL a 366 " --> pdb=" O ILE a 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 376 through 379 removed outlier: 3.523A pdb=" N VAL a 432 " --> pdb=" O GLU a 378 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL a 405 " --> pdb=" O ILE a 413 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 512 through 513 removed outlier: 3.724A pdb=" N LYS a 518 " --> pdb=" O SER a 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 587 through 589 removed outlier: 3.549A pdb=" N LEU a 588 " --> pdb=" O ILE a 607 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 849 through 850 removed outlier: 6.967A pdb=" N THR a 856 " --> pdb=" O ILE a 864 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 1283 through 1292 removed outlier: 3.542A pdb=" N MET a1285 " --> pdb=" O VAL a1305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 1224 through 1228 removed outlier: 4.067A pdb=" N LEU a1236 " --> pdb=" O LEU a1197 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL a1242 " --> pdb=" O TRP a1191 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP a1191 " --> pdb=" O VAL a1242 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA a1149 " --> pdb=" O GLU a1196 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER a1150 " --> pdb=" O ARG i 45 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG i 45 " --> pdb=" O SER a1150 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE a1152 " --> pdb=" O VAL i 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 143 through 147 removed outlier: 5.608A pdb=" N VAL a1443 " --> pdb=" O ILE g 61 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY g 59 " --> pdb=" O ILE a1445 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'f' and resid 143 through 147 removed outlier: 5.608A pdb=" N VAL a1443 " --> pdb=" O ILE g 61 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY g 59 " --> pdb=" O ILE a1445 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE g 79 " --> pdb=" O ILE g 45 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE g 45 " --> pdb=" O PHE g 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 69 through 73 removed outlier: 3.548A pdb=" N GLY b 93 " --> pdb=" O ASP b 131 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP b 131 " --> pdb=" O GLY b 93 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE b 95 " --> pdb=" O PHE b 129 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE b 129 " --> pdb=" O ILE b 95 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL b 97 " --> pdb=" O GLY b 127 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLY b 127 " --> pdb=" O VAL b 97 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER b 126 " --> pdb=" O ARG b 169 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARG b 169 " --> pdb=" O SER b 126 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU b 128 " --> pdb=" O ILE b 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 101 through 103 removed outlier: 3.985A pdb=" N VAL b 102 " --> pdb=" O HIS b 110 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 203 through 204 Processing sheet with id=AC2, first strand: chain 'b' and resid 404 through 407 Processing sheet with id=AC3, first strand: chain 'b' and resid 224 through 227 removed outlier: 4.276A pdb=" N HIS b 236 " --> pdb=" O LEU b 258 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU b 258 " --> pdb=" O HIS b 236 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE b 240 " --> pdb=" O LEU b 254 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN b 255 " --> pdb=" O THR b 272 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR b 268 " --> pdb=" O TYR b 259 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE b 269 " --> pdb=" O ILE b 280 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE b 280 " --> pdb=" O ILE b 269 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ALA b 271 " --> pdb=" O GLN b 278 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN b 278 " --> pdb=" O ALA b 271 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU b 273 " --> pdb=" O ILE b 276 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 544 through 545 Processing sheet with id=AC5, first strand: chain 'b' and resid 650 through 651 removed outlier: 3.545A pdb=" N GLU b 650 " --> pdb=" O GLU b 641 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 585 through 590 removed outlier: 3.684A pdb=" N HIS b 587 " --> pdb=" O VAL b 580 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL b 580 " --> pdb=" O HIS b 587 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N VAL b 589 " --> pdb=" O THR b 578 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR b 578 " --> pdb=" O VAL b 589 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 792 through 796 removed outlier: 3.702A pdb=" N ILE b 795 " --> pdb=" O LEU b 854 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG b 857 " --> pdb=" O VAL b 968 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL b 966 " --> pdb=" O TYR b 859 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP b 861 " --> pdb=" O VAL b 964 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG b 967 " --> pdb=" O GLN b 951 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN b 951 " --> pdb=" O ARG b 967 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG b 969 " --> pdb=" O VAL b 949 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL b 949 " --> pdb=" O ARG b 969 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 978 through 981 removed outlier: 5.451A pdb=" N LYS b 979 " --> pdb=" O LEU b1095 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU b1095 " --> pdb=" O LYS b 979 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA b 981 " --> pdb=" O GLN b1093 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N PHE b1086 " --> pdb=" O ILE b 827 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE b 827 " --> pdb=" O PHE b1086 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N LEU b1010 " --> pdb=" O ASN b 822 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE b 824 " --> pdb=" O LEU b1010 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE b1012 " --> pdb=" O ILE b 824 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA b 826 " --> pdb=" O ILE b1012 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N MET b 839 " --> pdb=" O GLY b 991 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR b 993 " --> pdb=" O MET b 839 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET b 841 " --> pdb=" O THR b 993 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 978 through 981 removed outlier: 5.451A pdb=" N LYS b 979 " --> pdb=" O LEU b1095 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU b1095 " --> pdb=" O LYS b 979 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA b 981 " --> pdb=" O GLN b1093 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 910 through 912 removed outlier: 6.819A pdb=" N THR b 939 " --> pdb=" O ILE b 911 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'b' and resid 1158 through 1162 Processing sheet with id=AD3, first strand: chain 'c' and resid 8 through 13 removed outlier: 6.609A pdb=" N ASP c 19 " --> pdb=" O ARG c 11 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA c 13 " --> pdb=" O ASN c 17 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASN c 17 " --> pdb=" O ALA c 13 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE c 20 " --> pdb=" O MET c 230 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET c 230 " --> pdb=" O PHE c 20 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 119 through 120 removed outlier: 5.649A pdb=" N LYS c 160 " --> pdb=" O ILE c 46 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE c 46 " --> pdb=" O LYS c 160 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE l 67 " --> pdb=" O VAL c 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'c' and resid 72 through 74 removed outlier: 4.238A pdb=" N HIS c 131 " --> pdb=" O GLN c 73 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 111 through 112 Processing sheet with id=AD7, first strand: chain 'd' and resid 36 through 37 Processing sheet with id=AD8, first strand: chain 'e' and resid 60 through 62 removed outlier: 7.127A pdb=" N TRP e 79 " --> pdb=" O ILE e 109 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N VAL e 111 " --> pdb=" O TRP e 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 152 through 154 removed outlier: 3.761A pdb=" N LYS e 152 " --> pdb=" O ILE e 199 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE e 199 " --> pdb=" O LYS e 152 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 152 through 154 removed outlier: 3.761A pdb=" N LYS e 152 " --> pdb=" O ILE e 199 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE e 199 " --> pdb=" O LYS e 152 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'g' and resid 143 through 147 removed outlier: 3.683A pdb=" N VAL g 92 " --> pdb=" O GLU g 100 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLU g 100 " --> pdb=" O VAL g 92 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS g 107 " --> pdb=" O ALA g 159 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'h' and resid 95 through 98 removed outlier: 4.289A pdb=" N TYR h 95 " --> pdb=" O ILE h 144 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE h 144 " --> pdb=" O TYR h 95 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU h 27 " --> pdb=" O SER h 13 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL h 15 " --> pdb=" O ARG h 25 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG h 25 " --> pdb=" O VAL h 15 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU h 122 " --> pdb=" O ASP h 41 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR h 116 " --> pdb=" O MET h 123 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU h 125 " --> pdb=" O VAL h 114 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL h 114 " --> pdb=" O LEU h 125 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU h 111 " --> pdb=" O GLU h 106 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU h 106 " --> pdb=" O LEU h 111 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA h 113 " --> pdb=" O PHE h 104 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE h 104 " --> pdb=" O ALA h 113 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR h 115 " --> pdb=" O TYR h 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'i' and resid 14 through 18 Processing sheet with id=AE5, first strand: chain 'i' and resid 84 through 87 Processing sheet with id=AE6, first strand: chain 'k' and resid 19 through 24 removed outlier: 4.535A pdb=" N ALA k 30 " --> pdb=" O ASP k 24 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE k 71 " --> pdb=" O PHE k 35 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.605A pdb=" N VAL A 17 " --> pdb=" O ASP A1419 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 83 through 90 removed outlier: 10.202A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 11.266A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 106 through 107 Processing sheet with id=AF1, first strand: chain 'A' and resid 173 through 177 removed outlier: 3.756A pdb=" N THR A 173 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 343 through 345 removed outlier: 4.099A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.553A pdb=" N ALA A 349 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET A 456 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE A 463 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL A 366 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AF5, first strand: chain 'A' and resid 588 through 589 removed outlier: 