Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 26 00:23:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyl_0091/08_2023/6gyl_0091_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyl_0091/08_2023/6gyl_0091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyl_0091/08_2023/6gyl_0091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyl_0091/08_2023/6gyl_0091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyl_0091/08_2023/6gyl_0091_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyl_0091/08_2023/6gyl_0091_neut.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 112 5.49 5 Mg 1 5.21 5 S 230 5.16 5 C 27071 2.51 5 N 7588 2.21 5 O 8397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 123": "NH1" <-> "NH2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 812": "OE1" <-> "OE2" Residue "A GLU 1264": "OE1" <-> "OE2" Residue "A GLU 1280": "OE1" <-> "OE2" Residue "A GLU 1351": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B GLU 836": "OE1" <-> "OE2" Residue "B ARG 884": "NH1" <-> "NH2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 130": "NH1" <-> "NH2" Residue "I ARG 30": "NH1" <-> "NH2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "M ARG 215": "NH1" <-> "NH2" Residue "M ARG 320": "NH1" <-> "NH2" Residue "O ARG 79": "NH1" <-> "NH2" Residue "Q ARG 343": "NH1" <-> "NH2" Residue "Q ARG 398": "NH1" <-> "NH2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R ARG 251": "NH1" <-> "NH2" Residue "R ARG 271": "NH1" <-> "NH2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W ARG 65": "NH1" <-> "NH2" Residue "W ARG 108": "NH1" <-> "NH2" Residue "W ARG 144": "NH1" <-> "NH2" Residue "W ARG 174": "NH1" <-> "NH2" Residue "W ARG 193": "NH1" <-> "NH2" Residue "X ARG 197": "NH1" <-> "NH2" Residue "X ARG 276": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 43409 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 10997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1398, 10997 Classifications: {'peptide': 1398} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1333} Chain breaks: 5 Chain: "B" Number of atoms: 9178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9178 Classifications: {'peptide': 1152} Link IDs: {'PTRANS': 51, 'TRANS': 1100} Chain breaks: 7 Chain: "C" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2061 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 11, 'TRANS': 250} Chain: "D" Number of atoms: 1253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1253 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Chain breaks: 1 Chain: "E" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1744 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "F" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 670 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 1 Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 904 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2175 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 10, 'TRANS': 268} Chain breaks: 2 Chain: "N" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1129 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "O" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "Q" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1144 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 141} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1303 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 7, 'TRANS': 182} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 158 Chain: "T" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1149 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "U" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 757 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'TRANS': 91} Chain breaks: 1 Chain: "V" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 782 Classifications: {'peptide': 100} Link IDs: {'TRANS': 99} Chain breaks: 1 Chain: "W" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1469 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 8, 'TRANS': 182} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 58 Chain: "X" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1004 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 7, 'TRANS': 152} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 158 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 813 SG CYS A 107 90.335 128.252 128.144 1.00 0.00 S ATOM 837 SG CYS A 110 89.016 130.128 130.771 1.00 0.00 S ATOM 1142 SG CYS A 148 92.758 131.261 130.115 1.00 0.00 S ATOM 1211 SG CYS A 167 92.131 127.640 130.961 1.00 0.00 S ATOM 508 SG CYS A 67 49.090 121.848 103.505 1.00 0.00 S ATOM 530 SG CYS A 70 48.979 125.959 105.444 1.00 0.00 S ATOM 583 SG CYS A 77 50.583 124.457 101.901 1.00 0.00 S ATOM 19693 SG CYS B1163 53.771 136.633 114.926 1.00 0.00 S ATOM 19711 SG CYS B1166 57.635 134.486 114.489 1.00 0.00 S ATOM 19836 SG CYS B1182 54.251 132.763 113.861 1.00 0.00 S ATOM 19855 SG CYS B1185 54.921 134.164 116.994 1.00 0.00 S ATOM 20822 SG CYS C 86 23.864 128.122 40.062 1.00 0.00 S ATOM 20839 SG CYS C 88 24.580 125.308 42.115 1.00 0.00 S ATOM 20872 SG CYS C 92 24.456 125.123 38.621 1.00 0.00 S ATOM 20895 SG CYS C 95 27.578 126.406 39.453 1.00 