7.087A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.574A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 879 through 882 removed outlier: 3.610A pdb=" N GLN A 881 " --> pdb=" O TRP A 954 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'A' and resid 1283 through 1292 removed outlier: 3.547A pdb=" N TYR A1328 " --> pdb=" O THR A1117 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.356A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER A1150 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ARG I 45 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ILE A1152 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.974A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 48 through 49 removed outlier: 3.974A pdb=" N ILE D 48 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 68 through 70 removed outlier: 5.511A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AG5, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AG6, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AG7, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.522A pdb=" N GLN B 224 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 268 " --> pdb=" O TYR B 259 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 544 through 547 removed outlier: 6.538A pdb=" N CYS B 544 " --> pdb=" O VAL B 633 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL B 633 " --> pdb=" O CYS B 544 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER B 546 " --> pdb=" O GLY B 631 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.328A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AH2, first strand: chain 'B' and resid 792 through 796 removed outlier: 3.518A pdb=" N ALA B 793 " --> pdb=" O PHE B 856 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 795 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 4.466A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 981 " --> pdb=" O GLN B1093 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 1158 through 1162 Processing sheet with id=AH5, first strand: chain 'C' and resid 8 through 13 removed outlier: 6.800A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.144A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.856A pdb=" N GLN C 73 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.986A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AI1, first strand: chain 'E' and resid 78 through 80 removed outlier: 6.357A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.503A pdb=" N ARG E 200 " --> pdb=" O TYR E 208 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 86 through 93 removed outlier: 5.430A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.895A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 54 through 58 removed outlier: 3.782A pdb=" N ASP H 8 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU H 111 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU H 106 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'I' and resid 14 through 18 Processing sheet with id=AI7, first strand: chain 'I' and resid 84 through 87 Processing sheet with id=AI8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AI9, first strand: chain 'Q' and resid 102 through 104 removed outlier: 4.149A pdb=" N GLY M 93 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE M 104 " --> pdb=" O LEU M 122 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU M 221 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL M 68 " --> pdb=" O CYS M 219 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU M 221 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU M 70 " --> pdb=" O GLU M 221 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN M 223 " --> pdb=" O LEU M 70 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG M 72 " --> pdb=" O GLN M 223 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N MET M 225 " --> pdb=" O ARG M 72 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN M 67 " --> pdb=" O VAL Q 378 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL Q 378 " --> pdb=" O GLN M 67 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Q' and resid 102 through 104 removed outlier: 4.149A pdb=" N GLY M 93 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE M 104 " --> pdb=" O LEU M 122 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU M 221 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL M 134 " --> pdb=" O VAL M 215 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N THR M 217 " --> pdb=" O GLU M 132 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU M 132 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR Q 116 " --> pdb=" O LYS Q 391 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N TYR Q 393 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU Q 118 " --> pdb=" O TYR Q 393 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE Q 395 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS Q 120 " --> pdb=" O PHE Q 395 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLN Q 122 " --> pdb=" O ALA Q 397 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR Q 360 " --> pdb=" O ARG Q 398 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) 2556 hydrogen bonds defined for protein. 7089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 140 hydrogen bonds 280 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 120 stacking parallelities Total time for adding SS restraints: 39.68 Time building geometry restraints manager: 16.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 22184 1.34 - 1.46: 15427 1.46 - 1.58: 32329 1.58 - 1.71: 333 1.71 - 1.83: 602 Bond restraints: 70875 Sorted by residual: bond pdb=" O3' C R 15 " pdb=" P C R 16 " ideal model delta sigma weight residual 1.607 1.665 -0.058 1.50e-02 4.44e+03 1.51e+01 bond pdb=" C CYS b 523 " pdb=" N PRO b 524 " ideal model delta sigma weight residual 1.334 1.305 0.029 8.40e-03 1.42e+04 1.18e+01 bond pdb=" O3' A r 46 " pdb=" P U r 47 " ideal model delta sigma weight residual 1.607 1.555 0.052 1.50e-02 4.44e+03 1.18e+01 bond pdb=" O3' DA O -47 " pdb=" P DT O -46 " ideal model delta sigma weight residual 1.607 1.557 0.050 1.50e-02 4.44e+03 1.10e+01 bond pdb=" O3' U R 13 " pdb=" P C R 14 " ideal model delta sigma weight residual 1.607 1.656 -0.049 1.50e-02 4.44e+03 1.05e+01 ... (remaining 70870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 95329 2.98 - 5.96: 1056 5.96 - 8.94: 88 8.94 - 11.92: 11 11.92 - 14.90: 6 Bond angle restraints: 96490 Sorted by residual: angle pdb=" C CYS B1166 " pdb=" CA CYS B1166 " pdb=" CB CYS B1166 " ideal model delta sigma weight residual 110.88 96.70 14.18 1.57e+00 4.06e-01 8.15e+01 angle pdb=" O3' U r 40 " pdb=" C3' U r 40 " pdb=" C2' U r 40 " ideal model delta sigma weight residual 113.70 101.01 12.69 1.50e+00 4.44e-01 7.16e+01 angle pdb=" O2' U r 47 " pdb=" C2' U r 47 " pdb=" C1' U r 47 " ideal model delta sigma weight residual 108.40 96.13 12.27 1.50e+00 4.44e-01 6.69e+01 angle pdb=" O3' DG O -39 " pdb=" C3' DG O -39 " pdb=" C2' DG O -39 " ideal model delta sigma weight residual 111.50 99.50 12.00 1.50e+00 4.44e-01 6.40e+01 angle pdb=" N PRO Q 421 " pdb=" CA PRO Q 421 " pdb=" CB PRO Q 421 " ideal model delta sigma weight residual 103.27 110.17 -6.90 9.00e-01 1.23e+00 5.88e+01 ... (remaining 96485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 41555 35.82 - 71.64: 1387 71.64 - 107.45: 96 107.45 - 143.27: 7 143.27 - 179.09: 3 Dihedral angle restraints: 43048 sinusoidal: 19016 harmonic: 24032 Sorted by residual: dihedral pdb=" CA HIS B 363 " pdb=" C HIS B 363 " pdb=" N ILE B 364 " pdb=" CA ILE B 364 " ideal model delta harmonic sigma weight residual -180.00 -133.35 -46.65 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA LYS B 510 " pdb=" C LYS B 510 " pdb=" N PRO B 511 " pdb=" CA PRO B 511 " ideal model delta harmonic sigma weight residual -180.00 -134.49 -45.51 0 5.00e+00 4.00e-02 8.29e+01 dihedral pdb=" CA PHE A 252 " pdb=" C PHE A 252 " pdb=" N ASN A 253 " pdb=" CA ASN A 253 " ideal model delta harmonic sigma weight residual 180.00 138.67 41.33 0 5.00e+00 4.00e-02 6.83e+01 ... (remaining 43045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 10481 0.106 - 0.212: 378 0.212 - 0.319: 6 0.319 - 0.425: 3 0.425 - 0.531: 1 Chirality restraints: 10869 Sorted by residual: chirality pdb=" C2' U r 40 " pdb=" C3' U r 40 " pdb=" O2' U r 40 " pdb=" C1' U r 40 " both_signs ideal model delta sigma weight residual False -2.75 -2.22 -0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" CA CYS B1166 " pdb=" N CYS B1166 " pdb=" C CYS B1166 " pdb=" CB CYS B1166 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C3' DA O -42 " pdb=" C4' DA O -42 " pdb=" O3' DA O -42 " pdb=" C2' DA O -42 " both_signs ideal model delta sigma weight residual False -2.66 -2.30 -0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 10866 not shown) Planarity restraints: 11891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 510 " 0.065 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO B 511 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 511 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 511 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U r 40 " 0.035 2.00e-02 2.50e+03 2.06e-02 9.52e+00 pdb=" N1 U r 40 " -0.049 2.00e-02 2.50e+03 pdb=" C2 U r 40 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U r 40 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U r 40 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U r 40 " 0.011 2.00e-02 2.50e+03 pdb=" O4 U r 40 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U r 40 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U r 40 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C r 39 " 0.042 2.00e-02 2.50e+03 1.97e-02 8.71e+00 pdb=" N1 C r 39 " -0.015 2.00e-02 2.50e+03 pdb=" C2 C r 39 " -0.007 2.00e-02 2.50e+03 pdb=" O2 C r 39 " -0.016 2.00e-02 2.50e+03 pdb=" N3 C r 39 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C r 39 " 0.004 2.00e-02 2.50e+03 pdb=" N4 C r 39 " 0.024 2.00e-02 2.50e+03 pdb=" C5 C r 39 " -0.014 2.00e-02 2.50e+03 pdb=" C6 C r 39 " -0.019 2.00e-02 2.50e+03 ... (remaining 11888 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 3 1.97 - 2.71: 3993 2.71 - 3.44: 110854 3.44 - 4.17: 167907 4.17 - 4.90: 280550 Nonbonded interactions: 563307 Sorted by model distance: nonbonded pdb=" OP1 U R 13 " pdb="MG MG R 101 " model vdw 1.242 2.170 nonbonded pdb=" O CYS a 67 " pdb="ZN ZN a1802 " model vdw 1.888 2.230 nonbonded pdb=" OD2 ASP a 481 " pdb="MG MG a1803 " model vdw 1.934 2.170 nonbonded pdb=" OP2 C r 48 " pdb="MG MG a1803 " model vdw 1.984 2.170 nonbonded pdb=" O CYS A 67 " pdb="ZN ZN A1802 " model vdw 1.999 2.230 ... (remaining 563302 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 314 or (resid 315 through 318 and (name N or nam \ e CA or name C or name O or name CB )) or resid 319 through 1454 or resid 1801 t \ hrough 1803)) selection = (chain 'a' and (resid 2 through 174 or (resid 175 and (name N or name CA or name \ C or name O or name CB )) or resid 176 through 317 or (resid 318 and (name N or \ name CA or name C or name O or name CB )) or resid 319 through 325 or (resid 32 \ 6 through 327 and (name N or name CA or name C or name O or name CB )) or resid \ 328 through 329 or (resid 330 and (name N or name CA or name C or name O or name \ CB )) or resid 331 through 1403 or (resid 1404 and (name N or name CA or name C \ or name O or name CB )) or resid 1405 through 1406 or (resid 1407 and (name N o \ r name CA or name C or name O or name CB )) or resid 1408 through 1454 or resid \ 1801 through 1803)) } ncs_group { reference = (chain 'B' and (resid 20 through 502 or resid 509 through 867 or (resid 868 and \ (name N or name CA or name C or name O or name CB )) or resid 869 through 1223 o \ r resid 1301)) selection = (chain 'b' and (resid 20 through 469 or (resid 470 through 472 and (name N or na \ me CA or name C or name O or name CB )) or resid 473 through 1223 or resid 1301) \ ) } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = (chain 'g' and (resid 1 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 171)) } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } 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=0.95 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.350 Construct map_model_manager: 0.060 Extract box with map and model: 2.200 Check model and map are aligned: 0.410 Set scattering table: 0.490 Process input model: 158.830 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.560 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 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 : 0.005 0.062 70875 Z= 0.348 Angle : 0.830 14.899 96490 Z= 0.486 Chirality : 0.047 0.531 10869 Planarity : 0.004 0.097 11891 Dihedral : 16.975 179.091 27482 Min Nonbonded Distance : 1.242 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.32 % Favored : 88.61 % Rotamer: Outliers : 0.07 % Allowed : 0.57 % Favored : 99.36 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.11 % 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: -1.69 (0.09), residues: 8171 helix: 0.33 (0.10), residues: 2620 sheet: -0.98 (0.14), residues: 1258 loop : -2.17 (0.09), residues: 4293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP b 466 HIS 0.011 0.001 HIS A 399 PHE 0.027 0.002 PHE d 151 TYR 0.022 0.002 TYR b 833 ARG 0.014 0.001 ARG h 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 362 time to evaluate : 6.056 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: a 234 MET cc_start: 0.9197 (tpt) cc_final: 0.8918 (tpt) REVERT: a 455 MET cc_start: 0.8636 (pmm) cc_final: 0.8396 (pmm) REVERT: a 521 MET cc_start: 0.8842 (mmp) cc_final: 0.8285 (mmm) REVERT: a 605 MET cc_start: 0.7350 (tpp) cc_final: 0.6898 (mmp) REVERT: a 1267 MET cc_start: 0.9414 (mmp) cc_final: 0.9133 (mmm) REVERT: a 1336 MET cc_start: 0.9669 (tmm) cc_final: 0.9391 (tmm) REVERT: a 1368 MET cc_start: 0.8949 (mpp) cc_final: 0.8691 (mpp) REVERT: b 173 MET cc_start: 0.7051 (tmm) cc_final: 0.6741 (tmm) REVERT: b 313 MET cc_start: 0.9630 (mmm) cc_final: 0.9376 (mmm) REVERT: b 432 MET cc_start: 0.9401 (ptp) cc_final: 0.9046 (mmm) REVERT: b 615 MET cc_start: 0.9043 (pmm) cc_final: 0.8576 (pmm) REVERT: b 747 MET cc_start: 0.8793 (mmp) cc_final: 0.8524 (mmp) REVERT: b 778 MET cc_start: 0.6845 (pmm) cc_final: 0.6450 (pmm) REVERT: b 931 TYR cc_start: 0.8115 (m-10) cc_final: 0.7893 (m-10) REVERT: b 1098 MET cc_start: 0.8513 (mmp) cc_final: 0.8163 (mmp) REVERT: b 1133 MET cc_start: 0.9069 (mtp) cc_final: 0.8806 (mmm) REVERT: e 22 MET cc_start: 0.9018 (tmm) cc_final: 0.8747 (tmm) REVERT: A 341 MET cc_start: 0.9002 (mpp) cc_final: 0.8527 (mpp) REVERT: A 437 MET cc_start: 0.8385 (mtm) cc_final: 0.8159 (mtt) REVERT: A 453 MET cc_start: 0.9574 (mpp) cc_final: 0.9271 (mpp) REVERT: A 456 MET cc_start: 0.8418 (mpp) cc_final: 0.7647 (mpp) REVERT: A 1267 MET cc_start: 0.9380 (mmp) cc_final: 0.9081 (mmp) REVERT: A 1336 MET cc_start: 0.9632 (tmm) cc_final: 0.9422 (tmm) REVERT: A 1368 MET cc_start: 0.9400 (mtm) cc_final: 0.8608 (mpp) REVERT: A 1433 MET cc_start: 0.9243 (ppp) cc_final: 0.8940 (ppp) REVERT: A 1444 MET cc_start: 0.8838 (tpp) cc_final: 0.8583 (tpp) REVERT: B 101 MET cc_start: 0.8566 (tpt) cc_final: 0.8278 (tpp) REVERT: B 860 MET cc_start: 0.8772 (ppp) cc_final: 0.8286 (ppp) REVERT: B 1206 GLU cc_start: 0.9108 (mp0) cc_final: 0.8787 (pm20) REVERT: C 75 MET cc_start: 0.9520 (tpt) cc_final: 0.9086 (tpp) REVERT: C 125 MET cc_start: 0.9503 (pmm) cc_final: 0.9273 (pmm) REVERT: E 22 MET cc_start: 0.9393 (ttm) cc_final: 0.9158 (ttm) REVERT: E 58 MET cc_start: 0.9498 (ptp) cc_final: 0.8961 (ptp) REVERT: F 70 LYS cc_start: 0.6856 (mppt) cc_final: 0.6153 (pttt) REVERT: F 154 ASP cc_start: 0.7806 (t70) cc_final: 0.7415 (t0) REVERT: G 44 TYR cc_start: 0.8809 (t80) cc_final: 0.8293 (t80) REVERT: G 51 TYR cc_start: 0.8271 (t80) cc_final: 0.7751 (m-80) REVERT: G 52 ASP cc_start: 0.8958 (t0) cc_final: 0.8489 (p0) REVERT: G 65 ASP cc_start: 0.8771 (m-30) cc_final: 0.8548 (m-30) REVERT: H 1 MET cc_start: 0.5375 (pmm) cc_final: 0.5156 (pmm) REVERT: H 52 GLN cc_start: 0.9446 (tp-100) cc_final: 0.9190 (tp-100) REVERT: H 97 MET cc_start: 0.8906 (ppp) cc_final: 0.8465 (ppp) REVERT: H 123 MET cc_start: 0.9390 (ppp) cc_final: 0.9187 (ppp) REVERT: I 54 GLU cc_start: 0.8745 (pm20) cc_final: 0.8400 (pm20) REVERT: K 38 GLU cc_start: 0.9373 (mp0) cc_final: 0.9106 (pm20) REVERT: L 66 GLN cc_start: 0.8481 (pp30) cc_final: 0.7970 (pp30) REVERT: Q 329 THR cc_start: 0.3888 (m) cc_final: 0.3506 (p) outliers start: 5 outliers final: 1 residues processed: 367 average time/residue: 0.6801 time to fit residues: 437.4976 Evaluate side-chains 331 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 6.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 702 optimal weight: 8.9990 chunk 630 optimal weight: 8.9990 chunk 349 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 425 optimal weight: 20.0000 chunk 336 optimal weight: 0.0060 chunk 652 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 396 optimal weight: 3.9990 chunk 485 optimal weight: 0.9980 chunk 755 optimal weight: 5.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 611 GLN ** a 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 877 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1009 ASN ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 47 GLN b 357 GLN ** b 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 ASN e 54 GLN ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 22 ASN ** j 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 ASN A 447 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 881 ASN D 74 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 131 ASN I 87 GLN I 89 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 70875 Z= 0.238 Angle : 0.714 14.081 96490 Z= 0.379 Chirality : 0.045 0.216 10869 Planarity : 0.005 0.093 11891 Dihedral : 16.157 176.390 11110 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.18 % Favored : 89.79 % Rotamer: Outliers : 0.44 % Allowed : 8.36 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % 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: -1.45 (0.09), residues: 8171 helix: 0.61 (0.10), residues: 2699 sheet: -0.87 (0.15), residues: 1218 loop : -2.12 (0.09), residues: 4254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP b 308 HIS 0.009 0.001 HIS B 363 PHE 0.029 0.002 PHE d 151 TYR 0.023 0.001 TYR h 116 ARG 0.009 0.001 ARG a1100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 358 time to evaluate : 6.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.7970 (tpt) cc_final: 0.7522 (tpt) REVERT: a 108 MET cc_start: 0.9074 (pmm) cc_final: 0.8780 (pmm) REVERT: a 234 MET cc_start: 0.9248 (tpt) cc_final: 0.8776 (tpt) REVERT: a 304 MET cc_start: 0.9444 (mmm) cc_final: 0.9222 (tpt) REVERT: a 456 MET cc_start: 0.8990 (mpp) cc_final: 0.8777 (mpp) REVERT: a 521 MET cc_start: 0.8781 (mmp) cc_final: 0.8352 (mmm) REVERT: a 761 MET cc_start: 0.9370 (mmm) cc_final: 0.9033 (mmm) REVERT: a 1267 MET cc_start: 0.9374 (mmp) cc_final: 0.9102 (mmm) REVERT: a 1317 MET cc_start: 0.8935 (tmm) cc_final: 0.8350 (tmm) REVERT: a 1368 MET cc_start: 0.8987 (mpp) cc_final: 0.8715 (mpp) REVERT: b 313 MET cc_start: 0.9623 (mmm) cc_final: 0.9364 (mmm) REVERT: b 432 MET cc_start: 0.9290 (ptp) cc_final: 0.9026 (ptt) REVERT: b 778 MET cc_start: 0.7146 (pmm) cc_final: 0.6472 (pmm) REVERT: b 931 TYR cc_start: 0.8057 (m-10) cc_final: 0.7825 (m-10) REVERT: b 1021 MET cc_start: 0.7915 (mmt) cc_final: 0.7680 (mmp) REVERT: b 1098 MET cc_start: 0.8544 (mmp) cc_final: 0.8107 (mmp) REVERT: b 1138 MET cc_start: 0.9430 (mmp) cc_final: 0.9184 (mmp) REVERT: b 1208 MET cc_start: 0.9084 (pmm) cc_final: 0.8334 (pmm) REVERT: b 1210 MET cc_start: 0.8971 (mmm) cc_final: 0.8709 (mmm) REVERT: e 22 MET cc_start: 0.9080 (tmm) cc_final: 0.8812 (tmm) REVERT: A 108 MET cc_start: 0.9323 (pmm) cc_final: 0.8784 (pmm) REVERT: A 122 MET cc_start: 0.9230 (tmm) cc_final: 0.9004 (ppp) REVERT: A 146 MET cc_start: 0.8798 (mmm) cc_final: 0.8595 (mmm) REVERT: A 304 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8593 (mmp) REVERT: A 341 MET cc_start: 0.9104 (mpp) cc_final: 0.8563 (mpp) REVERT: A 437 MET cc_start: 0.8510 (mtm) cc_final: 0.8235 (mtt) REVERT: A 456 MET cc_start: 0.8688 (mpp) cc_final: 0.8075 (mpp) REVERT: A 605 MET cc_start: 0.8736 (tpp) cc_final: 0.8290 (tpp) REVERT: A 849 MET cc_start: 0.8759 (tmm) cc_final: 0.8471 (tmm) REVERT: A 1063 MET cc_start: 0.9233 (mmm) cc_final: 0.8986 (mmm) REVERT: A 1111 MET cc_start: 0.8086 (mmp) cc_final: 0.7860 (mmp) REVERT: A 1209 MET cc_start: 0.8723 (ppp) cc_final: 0.8371 (tmm) REVERT: A 1267 MET cc_start: 0.9372 (mmp) cc_final: 0.9089 (mmp) REVERT: A 1398 MET cc_start: 0.9063 (tmm) cc_final: 0.8811 (tmm) REVERT: A 1433 MET cc_start: 0.9259 (ppp) cc_final: 0.9047 (ppp) REVERT: B 101 MET cc_start: 0.8420 (tpt) cc_final: 0.8175 (tpp) REVERT: B 705 MET cc_start: 0.8952 (tpp) cc_final: 0.8673 (tpp) REVERT: B 860 MET cc_start: 0.8784 (ppp) cc_final: 0.8311 (ppp) REVERT: B 1206 GLU cc_start: 0.9053 (mp0) cc_final: 0.8741 (mp0) REVERT: B 1210 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8588 (tpp) REVERT: C 37 MET cc_start: 0.9396 (mtm) cc_final: 0.9094 (mtm) REVERT: C 75 MET cc_start: 0.9531 (tpt) cc_final: 0.9084 (tpp) REVERT: D 173 HIS cc_start: 0.8154 (t70) cc_final: 0.7952 (t70) REVERT: E 22 MET cc_start: 0.9408 (ttm) cc_final: 0.9049 (ttm) REVERT: E 58 MET cc_start: 0.9407 (ptp) cc_final: 0.9177 (ptp) REVERT: F 70 LYS cc_start: 0.7008 (mppt) cc_final: 0.6252 (pttt) REVERT: F 85 MET cc_start: 0.8546 (tmm) cc_final: 0.8281 (tmm) REVERT: F 120 ILE cc_start: 0.9798 (mm) cc_final: 0.9593 (mm) REVERT: F 122 MET cc_start: 0.9471 (mtp) cc_final: 0.9201 (mtp) REVERT: F 154 ASP cc_start: 0.7768 (t70) cc_final: 0.7395 (t0) REVERT: G 44 TYR cc_start: 0.8562 (t80) cc_final: 0.8149 (t80) REVERT: G 51 TYR cc_start: 0.8520 (t80) cc_final: 0.7972 (m-80) REVERT: G 52 ASP cc_start: 0.8982 (t0) cc_final: 0.8492 (p0) REVERT: H 52 GLN cc_start: 0.9445 (tp-100) cc_final: 0.9174 (tp-100) REVERT: H 97 MET cc_start: 0.8717 (ppp) cc_final: 0.8353 (ppp) REVERT: H 123 MET cc_start: 0.9278 (ppp) cc_final: 0.9023 (ppp) REVERT: I 54 GLU cc_start: 0.8717 (pm20) cc_final: 0.8489 (pm20) REVERT: K 38 GLU cc_start: 0.9360 (mp0) cc_final: 0.9149 (mp0) REVERT: L 66 GLN cc_start: 0.8574 (pp30) cc_final: 0.8065 (pp30) REVERT: L 68 GLU cc_start: 0.9076 (mp0) cc_final: 0.8861 (mp0) outliers start: 32 outliers final: 13 residues processed: 374 average time/residue: 0.7740 time to fit residues: 511.8675 Evaluate side-chains 347 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 332 time to evaluate : 6.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain M residue 97 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 419 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 628 optimal weight: 6.9990 chunk 514 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 756 optimal weight: 7.9990 chunk 817 optimal weight: 30.0000 chunk 674 optimal weight: 10.0000 chunk 750 optimal weight: 50.0000 chunk 258 optimal weight: 20.0000 chunk 607 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 209 ASN ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 851 HIS ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 146 HIS ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN ** j 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1427 ASN ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN G 24 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 70875 Z= 0.385 Angle : 0.744 13.986 96490 Z= 0.395 Chirality : 0.045 0.237 10869 Planarity : 0.005 0.090 11891 Dihedral : 16.182 177.508 11110 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.16 % Favored : 88.81 % Rotamer: Outliers : 1.06 % Allowed : 12.41 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % 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: -1.52 (0.09), residues: 8171 helix: 0.59 (0.10), residues: 2717 sheet: -1.02 (0.14), residues: 1240 loop : -2.17 (0.09), residues: 4214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP b 308 HIS 0.016 0.002 HIS A 451 PHE 0.023 0.002 PHE d 151 TYR 0.024 0.002 TYR b 833 ARG 0.010 0.001 ARG h 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 346 time to evaluate : 6.