0.00 S ATOM 28385 SG CYS I 7 143.345 110.639 85.304 1.00 0.00 S ATOM 28410 SG CYS I 10 141.267 107.799 87.542 1.00 0.00 S ATOM 28576 SG CYS I 29 141.130 111.997 87.933 1.00 0.00 S ATOM 28600 SG CYS I 32 143.874 109.861 88.665 1.00 0.00 S ATOM 28927 SG CYS I 75 134.628 130.777 45.585 1.00 0.00 S ATOM 28949 SG CYS I 78 135.146 128.000 42.825 1.00 0.00 S ATOM 29165 SG CYS I 103 132.166 127.298 44.291 1.00 0.00 S ATOM 29185 SG CYS I 106 135.744 126.804 46.204 1.00 0.00 S ATOM 29330 SG CYS J 7 59.178 129.901 32.220 1.00 0.00 S ATOM 29353 SG CYS J 10 57.669 132.031 29.929 1.00 0.00 S ATOM 29633 SG CYS J 45 60.981 133.567 30.316 1.00 0.00 S ATOM 29639 SG CYS J 46 59.816 130.465 28.489 1.00 0.00 S ATOM 30762 SG CYS L 31 54.372 90.589 53.582 1.00 0.00 S ATOM 30782 SG CYS L 34 53.510 88.753 50.615 1.00 0.00 S ATOM 30886 SG CYS L 48 52.642 88.314 54.892 1.00 0.00 S ATOM 30909 SG CYS L 51 55.898 87.634 53.758 1.00 0.00 S ATOM 31137 SG CYS M 24 28.773 126.975 87.662 1.00 0.00 S ATOM 31159 SG CYS M 27 26.541 126.178 85.730 1.00 0.00 S ATOM 31303 SG CYS M 45 29.463 124.143 84.323 1.00 0.00 S ATOM 31322 SG CYS M 48 28.298 128.317 84.550 1.00 0.00 S ATOM 41826 SG CYS W 124 35.061 114.115 116.841 1.00 0.00 S ATOM 41847 SG CYS W 127 37.745 114.885 114.702 1.00 0.00 S ATOM 42032 SG CYS W 149 35.318 117.715 115.408 1.00 0.00 S ATOM 42052 SG CYS W 152 34.656 114.547 112.818 1.00 0.00 S Residues with excluded nonbonded symmetry interactions: 92 residue: pdb=" P DT N 5 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT N 5 " occ=0.00 residue: pdb=" P DG N 6 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 6 " occ=0.00 residue: pdb=" P DC N 7 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 7 " occ=0.00 residue: pdb=" P DC N 8 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 8 " occ=0.00 residue: pdb=" P DC N 9 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 9 " occ=0.00 residue: pdb=" P DG N 10 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 10 " occ=0.00 residue: pdb=" P DG N 11 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 11 " occ=0.00 residue: pdb=" P DC N 12 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 12 " occ=0.00 residue: pdb=" P DC N 13 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 13 " occ=0.00 residue: pdb=" P DC N 14 " occ=0.00 ... (17 atoms not shown) pdb=" C6 DC N 14 " occ=0.00 residue: pdb=" P DA N 15 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA N 15 " occ=0.00 residue: pdb=" P DG N 16 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG N 16 " occ=0.00 ... (remaining 80 not shown) Time building chain proxies: 20.92, per 1000 atoms: 0.48 Number of scatterers: 43409 At special positions: 0 Unit cell: (165.9, 220.5, 168, 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 10 29.99 S 230 16.00 P 112 15.00 Mg 1 11.99 O 8397 8.00 N 7588 7.00 C 27071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 38901 O4' DA T 58 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.05 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " 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 ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " 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 103 " 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 J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " 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 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 48 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 45 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 24 " pdb=" ZN W 601 " pdb="ZN ZN W 601 " - pdb=" SG CYS W 124 " pdb="ZN ZN W 601 " - pdb=" SG CYS W 152 " pdb="ZN ZN W 601 " - pdb=" SG CYS W 149 " pdb="ZN ZN W 601 " - pdb=" SG CYS W 127 " Number of angles added : 57 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9914 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 59 sheets defined 41.0% alpha, 19.9% beta 46 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 14.24 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.653A pdb=" N ALA A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 203 through 213 Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 230 through 234 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.641A pdb=" N ASN A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.772A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 374 Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.632A pdb=" N GLY A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.662A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.580A pdb=" N ARG A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.906A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.586A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.536A 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 removed outlier: 3.515A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 661 removed outlier: 4.116A pdb=" N VAL A 641 " --> pdb=" O LYS A 637 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 646 " --> pdb=" O CYS A 642 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 removed outlier: 3.615A pdb=" N LEU A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 