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8031 (tpt) cc_final: 0.7696 (tpt) REVERT: a 108 MET cc_start: 0.9136 (pmm) cc_final: 0.8932 (pmm) REVERT: a 304 MET cc_start: 0.9466 (mmm) cc_final: 0.9023 (tpt) REVERT: a 455 MET cc_start: 0.8010 (pmm) cc_final: 0.7641 (pmm) REVERT: a 456 MET cc_start: 0.9068 (mpp) cc_final: 0.8181 (mpp) REVERT: a 512 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8685 (p) REVERT: a 605 MET cc_start: 0.7658 (tpp) cc_final: 0.7119 (mmp) REVERT: a 761 MET cc_start: 0.9502 (mmm) cc_final: 0.9276 (mmm) REVERT: a 1267 MET cc_start: 0.9350 (mmp) cc_final: 0.9094 (mmm) REVERT: a 1317 MET cc_start: 0.9006 (tmm) cc_final: 0.8760 (tmm) REVERT: a 1368 MET cc_start: 0.8971 (mpp) cc_final: 0.8646 (mpp) REVERT: b 173 MET cc_start: 0.7056 (tmm) cc_final: 0.6709 (tmm) REVERT: b 210 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8713 (mmmt) REVERT: b 313 MET cc_start: 0.9625 (mmm) cc_final: 0.9284 (mmm) REVERT: b 432 MET cc_start: 0.9248 (ptp) cc_final: 0.8933 (ptt) REVERT: b 778 MET cc_start: 0.7424 (pmm) cc_final: 0.6652 (pmm) REVERT: b 931 TYR cc_start: 0.8074 (m-10) cc_final: 0.7803 (m-10) REVERT: b 1098 MET cc_start: 0.8592 (mmp) cc_final: 0.8095 (mmp) REVERT: b 1138 MET cc_start: 0.9466 (mmp) cc_final: 0.9156 (mmp) REVERT: b 1208 MET cc_start: 0.9138 (pmm) cc_final: 0.8419 (pmm) REVERT: b 1210 MET cc_start: 0.8897 (mmm) cc_final: 0.8653 (mmm) REVERT: e 22 MET cc_start: 0.9063 (tmm) cc_final: 0.8827 (tmm) REVERT: A 234 MET cc_start: 0.9462 (ttm) cc_final: 0.8720 (tpp) REVERT: A 341 MET cc_start: 0.9182 (mpp) cc_final: 0.8591 (mpp) REVERT: A 437 MET cc_start: 0.8466 (mtm) cc_final: 0.8182 (mtt) REVERT: A 456 MET cc_start: 0.8736 (mpp) cc_final: 0.8138 (mpp) REVERT: A 487 MET cc_start: 0.8893 (tpp) cc_final: 0.8674 (tpp) REVERT: A 605 MET cc_start: 0.8624 (tpp) cc_final: 0.8267 (tpp) REVERT: A 849 MET cc_start: 0.8886 (tmm) cc_final: 0.8566 (tmm) REVERT: A 1267 MET cc_start: 0.9341 (mmp) cc_final: 0.9085 (mmm) REVERT: A 1375 MET cc_start: 0.9454 (ttp) cc_final: 0.9070 (tmm) REVERT: A 1398 MET cc_start: 0.9131 (tmm) cc_final: 0.8790 (tmm) REVERT: A 1433 MET cc_start: 0.9229 (ppp) cc_final: 0.8698 (ppp) REVERT: A 1444 MET cc_start: 0.8738 (tpp) cc_final: 0.8430 (mmm) REVERT: B 101 MET cc_start: 0.8386 (tpt) cc_final: 0.8031 (tpp) REVERT: B 381 MET cc_start: 0.9435 (tmm) cc_final: 0.8700 (tmm) REVERT: B 705 MET cc_start: 0.8989 (tpp) cc_final: 0.8687 (tpp) REVERT: B 809 MET cc_start: 0.8846 (pmm) cc_final: 0.8537 (pmm) REVERT: B 860 MET cc_start: 0.8823 (ppp) cc_final: 0.8387 (ppp) REVERT: B 1152 MET cc_start: 0.8783 (mmm) cc_final: 0.8416 (mmm) REVERT: C 37 MET cc_start: 0.9411 (mtm) cc_final: 0.9100 (mtm) REVERT: C 75 MET cc_start: 0.9563 (tpt) cc_final: 0.9119 (tpp) REVERT: D 143 ASN cc_start: 0.8613 (m-40) cc_final: 0.8236 (t0) REVERT: E 22 MET cc_start: 0.9373 (ttm) cc_final: 0.9064 (ttp) REVERT: E 58 MET cc_start: 0.9295 (ptp) cc_final: 0.9081 (ptp) REVERT: F 70 LYS cc_start: 0.7105 (mppt) cc_final: 0.6327 (pttt) REVERT: F 103 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8588 (ppp) REVERT: F 120 ILE cc_start: 0.9800 (mm) cc_final: 0.9596 (mm) REVERT: F 122 MET cc_start: 0.9555 (mtp) cc_final: 0.9351 (mtp) REVERT: F 154 ASP cc_start: 0.7768 (t70) cc_final: 0.7403 (t0) REVERT: G 44 TYR cc_start: 0.8522 (t80) cc_final: 0.7881 (t80) REVERT: G 51 TYR cc_start: 0.8572 (t80) cc_final: 0.8352 (t80) REVERT: G 52 ASP cc_start: 0.9030 (t0) cc_final: 0.8765 (p0) REVERT: H 123 MET cc_start: 0.9335 (ppp) cc_final: 0.9019 (ppp) REVERT: I 54 GLU cc_start: 0.8753 (pm20) cc_final: 0.8515 (pm20) REVERT: K 38 GLU cc_start: 0.9336 (mp0) cc_final: 0.9062 (mp0) outliers start: 76 outliers final: 31 residues processed: 404 average time/residue: 0.7186 time to fit residues: 515.0905 Evaluate side-chains 367 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 333 time to evaluate : 6.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain b residue 210 LYS Chi-restraints excluded: chain b residue 399 ASP Chi-restraints excluded: chain b residue 773 MET Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain d residue 23 ASN Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 116 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 747 optimal weight: 7.9990 chunk 569 optimal weight: 10.0000 chunk 392 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 361 optimal weight: 9.9990 chunk 508 optimal weight: 5.9990 chunk 759 optimal weight: 0.5980 chunk 804 optimal weight: 30.0000 chunk 396 optimal weight: 10.0000 chunk 719 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 395 GLN ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 ASN e 5 ASN ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 53 HIS ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 447 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN H 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 70875 Z= 0.286 Angle : 0.686 13.427 96490 Z= 0.364 Chirality : 0.044 0.230 10869 Planarity : 0.005 0.086 11891 Dihedral : 16.150 178.940 11110 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.16 % Favored : 89.82 % Rotamer: Outliers : 1.68 % Allowed : 14.33 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.09), residues: 8171 helix: 0.78 (0.10), residues: 2711 sheet: -0.98 (0.14), residues: 1244 loop : -2.10 (0.09), residues: 4216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 81 HIS 0.010 0.001 HIS A 399 PHE 0.024 0.001 PHE k 10 TYR 0.020 0.001 TYR b 833 ARG 0.010 0.000 ARG h 145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 345 time to evaluate : 6.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8135 (tpt) cc_final: 0.7731 (tpt) REVERT: a 108 MET cc_start: 0.9167 (pmm) cc_final: 0.8963 (pmm) REVERT: a 234 MET cc_start: 0.9236 (tpt) cc_final: 0.8812 (tpt) REVERT: a 304 MET cc_start: 0.9416 (mmm) cc_final: 0.9076 (tpt) REVERT: a 340 LEU cc_start: 0.9568 (tp) cc_final: 0.9353 (tp) REVERT: a 512 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8661 (p) REVERT: a 521 MET cc_start: 0.9057 (mmm) cc_final: 0.8746 (mmm) REVERT: a 761 MET cc_start: 0.9572 (mmm) cc_final: 0.9048 (mmm) REVERT: a 1267 MET cc_start: 0.9301 (mmp) cc_final: 0.9056 (mmm) REVERT: a 1317 MET cc_start: 0.9128 (tmm) cc_final: 0.8852 (tmm) REVERT: a 1368 MET cc_start: 0.8969 (mpp) cc_final: 0.8633 (mpp) REVERT: b 173 MET cc_start: 0.6888 (tmm) cc_final: 0.6669 (tmm) REVERT: b 313 MET cc_start: 0.9622 (mmm) cc_final: 0.9276 (mmm) REVERT: b 432 MET cc_start: 0.9247 (ptp) cc_final: 0.8949 (ptt) REVERT: b 747 MET cc_start: 0.9122 (mmp) cc_final: 0.8911 (mmp) REVERT: b 778 MET cc_start: 0.7483 (pmm) cc_final: 0.6595 (pmm) REVERT: b 1021 MET cc_start: 0.7960 (mmt) cc_final: 0.7630 (mmt) REVERT: b 1098 MET cc_start: 0.8543 (mmp) cc_final: 0.8029 (mmp) REVERT: b 1111 MET cc_start: 0.9303 (mmp) cc_final: 0.9047 (tpp) REVERT: b 1138 MET cc_start: 0.9444 (mmp) cc_final: 0.9106 (mmp) REVERT: b 1208 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8401 (pmm) REVERT: b 1210 MET cc_start: 0.8921 (mmm) cc_final: 0.8700 (mmm) REVERT: e 22 MET cc_start: 0.9080 (tmm) cc_final: 0.8858 (tmm) REVERT: A 41 MET cc_start: 0.7421 (tpt) cc_final: 0.6998 (tpt) REVERT: A 108 MET cc_start: 0.9330 (pmm) cc_final: 0.8908 (pmm) REVERT: A 341 MET cc_start: 0.9222 (mpp) cc_final: 0.8608 (mpp) REVERT: A 437 MET cc_start: 0.8511 (mtm) cc_final: 0.8249 (mtt) REVERT: A 456 MET cc_start: 0.8720 (mpp) cc_final: 0.8101 (mpp) REVERT: A 487 MET cc_start: 0.8926 (tpp) cc_final: 0.8599 (tpp) REVERT: A 605 MET cc_start: 0.8472 (tpp) cc_final: 0.8058 (tpp) REVERT: A 849 MET cc_start: 0.8970 (tmm) cc_final: 0.8636 (tmm) REVERT: A 1111 MET cc_start: 0.8246 (mmp) cc_final: 0.7951 (mmm) REVERT: A 1267 MET cc_start: 0.9307 (mmp) cc_final: 0.9039 (mmp) REVERT: A 1279 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8966 (mp) REVERT: A 1375 MET cc_start: 0.9443 (ttp) cc_final: 0.9031 (tmm) REVERT: A 1398 MET cc_start: 0.9172 (tmm) cc_final: 0.8729 (tmm) REVERT: A 1433 MET cc_start: 0.9214 (ppp) cc_final: 0.8909 (ppp) REVERT: A 1444 MET cc_start: 0.8721 (tpp) cc_final: 0.8500 (mmm) REVERT: B 101 MET cc_start: 0.8424 (tpt) cc_final: 0.8107 (tpp) REVERT: B 381 MET cc_start: 0.9465 (tmm) cc_final: 0.8668 (tmm) REVERT: B 705 MET cc_start: 0.8975 (tpp) cc_final: 0.8631 (tpp) REVERT: B 860 MET cc_start: 0.8816 (ppp) cc_final: 0.8383 (ppp) REVERT: C 37 MET cc_start: 0.9406 (mtm) cc_final: 0.9155 (mtm) REVERT: C 75 MET cc_start: 0.9579 (tpt) cc_final: 0.9127 (tpp) REVERT: C 265 MET cc_start: 0.9111 (tpp) cc_final: 0.8532 (tmm) REVERT: D 143 ASN cc_start: 0.8607 (m-40) cc_final: 0.8217 (t0) REVERT: E 22 MET cc_start: 0.9334 (ttm) cc_final: 0.9000 (ttp) REVERT: E 58 MET cc_start: 0.9262 (ptp) cc_final: 0.9027 (ptp) REVERT: F 70 LYS cc_start: 0.7108 (mppt) cc_final: 0.6323 (pttt) REVERT: F 85 MET cc_start: 0.8708 (tmm) cc_final: 0.8397 (tmm) REVERT: F 100 GLN cc_start: 0.9350 (OUTLIER) cc_final: 0.8971 (pp30) REVERT: F 103 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8542 (ppp) REVERT: F 120 ILE cc_start: 0.9811 (mm) cc_final: 0.9608 (mm) REVERT: F 122 MET cc_start: 0.9548 (mtp) cc_final: 0.9304 (mtp) REVERT: F 154 ASP cc_start: 0.7774 (t70) cc_final: 0.7422 (t0) REVERT: G 44 TYR cc_start: 0.8492 (t80) cc_final: 0.7880 (t80) REVERT: G 51 TYR cc_start: 0.8565 (t80) cc_final: 0.8339 (t80) REVERT: G 52 ASP cc_start: 0.9063 (t0) cc_final: 0.8780 (p0) REVERT: G 61 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9026 (mp) REVERT: H 97 MET cc_start: 0.8863 (ppp) cc_final: 0.8658 (ppp) REVERT: H 123 MET cc_start: 0.9352 (ppp) cc_final: 0.8987 (ppp) REVERT: K 38 GLU cc_start: 0.9305 (mp0) cc_final: 0.9026 (mp0) REVERT: Q 352 MET cc_start: 0.7486 (tmm) cc_final: 0.7152 (tmm) outliers start: 121 outliers final: 55 residues processed: 443 average time/residue: 0.6293 time to fit residues: 492.3702 Evaluate side-chains 395 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 334 time to evaluate : 6.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 650 GLN Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1382 THR Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1394 THR Chi-restraints excluded: chain b residue 522 VAL Chi-restraints excluded: chain b residue 527 THR Chi-restraints excluded: chain b residue 773 MET Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain h residue 109 LYS Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1111 MET Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain Q residue 372 SER Chi-restraints excluded: chain M residue 97 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 669 optimal weight: 3.9990 chunk 456 optimal weight: 0.0970 chunk 11 optimal weight: 10.0000 chunk 598 optimal weight: 6.9990 chunk 331 optimal weight: 3.9990 chunk 686 optimal weight: 8.9990 chunk 555 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 410 optimal weight: 9.9990 chunk 721 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 253 ASN ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN ** e 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 70875 Z= 0.264 Angle : 0.679 12.840 96490 Z= 0.357 Chirality : 0.043 0.229 10869 Planarity : 0.004 0.079 11891 Dihedral : 16.112 179.419 11110 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.30 % Favored : 89.67 % Rotamer: Outliers : 1.97 % Allowed : 15.66 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % 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: -1.28 (0.09), residues: 8171 helix: 0.87 (0.10), residues: 2719 sheet: -0.94 (0.14), residues: 1231 loop : -2.06 (0.09), residues: 4221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP a 185 HIS 0.009 0.001 HIS A 399 PHE 0.026 0.001 PHE k 10 TYR 0.020 0.001 TYR b 833 ARG 0.009 0.000 ARG G 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 339 time to evaluate : 7.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8143 (tpt) cc_final: 0.7790 (tpt) REVERT: a 234 MET cc_start: 0.9267 (tpt) cc_final: 0.9061 (tpt) REVERT: a 304 MET cc_start: 0.9426 (mmm) cc_final: 0.9103 (tpt) REVERT: a 341 MET cc_start: 0.8976 (tpp) cc_final: 0.8533 (tpp) REVERT: a 512 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8596 (p) REVERT: a 550 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8373 (tp) REVERT: a 605 MET cc_start: 0.7600 (tpp) cc_final: 0.7097 (mmp) REVERT: a 761 MET cc_start: 0.9621 (mmm) cc_final: 0.9068 (mmm) REVERT: a 1267 MET cc_start: 0.9281 (mmp) cc_final: 0.9044 (mmm) REVERT: a 1317 MET cc_start: 0.9093 (tmm) cc_final: 0.8774 (tmm) REVERT: a 1363 VAL cc_start: 0.9670 (OUTLIER) cc_final: 0.9418 (p) REVERT: a 1368 MET cc_start: 0.8946 (mpp) cc_final: 0.8534 (mpp) REVERT: b 313 MET cc_start: 0.9621 (mmm) cc_final: 0.9269 (mmm) REVERT: b 705 MET cc_start: 0.7515 (tmm) cc_final: 0.7207 (tpp) REVERT: b 778 MET cc_start: 0.7491 (pmm) cc_final: 0.6614 (pmm) REVERT: b 1021 MET cc_start: 0.8015 (mmt) cc_final: 0.7661 (mmt) REVERT: b 1098 MET cc_start: 0.8544 (mmp) cc_final: 0.8003 (mmp) REVERT: b 1111 MET cc_start: 0.9322 (mmp) cc_final: 0.9089 (tpp) REVERT: b 1138 MET cc_start: 0.9447 (mmp) cc_final: 0.9097 (mmp) REVERT: b 1152 MET cc_start: 0.8191 (tpp) cc_final: 0.7974 (tpt) REVERT: b 1208 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8372 (pmm) REVERT: b 1210 MET cc_start: 0.8919 (mmm) cc_final: 0.8699 (mmm) REVERT: e 22 MET cc_start: 0.9075 (tmm) cc_final: 0.8851 (tmm) REVERT: A 41 MET cc_start: 0.7472 (tpt) cc_final: 0.7070 (tpt) REVERT: A 108 MET cc_start: 0.9377 (pmm) cc_final: 0.8951 (pmm) REVERT: A 341 MET cc_start: 0.9265 (mpp) cc_final: 0.8663 (mpp) REVERT: A 437 MET cc_start: 0.8509 (mtm) cc_final: 0.8240 (mtt) REVERT: A 451 HIS cc_start: 0.9107 (OUTLIER) cc_final: 0.8654 (p90) REVERT: A 456 MET cc_start: 0.8720 (mpp) cc_final: 0.8317 (mpp) REVERT: A 486 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: A 487 MET cc_start: 0.8920 (tpp) cc_final: 0.7693 (mmm) REVERT: A 605 MET cc_start: 0.8403 (tpp) cc_final: 0.7981 (tpp) REVERT: A 849 MET cc_start: 0.8998 (tmm) cc_final: 0.8646 (tmm) REVERT: A 1111 MET cc_start: 0.8326 (mmp) cc_final: 0.8065 (mmm) REVERT: A 1267 MET cc_start: 0.9272 (mmp) cc_final: 0.9039 (mmp) REVERT: A 1279 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.9000 (mp) REVERT: A 1375 MET cc_start: 0.9450 (ttp) cc_final: 0.9034 (tmm) REVERT: A 1398 MET cc_start: 0.9225 (tmm) cc_final: 0.8820 (tmm) REVERT: A 1433 MET cc_start: 0.9235 (ppp) cc_final: 0.8754 (ppp) REVERT: B 101 MET cc_start: 0.8450 (tpt) cc_final: 0.8069 (tpp) REVERT: B 381 MET cc_start: 0.9484 (tmm) cc_final: 0.8646 (tmm) REVERT: B 705 MET cc_start: 0.8990 (tpp) cc_final: 0.8666 (tpp) REVERT: B 860 MET cc_start: 0.8830 (ppp) cc_final: 0.8388 (ppp) REVERT: C 37 MET cc_start: 0.9398 (mtm) cc_final: 0.9150 (mtm) REVERT: C 75 MET cc_start: 0.9576 (tpt) cc_final: 0.9120 (tpp) REVERT: C 265 MET cc_start: 0.9091 (tpp) cc_final: 0.8490 (tmm) REVERT: E 22 MET cc_start: 0.9318 (ttm) cc_final: 0.8896 (ttp) REVERT: E 58 MET cc_start: 0.9255 (ptp) cc_final: 0.9014 (ptp) REVERT: F 70 LYS cc_start: 0.7120 (mppt) cc_final: 0.6333 (pttt) REVERT: F 85 MET cc_start: 0.8713 (tmm) cc_final: 0.8365 (tmm) REVERT: F 100 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8976 (pp30) REVERT: F 103 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8533 (tmm) REVERT: F 122 MET cc_start: 0.9549 (mtp) cc_final: 0.9292 (mtp) REVERT: F 154 ASP cc_start: 0.7803 (t70) cc_final: 0.7445 (t0) REVERT: G 1 MET cc_start: 0.9438 (pmm) cc_final: 0.9219 (ppp) REVERT: G 44 TYR cc_start: 0.8478 (t80) cc_final: 0.7897 (t80) REVERT: G 51 TYR cc_start: 0.8571 (t80) cc_final: 0.8272 (t80) REVERT: G 69 GLU cc_start: 0.7484 (tp30) cc_final: 0.6764 (tp30) REVERT: H 123 MET cc_start: 0.9378 (ppp) cc_final: 0.8989 (ppp) REVERT: Q 352 MET cc_start: 0.7521 (tmm) cc_final: 0.7034 (tmm) outliers start: 142 outliers final: 76 residues processed: 460 average time/residue: 0.6508 time to fit residues: 537.8268 Evaluate side-chains 415 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 330 time to evaluate : 6.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1133 LEU Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1382 THR Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1394 THR Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain a residue 1433 MET Chi-restraints excluded: chain b residue 357 GLN Chi-restraints excluded: chain b residue 399 ASP Chi-restraints excluded: chain b residue 522 VAL Chi-restraints excluded: chain b residue 527 THR Chi-restraints excluded: chain b residue 773 MET Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 238 ILE Chi-restraints excluded: chain e residue 5 ASN Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain I residue 49 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain Q residue 372 SER Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 228 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 270 optimal weight: 1.9990 chunk 724 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 472 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 804 optimal weight: 9.9990 chunk 668 optimal weight: 10.0000 chunk 372 optimal weight: 0.0070 chunk 66 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 chunk 422 optimal weight: 30.0000 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 GLN ** a 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 786 HIS ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 ASN ** b 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b1195 HIS e 147 HIS ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 HIS ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 ASN ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 70875 Z= 0.207 Angle : 0.666 13.051 96490 Z= 0.348 Chirality : 0.043 0.233 10869 Planarity : 0.004 0.072 11891 Dihedral : 16.035 179.943 11110 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.62 % Favored : 90.36 % Rotamer: Outliers : 1.87 % Allowed : 16.81 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % 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: -1.14 (0.09), residues: 8171 helix: 0.99 (0.10), residues: 2718 sheet: -0.83 (0.15), residues: 1218 loop : -1.99 (0.09), residues: 4235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP b 31 HIS 0.006 0.001 HIS A 451 PHE 0.017 0.001 PHE b 370 TYR 0.019 0.001 TYR b 833 ARG 0.008 0.000 ARG h 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 342 time to evaluate : 6.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8211 (tpt) cc_final: 0.7791 (tpt) REVERT: a 108 MET cc_start: 0.8971 (pmm) cc_final: 0.8723 (pmm) REVERT: a 234 MET cc_start: 0.9257 (tpt) cc_final: 0.8827 (mmm) REVERT: a 304 MET cc_start: 0.9417 (mmm) cc_final: 0.9052 (tpt) REVERT: a 512 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8546 (p) REVERT: a 550 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8383 (tp) REVERT: a 605 MET cc_start: 0.7573 (tpp) cc_final: 0.7229 (tpp) REVERT: a 761 MET cc_start: 0.9661 (mmm) cc_final: 0.9146 (mmm) REVERT: a 1267 MET cc_start: 0.9219 (mmp) cc_final: 0.8988 (mmm) REVERT: a 1317 MET cc_start: 0.9065 (tmm) cc_final: 0.8711 (tmm) REVERT: a 1363 VAL cc_start: 0.9669 (OUTLIER) cc_final: 0.9436 (p) REVERT: a 1368 MET cc_start: 0.8929 (mpp) cc_final: 0.8525 (mpp) REVERT: a 1400 CYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8790 (p) REVERT: b 313 MET cc_start: 0.9621 (mmm) cc_final: 0.9252 (mmm) REVERT: b 432 MET cc_start: 0.9284 (ptt) cc_final: 0.8902 (mmm) REVERT: b 705 MET cc_start: 0.7459 (tmm) cc_final: 0.7108 (tpp) REVERT: b 778 MET cc_start: 0.7625 (pmm) cc_final: 0.6735 (pmm) REVERT: b 1021 MET cc_start: 0.8039 (mmt) cc_final: 0.7732 (mmt) REVERT: b 1098 MET cc_start: 0.8547 (mmp) cc_final: 0.7981 (mmp) REVERT: b 1111 MET cc_start: 0.9314 (mmp) cc_final: 0.9074 (tpp) REVERT: b 1138 MET cc_start: 0.9442 (mmp) cc_final: 0.9108 (mmp) REVERT: b 1152 MET cc_start: 0.8154 (tpp) cc_final: 0.7889 (mmm) REVERT: b 1169 MET cc_start: 0.7037 (mmm) cc_final: 0.6824 (mmm) REVERT: b 1208 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8320 (pmm) REVERT: b 1210 MET cc_start: 0.8898 (mmm) cc_final: 0.8634 (mmm) REVERT: e 22 MET cc_start: 0.9090 (tmm) cc_final: 0.8844 (tmm) REVERT: A 41 MET cc_start: 0.7492 (tpt) cc_final: 0.7059 (tpt) REVERT: A 108 MET cc_start: 0.9410 (pmm) cc_final: 0.9009 (pmm) REVERT: A 146 MET cc_start: 0.9144 (mmm) cc_final: 0.8759 (mmm) REVERT: A 341 MET cc_start: 0.9282 (mpp) cc_final: 0.8717 (mpp) REVERT: A 437 MET cc_start: 0.8506 (mtm) cc_final: 0.8242 (mtt) REVERT: A 451 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8328 (p90) REVERT: A 456 MET cc_start: 0.8716 (mpp) cc_final: 0.8306 (mpp) REVERT: A 486 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: A 487 MET cc_start: 0.8941 (tpp) cc_final: 0.7777 (mmm) REVERT: A 605 MET cc_start: 0.8293 (tpp) cc_final: 0.7812 (tpp) REVERT: A 849 MET cc_start: 0.8953 (tmm) cc_final: 0.8521 (tmm) REVERT: A 1209 MET cc_start: 0.8831 (ppp) cc_final: 0.8556 (tmm) REVERT: A 1267 MET cc_start: 0.9253 (mmp) cc_final: 0.9027 (mmp) REVERT: A 1279 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8986 (mp) REVERT: A 1375 MET cc_start: 0.9445 (ttp) cc_final: 0.9015 (tmm) REVERT: A 1398 MET cc_start: 0.9236 (tmm) cc_final: 0.8777 (tmm) REVERT: A 1433 MET cc_start: 0.9225 (ppp) cc_final: 0.8487 (ppp) REVERT: A 1444 MET cc_start: 0.9008 (mmm) cc_final: 0.8696 (mmm) REVERT: B 101 MET cc_start: 0.8436 (tpt) cc_final: 0.8048 (tpp) REVERT: B 381 MET cc_start: 0.9488 (tmm) cc_final: 0.8646 (tmm) REVERT: B 526 GLU cc_start: 0.7587 (mt-10) cc_final: 0.6387 (mp0) REVERT: B 705 MET cc_start: 0.8980 (tpp) cc_final: 0.8693 (tpp) REVERT: B 860 MET cc_start: 0.8927 (ppp) cc_final: 0.8561 (ppp) REVERT: C 37 MET cc_start: 0.9367 (mtm) cc_final: 0.9108 (mtm) REVERT: C 75 MET cc_start: 0.9584 (tpt) cc_final: 0.9138 (tpp) REVERT: C 265 MET cc_start: 0.9110 (tpp) cc_final: 0.8482 (tmm) REVERT: E 22 MET cc_start: 0.9292 (ttm) cc_final: 0.8867 (ttp) REVERT: E 58 MET cc_start: 0.9239 (ptp) cc_final: 0.9013 (ptp) REVERT: F 70 LYS cc_start: 0.7127 (mppt) cc_final: 0.6324 (pttt) REVERT: F 85 MET cc_start: 0.8672 (tmm) cc_final: 0.8320 (tmm) REVERT: F 100 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.8874 (pp30) REVERT: F 103 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8322 (tmm) REVERT: F 111 LEU cc_start: 0.9761 (mp) cc_final: 0.9262 (tp) REVERT: F 122 MET cc_start: 0.9545 (mtp) cc_final: 0.9250 (mtp) REVERT: F 154 ASP cc_start: 0.7773 (t70) cc_final: 0.7570 (t0) REVERT: G 24 GLN cc_start: 0.9250 (mt0) cc_final: 0.8648 (mm110) REVERT: G 44 TYR cc_start: 0.8479 (t80) cc_final: 0.7860 (t80) REVERT: H 97 MET cc_start: 0.8748 (ppp) cc_final: 0.8546 (ppp) REVERT: H 123 MET cc_start: 0.9394 (ppp) cc_final: 0.9009 (ppp) REVERT: K 38 GLU cc_start: 0.9239 (mp0) cc_final: 0.8964 (mp0) REVERT: Q 31 PHE cc_start: 0.5085 (t80) cc_final: 0.4725 (t80) REVERT: Q 352 MET cc_start: 0.7525 (tmm) cc_final: 0.6960 (tmm) outliers start: 135 outliers final: 73 residues processed: 459 average time/residue: 0.6345 time to fit residues: 514.6739 Evaluate side-chains 415 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 332 time to evaluate : 6.