removed outlier: 3.521A pdb=" N GLN A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 762 removed outlier: 3.711A pdb=" N ILE A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.982A pdb=" N PHE A 815 " --> pdb=" O GLN A 811 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 889 through 897 Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.626A pdb=" N LEU A 913 " --> pdb=" O PRO A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.595A pdb=" N LEU A 920 " --> pdb=" O GLY A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 947 removed outlier: 3.599A pdb=" N GLN A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 3.727A pdb=" N ILE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.665A pdb=" N ILE A 986 " --> pdb=" O THR A 982 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1026 removed outlier: 5.543A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1056 Processing helix chain 'A' and resid 1063 through 1078 removed outlier: 3.616A pdb=" N LEU A1067 " --> pdb=" O MET A1063 " (cutoff:3.500A) Proline residue: A1075 - end of helix removed outlier: 4.002A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1107 removed outlier: 4.048A pdb=" N ARG A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1139 removed outlier: 3.776A pdb=" N ALA A1131 " --> pdb=" O ASP A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 3.834A pdb=" N PHE A1174 " --> pdb=" O ILE A1170 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1255 through 1271 removed outlier: 4.303A pdb=" N MET A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1319 removed outlier: 3.510A pdb=" N VAL A1316 " --> pdb=" O ASN A1312 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A1319 " --> pdb=" O GLU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1359 removed outlier: 3.703A pdb=" N ILE A1335 " --> pdb=" O SER A1331 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A1341 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N GLU A1342 " --> pdb=" O VAL A1338 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1355 " --> pdb=" O GLU A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.861A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1403 removed outlier: 4.164A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLU A1403 " --> pdb=" O ARG A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1415 removed outlier: 3.530A pdb=" N ILE A1408 " --> pdb=" O GLU A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1441 removed outlier: 3.935A pdb=" N PHE A1441 " --> pdb=" O THR A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1451 removed outlier: 3.606A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL A1451 " --> pdb=" O GLU A1447 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1446 through 1451' Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.880A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.106A pdb=" N LEU B 48 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.719A pdb=" N SER B 182 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 179 through 183' Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.762A pdb=" N ILE B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 324 removed outlier: 3.559A pdb=" N LYS B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 344 through 358 removed outlier: 3.872A pdb=" N GLN B 350 " --> pdb=" O GLU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 439 removed outlier: 3.568A pdb=" N LEU B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 448 removed outlier: 3.727A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 463 Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.735A pdb=" N TRP B 519 " --> pdb=" O ASN B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 559 removed outlier: 3.585A pdb=" N SER B 559 " --> pdb=" O ILE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' 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 Processing helix chain 'B' and resid 654 through 668 removed outlier: 3.824A pdb=" N ILE B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 removed outlier: 3.540A pdb=" N GLU B 687 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.810A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 711 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.649A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 755 removed outlier: 3.900A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 783 through 788 removed outlier: 4.213A pdb=" N ASN B 786 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 788 " --> pdb=" O TYR B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 812 removed outlier: 4.084A pdb=" N GLU B 810 " --> pdb=" O THR B 806 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR B 811 " --> pdb=" O ARG B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 927 through 932 Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.361A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1039 removed outlier: 3.522A pdb=" N CYS B1029 " --> pdb=" O HIS B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 removed outlier: 3.645A pdb=" N ILE B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1151 removed outlier: 