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1382 THR Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1394 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain a residue 1433 MET Chi-restraints excluded: chain a residue 1438 THR Chi-restraints excluded: chain b residue 399 ASP Chi-restraints excluded: chain b residue 527 THR Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 989 THR Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1171 VAL Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain e residue 5 ASN Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 33 GLU Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain Q residue 96 ASN Chi-restraints excluded: chain Q residue 372 SER Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 228 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 776 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 458 optimal weight: 8.9990 chunk 587 optimal weight: 7.9990 chunk 455 optimal weight: 9.9990 chunk 677 optimal weight: 0.0040 chunk 449 optimal weight: 9.9990 chunk 801 optimal weight: 7.9990 chunk 501 optimal weight: 6.9990 chunk 488 optimal weight: 5.9990 chunk 370 optimal weight: 9.9990 overall best weight: 5.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 203 GLN ** d 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 HIS ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 70875 Z= 0.292 Angle : 0.698 14.320 96490 Z= 0.365 Chirality : 0.044 0.234 10869 Planarity : 0.004 0.068 11891 Dihedral : 16.048 179.946 11110 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.38 % Favored : 89.60 % Rotamer: Outliers : 2.05 % Allowed : 17.53 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.09), residues: 8171 helix: 0.97 (0.10), residues: 2723 sheet: -0.85 (0.15), residues: 1225 loop : -1.99 (0.09), residues: 4223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP b 31 HIS 0.011 0.001 HIS A 399 PHE 0.018 0.001 PHE C 20 TYR 0.023 0.001 TYR B 486 ARG 0.023 0.000 ARG h 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 341 time to evaluate : 6.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8240 (tpt) cc_final: 0.7873 (tpt) REVERT: a 234 MET cc_start: 0.9263 (tpt) cc_final: 0.8822 (mmm) REVERT: a 304 MET cc_start: 0.9428 (mmm) cc_final: 0.8953 (tpt) REVERT: a 340 LEU cc_start: 0.9569 (tp) cc_final: 0.9362 (tp) REVERT: a 512 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8623 (p) REVERT: a 550 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8393 (tp) REVERT: a 761 MET cc_start: 0.9656 (mmm) cc_final: 0.9122 (mmm) REVERT: a 1317 MET cc_start: 0.9076 (tmm) cc_final: 0.8710 (tmm) REVERT: a 1363 VAL cc_start: 0.9684 (OUTLIER) cc_final: 0.9447 (p) REVERT: a 1368 MET cc_start: 0.8919 (mpp) cc_final: 0.8533 (mpp) REVERT: a 1381 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9049 (pp) REVERT: a 1400 CYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8792 (p) REVERT: b 313 MET cc_start: 0.9620 (mmm) cc_final: 0.9266 (mmm) REVERT: b 778 MET cc_start: 0.7634 (pmm) cc_final: 0.7116 (pmm) REVERT: b 1021 MET cc_start: 0.8078 (mmt) cc_final: 0.7781 (mmt) REVERT: b 1098 MET cc_start: 0.8539 (mmp) cc_final: 0.7958 (mmp) REVERT: b 1138 MET cc_start: 0.9474 (mmp) cc_final: 0.9198 (mmp) REVERT: b 1152 MET cc_start: 0.8198 (tpp) cc_final: 0.7979 (tpt) REVERT: b 1169 MET cc_start: 0.7007 (mmm) cc_final: 0.6750 (mmm) REVERT: b 1208 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8368 (pmm) REVERT: b 1210 MET cc_start: 0.8947 (mmm) cc_final: 0.8601 (mmm) REVERT: e 22 MET cc_start: 0.9092 (tmm) cc_final: 0.8873 (tmm) REVERT: A 41 MET cc_start: 0.7449 (tpt) cc_final: 0.7027 (tpt) REVERT: A 108 MET cc_start: 0.9405 (pmm) cc_final: 0.8998 (pmm) REVERT: A 341 MET cc_start: 0.9325 (mpp) cc_final: 0.8805 (mpp) REVERT: A 437 MET cc_start: 0.8516 (mtm) cc_final: 0.8247 (mtt) REVERT: A 451 HIS cc_start: 0.9042 (OUTLIER) cc_final: 0.8622 (p90) REVERT: A 456 MET cc_start: 0.8701 (mpp) cc_final: 0.8285 (mpp) REVERT: A 486 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: A 605 MET cc_start: 0.8269 (tpp) cc_final: 0.7800 (tpp) REVERT: A 708 MET cc_start: 0.8495 (pmm) cc_final: 0.7827 (pmm) REVERT: A 849 MET cc_start: 0.8883 (tmm) cc_final: 0.8537 (tmm) REVERT: A 1111 MET cc_start: 0.8605 (mmm) cc_final: 0.7940 (tpp) REVERT: A 1209 MET cc_start: 0.8805 (ppp) cc_final: 0.8519 (tmm) REVERT: A 1267 MET cc_start: 0.9253 (mmp) cc_final: 0.9045 (mmp) REVERT: A 1279 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9022 (mp) REVERT: A 1375 MET cc_start: 0.9454 (ttp) cc_final: 0.9015 (tmm) REVERT: A 1398 MET cc_start: 0.9226 (tmm) cc_final: 0.8794 (tmm) REVERT: A 1400 CYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8988 (p) REVERT: A 1444 MET cc_start: 0.8962 (mmm) cc_final: 0.8669 (mmm) REVERT: B 101 MET cc_start: 0.8386 (tpt) cc_final: 0.8151 (tpp) REVERT: B 273 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7304 (pt) REVERT: B 381 MET cc_start: 0.9503 (tmm) cc_final: 0.8686 (tmm) REVERT: B 705 MET cc_start: 0.9038 (tpp) cc_final: 0.8733 (tpp) REVERT: B 860 MET cc_start: 0.8906 (ppp) cc_final: 0.8552 (ppp) REVERT: B 1100 ASP cc_start: 0.9116 (m-30) cc_final: 0.8656 (p0) REVERT: C 37 MET cc_start: 0.9388 (mtm) cc_final: 0.9129 (mtm) REVERT: C 75 MET cc_start: 0.9607 (tpt) cc_final: 0.9191 (tpp) REVERT: C 125 MET cc_start: 0.9493 (pmm) cc_final: 0.9256 (pmm) REVERT: C 134 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9234 (mm) REVERT: C 265 MET cc_start: 0.9137 (tpp) cc_final: 0.8490 (tmm) REVERT: E 22 MET cc_start: 0.9270 (ttm) cc_final: 0.8841 (ttm) REVERT: E 58 MET cc_start: 0.9254 (ptp) cc_final: 0.8887 (ptp) REVERT: F 70 LYS cc_start: 0.7147 (mppt) cc_final: 0.6342 (pttt) REVERT: F 81 THR cc_start: 0.9050 (OUTLIER) cc_final: 0.8611 (p) REVERT: F 85 MET cc_start: 0.8712 (tmm) cc_final: 0.8477 (tmm) REVERT: F 100 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8826 (pp30) REVERT: F 103 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8357 (tmm) REVERT: F 122 MET cc_start: 0.9558 (mtp) cc_final: 0.9293 (mtp) REVERT: F 154 ASP cc_start: 0.7969 (t70) cc_final: 0.7609 (t0) REVERT: G 24 GLN cc_start: 0.9243 (mt0) cc_final: 0.8659 (mm110) REVERT: G 44 TYR cc_start: 0.8505 (t80) cc_final: 0.7821 (t80) REVERT: G 51 TYR cc_start: 0.8264 (t80) cc_final: 0.7976 (m-80) REVERT: G 52 ASP cc_start: 0.9091 (t0) cc_final: 0.8600 (p0) REVERT: H 123 MET cc_start: 0.9395 (ppp) cc_final: 0.9024 (ppp) REVERT: Q 352 MET cc_start: 0.7580 (tmm) cc_final: 0.6967 (tmm) outliers start: 148 outliers final: 87 residues processed: 468 average time/residue: 0.6316 time to fit residues: 525.4078 Evaluate side-chains 437 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 335 time to evaluate : 6.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 550 LEU Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1381 LEU Chi-restraints excluded: chain a residue 1382 THR Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1394 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain a residue 1433 MET Chi-restraints excluded: chain b residue 399 ASP Chi-restraints excluded: chain b residue 522 VAL Chi-restraints excluded: chain b residue 527 THR Chi-restraints excluded: chain b residue 690 VAL Chi-restraints excluded: chain b residue 773 MET Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 854 LEU Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1171 VAL Chi-restraints excluded: chain b residue 1182 CYS Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 88 CYS Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 33 GLU Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain Q residue 96 ASN Chi-restraints excluded: chain Q residue 372 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 228 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 496 optimal weight: 20.0000 chunk 320 optimal weight: 7.9990 chunk 478 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 509 optimal weight: 9.9990 chunk 546 optimal weight: 3.9990 chunk 396 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 630 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 209 ASN ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 70875 Z= 0.281 Angle : 0.703 12.526 96490 Z= 0.366 Chirality : 0.044 0.236 10869 Planarity : 0.004 0.067 11891 Dihedral : 16.060 179.335 11110 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.11 % Favored : 89.87 % Rotamer: Outliers : 1.86 % Allowed : 17.99 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.09), residues: 8171 helix: 0.98 (0.10), residues: 2722 sheet: -0.84 (0.15), residues: 1227 loop : -1.99 (0.09), residues: 4222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP b 31 HIS 0.010 0.001 HIS A 399 PHE 0.018 0.001 PHE C 20 TYR 0.021 0.001 TYR B 486 ARG 0.020 0.000 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 341 time to evaluate : 6.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8274 (tpt) cc_final: 0.7857 (tpt) REVERT: a 304 MET cc_start: 0.9416 (mmm) cc_final: 0.8916 (tpt) REVERT: a 341 MET cc_start: 0.8915 (tpp) cc_final: 0.8260 (tpp) REVERT: a 512 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8594 (p) REVERT: a 605 MET cc_start: 0.7730 (tpp) cc_final: 0.7286 (mmp) REVERT: a 761 MET cc_start: 0.9662 (mmm) cc_final: 0.9117 (mmm) REVERT: a 1317 MET cc_start: 0.9072 (tmm) cc_final: 0.8694 (tmm) REVERT: a 1363 VAL cc_start: 0.9685 (OUTLIER) cc_final: 0.9449 (p) REVERT: a 1368 MET cc_start: 0.8927 (mpp) cc_final: 0.8534 (mpp) REVERT: a 1381 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9050 (pp) REVERT: a 1400 CYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8780 (p) REVERT: b 313 MET cc_start: 0.9626 (mmm) cc_final: 0.9262 (mmm) REVERT: b 705 MET cc_start: 0.7420 (tmm) cc_final: 0.7119 (tpp) REVERT: b 778 MET cc_start: 0.7668 (pmm) cc_final: 0.7137 (pmm) REVERT: b 1021 MET cc_start: 0.8096 (mmt) cc_final: 0.7781 (mmt) REVERT: b 1098 MET cc_start: 0.8518 (mmp) cc_final: 0.7921 (mmp) REVERT: b 1111 MET cc_start: 0.9118 (tpp) cc_final: 0.8788 (tpp) REVERT: b 1138 MET cc_start: 0.9484 (mmp) cc_final: 0.9245 (mmp) REVERT: b 1208 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8337 (pmm) REVERT: b 1210 MET cc_start: 0.8950 (mmm) cc_final: 0.8587 (mmm) REVERT: e 22 MET cc_start: 0.9097 (tmm) cc_final: 0.8877 (tmm) REVERT: h 97 MET cc_start: 0.8556 (tmm) cc_final: 0.8307 (tmm) REVERT: A 108 MET cc_start: 0.9399 (pmm) cc_final: 0.8998 (pmm) REVERT: A 304 MET cc_start: 0.9291 (tpt) cc_final: 0.9057 (tpt) REVERT: A 341 MET cc_start: 0.9330 (mpp) cc_final: 0.8956 (mpp) REVERT: A 437 MET cc_start: 0.8561 (mtm) cc_final: 0.8272 (mtt) REVERT: A 451 HIS cc_start: 0.9030 (OUTLIER) cc_final: 0.8258 (p90) REVERT: A 456 MET cc_start: 0.8713 (mpp) cc_final: 0.8287 (mpp) REVERT: A 486 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: A 605 MET cc_start: 0.8258 (tpp) cc_final: 0.7787 (tpp) REVERT: A 708 MET cc_start: 0.8435 (pmm) cc_final: 0.7802 (pmm) REVERT: A 849 MET cc_start: 0.8924 (tmm) cc_final: 0.8586 (tmm) REVERT: A 1111 MET cc_start: 0.8585 (mmm) cc_final: 0.7785 (tpp) REVERT: A 1209 MET cc_start: 0.8798 (ppp) cc_final: 0.8499 (tmm) REVERT: A 1267 MET cc_start: 0.9247 (mmp) cc_final: 0.9036 (mmp) REVERT: A 1279 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.9024 (mp) REVERT: A 1336 MET cc_start: 0.9592 (tmm) cc_final: 0.9305 (tmm) REVERT: A 1375 MET cc_start: 0.9454 (ttp) cc_final: 0.8995 (tmm) REVERT: A 1398 MET cc_start: 0.9249 (tmm) cc_final: 0.8800 (tmm) REVERT: A 1400 CYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8969 (p) REVERT: A 1433 MET cc_start: 0.9207 (ppp) cc_final: 0.8829 (ppp) REVERT: A 1444 MET cc_start: 0.8941 (mmm) cc_final: 0.8639 (mmm) REVERT: B 101 MET cc_start: 0.8385 (tpt) cc_final: 0.8151 (tpp) REVERT: B 273 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7308 (pt) REVERT: B 381 MET cc_start: 0.9514 (tmm) cc_final: 0.8665 (tmm) REVERT: B 526 GLU cc_start: 0.7727 (mt-10) cc_final: 0.6442 (mp0) REVERT: B 705 MET cc_start: 0.9049 (tpp) cc_final: 0.8729 (tpp) REVERT: B 792 MET cc_start: 0.8561 (mmm) cc_final: 0.8284 (mmm) REVERT: B 860 MET cc_start: 0.8910 (ppp) cc_final: 0.8599 (ppp) REVERT: B 1100 ASP cc_start: 0.9142 (m-30) cc_final: 0.8642 (p0) REVERT: C 37 MET cc_start: 0.9380 (mtm) cc_final: 0.9122 (mtm) REVERT: C 75 MET cc_start: 0.9614 (tpt) cc_final: 0.9208 (tpp) REVERT: C 125 MET cc_start: 0.9469 (pmm) cc_final: 0.9251 (pmm) REVERT: C 134 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9253 (mm) REVERT: C 265 MET cc_start: 0.9144 (tpp) cc_final: 0.8486 (tmm) REVERT: E 22 MET cc_start: 0.9280 (ttm) cc_final: 0.8835 (ttm) REVERT: E 58 MET cc_start: 0.9237 (ptp) cc_final: 0.8876 (ptp) REVERT: F 70 LYS cc_start: 0.7104 (mppt) cc_final: 0.6276 (pttt) REVERT: F 81 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8611 (p) REVERT: F 85 MET cc_start: 0.8697 (tmm) cc_final: 0.8452 (tmm) REVERT: F 100 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.8839 (pp30) REVERT: F 103 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8347 (tmm) REVERT: F 122 MET cc_start: 0.9557 (mtp) cc_final: 0.9286 (mtp) REVERT: F 154 ASP cc_start: 0.7963 (t70) cc_final: 0.7601 (t0) REVERT: G 44 TYR cc_start: 0.8497 (t80) cc_final: 0.7786 (t80) REVERT: G 51 TYR cc_start: 0.8311 (t80) cc_final: 0.7964 (m-80) REVERT: G 52 ASP cc_start: 0.9094 (t0) cc_final: 0.8861 (t0) REVERT: H 123 MET cc_start: 0.9375 (ppp) cc_final: 0.8996 (ppp) REVERT: I 51 ASN cc_start: 0.7488 (t0) cc_final: 0.7278 (t0) REVERT: J 1 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8091 (mtt) REVERT: Q 31 PHE cc_start: 0.4872 (t80) cc_final: 0.4447 (t80) REVERT: Q 352 MET cc_start: 0.7575 (tmm) cc_final: 0.6944 (tmm) REVERT: Q 385 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8508 (p) outliers start: 134 outliers final: 94 residues processed: 453 average time/residue: 0.6824 time to fit residues: 548.2551 Evaluate side-chains 447 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 337 time to evaluate : 6.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 981 LEU Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1381 LEU Chi-restraints excluded: chain a residue 1382 THR Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1394 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain a residue 1433 MET Chi-restraints excluded: chain a residue 1438 THR Chi-restraints excluded: chain b residue 399 ASP Chi-restraints excluded: chain b residue 522 VAL Chi-restraints excluded: chain b residue 527 THR Chi-restraints excluded: chain b residue 690 VAL Chi-restraints excluded: chain b residue 773 MET Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 854 LEU Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1171 VAL Chi-restraints excluded: chain b residue 1182 CYS Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 88 CYS Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 33 GLU Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 451 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain Q residue 96 ASN Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain Q residue 413 MET Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 228 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 729 optimal weight: 1.9990 chunk 768 optimal weight: 20.0000 chunk 700 optimal weight: 50.0000 chunk 747 optimal weight: 3.9990 chunk 449 optimal weight: 9.9990 chunk 325 optimal weight: 7.9990 chunk 586 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 675 optimal weight: 5.9990 chunk 706 optimal weight: 7.9990 chunk 744 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 415 GLN ** b 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 70875 Z= 0.276 Angle : 0.711 12.754 96490 Z= 0.367 Chirality : 0.043 0.235 10869 Planarity : 0.004 0.066 11891 Dihedral : 16.060 178.681 11110 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.38 % Favored : 89.60 % Rotamer: Outliers : 1.85 % Allowed : 18.33 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.09), residues: 8171 helix: 0.95 (0.10), residues: 2733 sheet: -0.83 (0.15), residues: 1239 loop : -1.98 (0.09), residues: 4199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP b 31 HIS 0.009 0.001 HIS A 399 PHE 0.018 0.001 PHE c 20 TYR 0.021 0.001 TYR b 833 ARG 0.019 0.000 ARG h 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 342 time to evaluate : 6.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8274 (tpt) cc_final: 0.7847 (tpt) REVERT: a 261 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7693 (t70) REVERT: a 304 MET cc_start: 0.9417 (mmm) cc_final: 0.8850 (tpt) REVERT: a 341 MET cc_start: 0.8858 (tpp) cc_final: 0.8179 (tpp) REVERT: a 512 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8587 (p) REVERT: a 605 MET cc_start: 0.7719 (tpp) cc_final: 0.7446 (tpp) REVERT: a 761 MET cc_start: 0.9665 (mmm) cc_final: 0.9111 (mmm) REVERT: a 1317 MET cc_start: 0.9068 (tmm) cc_final: 0.8681 (tmm) REVERT: a 1363 VAL cc_start: 0.9686 (OUTLIER) cc_final: 0.9447 (p) REVERT: a 1368 MET cc_start: 0.8922 (mpp) cc_final: 0.8529 (mpp) REVERT: a 1381 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9054 (pp) REVERT: a 1400 CYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8771 (p) REVERT: b 173 MET cc_start: 0.7018 (tmm) cc_final: 0.6606 (tmm) REVERT: b 174 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8315 (mt) REVERT: b 313 MET cc_start: 0.9620 (mmm) cc_final: 0.9247 (mmm) REVERT: b 705 MET cc_start: 0.7372 (tmm) cc_final: 0.7099 (tpp) REVERT: b 778 MET cc_start: 0.7681 (pmm) cc_final: 0.7143 (pmm) REVERT: b 1021 MET cc_start: 0.8103 (mmt) cc_final: 0.7781 (mmt) REVERT: b 1098 MET cc_start: 0.8476 (mmp) cc_final: 0.7868 (mmp) REVERT: b 1111 MET cc_start: 0.9129 (tpp) cc_final: 0.8769 (tpp) REVERT: b 1138 MET cc_start: 0.9470 (mmp) cc_final: 0.9237 (mmp) REVERT: b 1169 MET cc_start: 0.7795 (mmm) cc_final: 0.7490 (mmm) REVERT: b 1208 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8330 (pmm) REVERT: b 1210 MET cc_start: 0.8949 (mmm) cc_final: 0.8563 (mmm) REVERT: e 22 MET cc_start: 0.9103 (tmm) cc_final: 0.8875 (tmm) REVERT: h 97 MET cc_start: 0.8573 (tmm) cc_final: 0.8323 (tmm) REVERT: A 41 MET cc_start: 0.6314 (tpp) cc_final: 0.6035 (tpp) REVERT: A 108 MET cc_start: 0.9391 (pmm) cc_final: 0.8942 (pmm) REVERT: A 341 MET cc_start: 0.9340 (mpp) cc_final: 0.8915 (mpp) REVERT: A 437 MET cc_start: 0.8545 (mtm) cc_final: 0.8270 (mtt) REVERT: A 456 MET cc_start: 0.8683 (mpp) cc_final: 0.8273 (mpp) REVERT: A 486 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: A 605 MET cc_start: 0.8224 (tpp) cc_final: 0.7713 (tpp) REVERT: A 708 MET cc_start: 0.8363 (pmm) cc_final: 0.7950 (pmm) REVERT: A 849 MET cc_start: 0.8902 (tmm) cc_final: 0.8557 (tmm) REVERT: A 1111 MET cc_start: 0.8604 (mmm) cc_final: 0.7679 (tpp) REVERT: A 1209 MET cc_start: 0.8794 (ppp) cc_final: 0.8497 (tmm) REVERT: A 1267 MET cc_start: 0.9241 (mmp) cc_final: 0.9034 (mmp) REVERT: A 1279 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9030 (mp) REVERT: A 1336 MET cc_start: 0.9569 (tmm) cc_final: 0.9325 (tmm) REVERT: A 1375 MET cc_start: 0.9453 (ttp) cc_final: 0.8975 (tmm) REVERT: A 1398 MET cc_start: 0.9268 (tmm) cc_final: 0.8815 (tmm) REVERT: A 1400 CYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8980 (p) REVERT: A 1433 MET cc_start: 0.9263 (ppp) cc_final: 0.8895 (ppp) REVERT: A 1444 MET cc_start: 0.8972 (mmm) cc_final: 0.8679 (mmm) REVERT: B 101 MET cc_start: 0.8394 (tpt) cc_final: 0.8164 (tpp) REVERT: B 273 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7410 (pt) REVERT: B 276 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7763 (mt) REVERT: B 381 MET cc_start: 0.9460 (tmm) cc_final: 0.8674 (tmm) REVERT: B 526 GLU cc_start: 0.7621 (mt-10) cc_final: 0.6390 (mp0) REVERT: B 705 MET cc_start: 0.9048 (tpp) cc_final: 0.8708 (tpp) REVERT: B 792 MET cc_start: 0.8451 (mmm) cc_final: 0.8241 (mmm) REVERT: B 860 MET cc_start: 0.8930 (ppp) cc_final: 0.8611 (ppp) REVERT: B 1100 ASP cc_start: 0.9193 (m-30) cc_final: 0.8640 (p0) REVERT: C 37 MET cc_start: 0.9375 (mtm) cc_final: 0.9118 (mtm) REVERT: C 75 MET cc_start: 0.9615 (tpt) cc_final: 0.9208 (tpp) REVERT: C 125 MET cc_start: 0.9480 (pmm) cc_final: 0.9258 (pmm) REVERT: C 134 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9264 (mm) REVERT: C 265 MET cc_start: 0.9148 (tpp) cc_final: 0.8487 (tmm) REVERT: E 22 MET cc_start: 0.9279 (ttm) cc_final: 0.8833 (ttp) REVERT: E 58 MET cc_start: 0.9260 (ptp) cc_final: 0.9019 (ptp) REVERT: F 70 LYS cc_start: 0.7091 (mppt) cc_final: 0.6292 (pttt) REVERT: F 81 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8610 (p) REVERT: F 85 MET cc_start: 0.8702 (tmm) cc_final: 0.8471 (tmm) REVERT: F 100 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.8815 (pp30) REVERT: F 103 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8380 (tmm) REVERT: F 154 ASP cc_start: 0.7950 (t70) cc_final: 0.7603 (t0) REVERT: G 44 TYR cc_start: 0.8502 (t80) cc_final: 0.7830 (t80) REVERT: G 51 TYR cc_start: 0.8310 (t80) cc_final: 0.7983 (m-80) REVERT: G 52 ASP cc_start: 0.9089 (t0) cc_final: 0.8829 (t0) REVERT: H 123 MET cc_start: 0.9378 (ppp) cc_final: 0.8999 (ppp) REVERT: J 1 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8103 (mtt) REVERT: Q 352 MET cc_start: 0.7560 (tmm) cc_final: 0.6974 (tmm) REVERT: Q 385 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8449 (p) outliers start: 133 outliers final: 101 residues processed: 453 average time/residue: 0.6434 time to fit residues: 516.3774 Evaluate side-chains 459 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 340 time to evaluate : 6.