3.744A pdb=" N LEU B1147 " --> pdb=" O ALA B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 39 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 75 through 80 removed outlier: 4.287A pdb=" N GLU C 78 " --> pdb=" O MET C 75 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 79 " --> pdb=" O ASP C 76 " (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 removed outlier: 3.539A pdb=" N GLY C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 201 removed outlier: 3.501A pdb=" N GLU C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 239 through 264 removed outlier: 3.505A pdb=" N GLN C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 73 removed outlier: 3.720A pdb=" N LEU D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 132 removed outlier: 3.669A pdb=" N LEU D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.718A pdb=" N ALA D 191 " --> pdb=" O THR D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.500A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.624A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.556A pdb=" N MET E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 Processing helix chain 'E' and resid 143 through 147 removed outlier: 3.585A pdb=" N HIS E 146 " --> pdb=" O ASN E 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS E 147 " --> pdb=" O ILE E 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 147' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.734A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.728A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.586A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 removed outlier: 3.773A pdb=" N PHE G 18 " --> pdb=" O PRO G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.633A pdb=" N TYR G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 removed outlier: 3.794A pdb=" N GLY G 66 " --> pdb=" O PRO G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 63 through 66' Processing helix chain 'G' and resid 112 through 115 Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.553A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER I 64 " --> pdb=" O ASP I 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 29 Processing helix chain 'J' and resid 31 through 40 removed outlier: 3.696A pdb=" N GLY J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.176A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 62 removed outlier: 3.782A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.521A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.770A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU K 49 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.600A pdb=" N ALA K 86 " --> pdb=" O ASP K 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 64 Processing helix chain 'M' and resid 85 through 89 Processing helix chain 'M' and resid 103 through 118 removed outlier: 3.635A pdb=" N THR M 107 " --> pdb=" O ASP M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 121 No H-bonds generated for 'chain 'M' and resid 119 through 121' Processing helix chain 'M' and resid 123 through 141 removed outlier: 3.651A pdb=" N GLN M 127 " --> pdb=" O ASP M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 158 Processing helix chain 'M' and resid 165 through 168 removed outlier: 4.423A pdb=" N MET M 168 " --> pdb=" O GLY M 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 165 through 168' Processing helix chain 'M' and resid 169 through 183 Processing helix chain 'M' and resid 188 through 196 removed outlier: 3.518A pdb=" N ILE M 192 " --> pdb=" O THR M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 217 Processing helix chain 'M' and resid 237 through 247 removed outlier: 4.207A pdb=" N ARG M 241 " --> pdb=" O THR M 237 " (cutoff:3.500A) Processing helix chain 'M' and resid 249 through 267 removed outlier: 3.887A pdb=" N LYS M 267 " --> pdb=" O CYS M 263 " (cutoff:3.500A) Processing helix chain 'M' and resid 273 through 289 removed outlier: 3.946A pdb=" N ILE M 277 " --> pdb=" O SER M 273 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE M 289 " --> pdb=" O ASN M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 302 removed outlier: 4.045A pdb=" N LYS M 297 " --> pdb=" O ILE M 293 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL M 298 " --> pdb=" O THR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 319 removed outlier: 3.790A pdb=" N ILE M 315 " --> pdb=" O SER M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 324 removed outlier: 3.627A pdb=" N LEU M 323 " --> pdb=" O ARG M 320 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL M 324 " --> pdb=" O ASP M 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 320 through 324' Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 128 through 147 removed outlier: 3.621A pdb=" N GLY O 147 " --> pdb=" O ILE O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 179 Processing helix chain 'O' and resid 219 through 237 removed outlier: 3.854A pdb=" N ILE O 223 " --> pdb=" O GLN O 219 " (cutoff:3.500A) Proline residue: O 232 - end of helix Processing helix chain 'Q' and resid 26 through 35 removed outlier: 3.525A pdb=" N ASN Q 30 " --> pdb=" O