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 261 ASP Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 584 ASN Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 981 LEU Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1381 LEU Chi-restraints excluded: chain a residue 1382 THR Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1394 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain a residue 1433 MET Chi-restraints excluded: chain a residue 1438 THR Chi-restraints excluded: chain b residue 174 LEU Chi-restraints excluded: chain b residue 399 ASP Chi-restraints excluded: chain b residue 522 VAL Chi-restraints excluded: chain b residue 527 THR Chi-restraints excluded: chain b residue 690 VAL Chi-restraints excluded: chain b residue 773 MET Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 854 LEU Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1171 VAL Chi-restraints excluded: chain b residue 1182 CYS Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 88 CYS Chi-restraints excluded: chain e residue 5 ASN Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 33 GLU Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 63 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1370 LEU Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 809 MET Chi-restraints excluded: chain B residue 1062 HIS Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain Q residue 96 ASN Chi-restraints excluded: chain Q residue 372 SER Chi-restraints excluded: chain Q residue 385 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 224 VAL Chi-restraints excluded: chain M residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 490 optimal weight: 3.9990 chunk 790 optimal weight: 0.8980 chunk 482 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 chunk 549 optimal weight: 1.9990 chunk 828 optimal weight: 9.9990 chunk 762 optimal weight: 2.9990 chunk 660 optimal weight: 0.0770 chunk 68 optimal weight: 0.9980 chunk 509 optimal weight: 4.9990 chunk 404 optimal weight: 20.0000 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1432 GLN b 587 HIS ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 5 ASN ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS ** A 587 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 70875 Z= 0.184 Angle : 0.704 12.692 96490 Z= 0.361 Chirality : 0.043 0.233 10869 Planarity : 0.004 0.065 11891 Dihedral : 16.031 178.154 11110 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.52 % Favored : 90.45 % Rotamer: Outliers : 1.64 % Allowed : 18.69 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.84 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.09), residues: 8171 helix: 0.98 (0.10), residues: 2723 sheet: -0.77 (0.15), residues: 1205 loop : -1.93 (0.09), residues: 4243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP b 31 HIS 0.008 0.001 HIS G 113 PHE 0.032 0.001 PHE k 10 TYR 0.026 0.001 TYR B 486 ARG 0.017 0.000 ARG h 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16342 Ramachandran restraints generated. 8171 Oldfield, 0 Emsley, 8171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 346 time to evaluate : 6.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 41 MET cc_start: 0.8253 (tpt) cc_final: 0.7766 (tpt) REVERT: a 261 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7566 (t70) REVERT: a 304 MET cc_start: 0.9403 (mmm) cc_final: 0.8885 (tpt) REVERT: a 340 LEU cc_start: 0.9573 (tp) cc_final: 0.9357 (tp) REVERT: a 456 MET cc_start: 0.8980 (mpp) cc_final: 0.8069 (mpp) REVERT: a 512 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8542 (p) REVERT: a 605 MET cc_start: 0.7713 (tpp) cc_final: 0.7426 (tpp) REVERT: a 761 MET cc_start: 0.9685 (mmm) cc_final: 0.9072 (mmp) REVERT: a 1317 MET cc_start: 0.9029 (tmm) cc_final: 0.8635 (tmm) REVERT: a 1363 VAL cc_start: 0.9676 (OUTLIER) cc_final: 0.9434 (p) REVERT: a 1368 MET cc_start: 0.8902 (mpp) cc_final: 0.8491 (mpp) REVERT: a 1381 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9039 (pp) REVERT: a 1400 CYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8741 (p) REVERT: b 173 MET cc_start: 0.6883 (tmm) cc_final: 0.6509 (tmm) REVERT: b 174 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8285 (mt) REVERT: b 313 MET cc_start: 0.9625 (mmm) cc_final: 0.9248 (mmm) REVERT: b 705 MET cc_start: 0.7394 (tmm) cc_final: 0.7103 (tpp) REVERT: b 778 MET cc_start: 0.7654 (pmm) cc_final: 0.6734 (pmm) REVERT: b 1021 MET cc_start: 0.8062 (mmt) cc_final: 0.7489 (mmt) REVERT: b 1098 MET cc_start: 0.8468 (mmp) cc_final: 0.7864 (mmp) REVERT: b 1111 MET cc_start: 0.9152 (tpp) cc_final: 0.8745 (tpp) REVERT: b 1138 MET cc_start: 0.9409 (mmp) cc_final: 0.9152 (mmp) REVERT: b 1152 MET cc_start: 0.8207 (tpp) cc_final: 0.7937 (mmm) REVERT: b 1169 MET cc_start: 0.7778 (mmm) cc_final: 0.7444 (mmm) REVERT: b 1208 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8283 (pmm) REVERT: b 1210 MET cc_start: 0.8928 (mmm) cc_final: 0.8538 (mmm) REVERT: e 22 MET cc_start: 0.9101 (tmm) cc_final: 0.8868 (tmm) REVERT: h 97 MET cc_start: 0.8544 (tmm) cc_final: 0.8283 (tmm) REVERT: j 1 MET cc_start: 0.6932 (mmm) cc_final: 0.6565 (mmm) REVERT: A 41 MET cc_start: 0.6466 (tpp) cc_final: 0.6197 (tpp) REVERT: A 108 MET cc_start: 0.9389 (pmm) cc_final: 0.8978 (pmm) REVERT: A 146 MET cc_start: 0.9125 (mmm) cc_final: 0.8707 (mmm) REVERT: A 341 MET cc_start: 0.9339 (mpp) cc_final: 0.8862 (mpp) REVERT: A 437 MET cc_start: 0.8535 (mtm) cc_final: 0.8317 (mtt) REVERT: A 456 MET cc_start: 0.8672 (mpp) cc_final: 0.8260 (mpp) REVERT: A 486 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: A 605 MET cc_start: 0.8191 (tpp) cc_final: 0.7733 (tpp) REVERT: A 708 MET cc_start: 0.8387 (pmm) cc_final: 0.7815 (pmm) REVERT: A 849 MET cc_start: 0.8860 (tmm) cc_final: 0.8548 (tmm) REVERT: A 1111 MET cc_start: 0.8617 (mmm) cc_final: 0.7613 (tpp) REVERT: A 1209 MET cc_start: 0.8780 (ppp) cc_final: 0.8468 (tmm) REVERT: A 1267 MET cc_start: 0.9223 (mmp) cc_final: 0.9017 (mmp) REVERT: A 1279 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9055 (mp) REVERT: A 1336 MET cc_start: 0.9555 (tmm) cc_final: 0.9306 (tmm) REVERT: A 1375 MET cc_start: 0.9440 (ttp) cc_final: 0.8951 (tmm) REVERT: A 1398 MET cc_start: 0.9250 (tmm) cc_final: 0.8807 (tmm) REVERT: A 1400 CYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8930 (p) REVERT: A 1433 MET cc_start: 0.9270 (ppp) cc_final: 0.8915 (ppp) REVERT: A 1444 MET cc_start: 0.8935 (mmm) cc_final: 0.8652 (mmm) REVERT: B 101 MET cc_start: 0.8392 (tpt) cc_final: 0.8139 (tpp) REVERT: B 273 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7334 (pt) REVERT: B 381 MET cc_start: 0.9447 (tmm) cc_final: 0.8647 (tmm) REVERT: B 526 GLU cc_start: 0.7593 (mt-10) cc_final: 0.6378 (mp0) REVERT: B 705 MET cc_start: 0.9006 (tpp) cc_final: 0.8698 (tpp) REVERT: B 792 MET cc_start: 0.8460 (mmm) cc_final: 0.8215 (mmm) REVERT: B 860 MET cc_start: 0.8932 (ppp) cc_final: 0.8604 (ppp) REVERT: B 1100 ASP cc_start: 0.9156 (m-30) cc_final: 0.8591 (p0) REVERT: C 37 MET cc_start: 0.9351 (mtm) cc_final: 0.9090 (mtm) REVERT: C 75 MET cc_start: 0.9605 (tpt) cc_final: 0.9195 (tpp) REVERT: C 125 MET cc_start: 0.9473 (pmm) cc_final: 0.9251 (pmm) REVERT: C 134 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9228 (mm) REVERT: C 265 MET cc_start: 0.9142 (tpp) cc_final: 0.8476 (tmm) REVERT: E 22 MET cc_start: 0.9263 (ttm) cc_final: 0.8816 (ttm) REVERT: E 58 MET cc_start: 0.9256 (ptp) cc_final: 0.9005 (ptp) REVERT: F 70 LYS cc_start: 0.7142 (mppt) cc_final: 0.6344 (pttt) REVERT: F 100 GLN cc_start: 0.9381 (OUTLIER) cc_final: 0.8912 (pp30) REVERT: F 103 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8391 (tmm) REVERT: F 110 ASP cc_start: 0.9293 (p0) cc_final: 0.9044 (p0) REVERT: G 44 TYR cc_start: 0.8472 (t80) cc_final: 0.7732 (t80) REVERT: G 51 TYR cc_start: 0.8344 (t80) cc_final: 0.8013 (m-80) REVERT: G 52 ASP cc_start: 0.9088 (t0) cc_final: 0.8863 (t0) REVERT: H 97 MET cc_start: 0.8302 (ppp) cc_final: 0.8027 (ppp) REVERT: H 123 MET cc_start: 0.9390 (ppp) cc_final: 0.9014 (ppp) REVERT: Q 352 MET cc_start: 0.7537 (tmm) cc_final: 0.6954 (tmm) outliers start: 118 outliers final: 86 residues processed: 447 average time/residue: 0.6502 time to fit residues: 516.3107 Evaluate side-chains 437 residues out of total 7299 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 337 time to evaluate : 6.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 261 ASP Chi-restraints excluded: chain a residue 460 VAL Chi-restraints excluded: chain a residue 491 VAL Chi-restraints excluded: chain a residue 512 VAL Chi-restraints excluded: chain a residue 584 ASN Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 1098 VAL Chi-restraints excluded: chain a residue 1107 VAL Chi-restraints excluded: chain a residue 1212 VAL Chi-restraints excluded: chain a residue 1327 ILE Chi-restraints excluded: chain a residue 1333 ILE Chi-restraints excluded: chain a residue 1363 VAL Chi-restraints excluded: chain a residue 1381 LEU Chi-restraints excluded: chain a residue 1382 THR Chi-restraints excluded: chain a residue 1385 THR Chi-restraints excluded: chain a residue 1394 THR Chi-restraints excluded: chain a residue 1400 CYS Chi-restraints excluded: chain a residue 1424 VAL Chi-restraints excluded: chain a residue 1433 MET Chi-restraints excluded: chain a residue 1438 THR Chi-restraints excluded: chain b residue 174 LEU Chi-restraints excluded: chain b residue 399 ASP Chi-restraints excluded: chain b residue 527 THR Chi-restraints excluded: chain b residue 690 VAL Chi-restraints excluded: chain b residue 809 MET Chi-restraints excluded: chain b residue 854 LEU Chi-restraints excluded: chain b residue 870 ILE Chi-restraints excluded: chain b residue 1163 CYS Chi-restraints excluded: chain b residue 1171 VAL Chi-restraints excluded: chain b residue 1182 CYS Chi-restraints excluded: chain b residue 1203 LEU Chi-restraints excluded: chain b residue 1205 GLN Chi-restraints excluded: chain b residue 1206 GLU Chi-restraints excluded: chain b residue 1208 MET Chi-restraints excluded: chain c residue 41 ILE Chi-restraints excluded: chain c residue 88 CYS Chi-restraints excluded: chain e residue 35 VAL Chi-restraints excluded: chain f residue 82 THR Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain g residue 33 GLU Chi-restraints excluded: chain h residue 129 TYR Chi-restraints excluded: chain i residue 7 CYS Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 106 GLU Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 189 ARG Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1107 VAL Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1243 VAL Chi-restraints excluded: chain A residue 1279 ILE Chi-restraints excluded: chain A residue 1318 THR Chi-restraints excluded: chain A residue 1370 LEU Chi-restraints excluded: chain A residue 1385 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1400 CYS Chi-restraints excluded: chain A residue 1450 LEU Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 210 LYS Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 1062 HIS Chi-restraints excluded: chain B residue 1082 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 102 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain L residue 31 CYS Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 51 CYS Chi-restraints excluded: chain Q residue 96 ASN Chi-restraints excluded: chain Q residue 372 SER Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 228 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 832 random chunks: chunk 524 optimal weight: 20.0000 chunk 703 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 608 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 661 optimal weight: 5.9990 chunk 276 optimal weight: 6.9990 chunk 678 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 HIS ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.046981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.032256 restraints weight = 573175.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.033313 restraints weight = 298646.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.034043 restraints weight = 197509.768| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 70875 Z= 0.189 Angle : 0.694 14.851 96490 Z= 0.355 Chirality : 0.043 0.234 10869 Planarity : 0.004 0.062 11891 Dihedral : 15.945 177.808 11110 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.35 % Favored : 90.63 % Rotamer: Outliers : 1.61 % Allowed : 18.80 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.52 % Cis-general : 0.38 % Twisted Proline : 0.56 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.09), residues: 8171 helix: 1.00 (0.10), residues: 2745 sheet: -0.67 (0.15), residues: 1186 loop : -1.88 (0.09), residues: 4240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP b 31 HIS 0.006 0.001 HIS G 113 PHE 0.018 0.001 PHE c 20 TYR 0.020 0.001 TYR G 51 ARG 0.017 0.000 ARG h 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12852.89 seconds wall clock time: 226 minutes 54.13 seconds (13614.13 seconds total)