ARG Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 114 removed outlier: 3.990A pdb=" N LEU Q 111 " --> pdb=" O PRO Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 346 removed outlier: 3.576A pdb=" N GLU Q 346 " --> pdb=" O LEU Q 342 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 413 Processing helix chain 'R' and resid 74 through 82 Processing helix chain 'R' and resid 234 through 244 Processing helix chain 'R' and resid 259 through 267 removed outlier: 3.855A pdb=" N GLY R 267 " --> pdb=" O MET R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 310 Processing helix chain 'R' and resid 315 through 323 removed outlier: 3.910A pdb=" N ARG R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 337 removed outlier: 3.684A pdb=" N LEU R 329 " --> pdb=" O PRO R 325 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS R 335 " --> pdb=" O GLU R 331 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL R 336 " --> pdb=" O CYS R 332 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA R 337 " --> pdb=" O LEU R 333 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 29 removed outlier: 3.882A pdb=" N SER U 7 " --> pdb=" O ASN U 3 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU U 23 " --> pdb=" O ASN U 19 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 47 removed outlier: 3.607A pdb=" N LEU U 35 " --> pdb=" O ASP U 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 8 through 12 removed outlier: 3.531A pdb=" N ARG V 11 " --> pdb=" O GLU V 8 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 29 Processing helix chain 'V' and resid 35 through 55 Processing helix chain 'W' and resid 5 through 21 Processing helix chain 'W' and resid 22 through 35 removed outlier: 4.238A pdb=" N VAL W 26 " --> pdb=" O GLY W 22 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS W 35 " --> pdb=" O ALA W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 48 Processing helix chain 'W' and resid 50 through 64 Proline residue: W 56 - end of helix Processing helix chain 'W' and resid 90 through 116 removed outlier: 3.805A pdb=" N ASP W 112 " --> pdb=" O ARG W 108 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU W 113 " --> pdb=" O LEU W 109 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP W 114 " --> pdb=" O LYS W 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS W 115 " --> pdb=" O ASP W 111 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN W 116 " --> pdb=" O ASP W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 132 through 139 Processing helix chain 'W' and resid 161 through 163 No H-bonds generated for 'chain 'W' and resid 161 through 163' Processing helix chain 'W' and resid 164 through 190 removed outlier: 3.718A pdb=" N LYS W 168 " --> pdb=" O LYS W 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN W 169 " --> pdb=" O ASN W 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP W 170 " --> pdb=" O LYS W 166 " (cutoff:3.500A) Proline residue: W 181 - end of helix Processing helix chain 'X' and resid 124 through 139 Processing helix chain 'X' and resid 143 through 151 Processing helix chain 'X' and resid 157 through 166 Processing helix chain 'X' and resid 188 through 198 Processing helix chain 'X' and resid 207 through 214 Processing helix chain 'X' and resid 216 through 224 removed outlier: 4.410A pdb=" N THR X 220 " --> pdb=" O GLN X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 256 through 265 Processing helix chain 'X' and resid 272 through 282 removed outlier: 3.553A pdb=" N ARG X 276 " --> pdb=" O ALA X 272 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU X 281 " --> pdb=" O LYS X 277 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.728A pdb=" N VAL A 17 " --> pdb=" O ASP A1419 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.663A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 10.704A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 4.595A pdb=" N LEU A 181 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 344 Processing sheet with id=AA7, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.586A pdb=" N HIS B1104 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 348 " --> pdb=" O ARG B1106 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N VAL A 364 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.866A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.524A pdb=" N SER A 513 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 518 " --> pdb=" O SER A 513 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 4.100A pdb=" N ILE A 566 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL H 96 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL H 107 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.844A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB5, first strand: chain 'A' and resid 848 through 850 removed outlier: 3.625A pdb=" N MET A 849 " --> pdb=" O ARG A 857 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN A 858 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 863 " --> pdb=" O ASN A 858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB7, first strand: chain 'A' and resid 1280 through 1287 removed outlier: 5.201A pdb=" N ARG A1281 " --> pdb=" O ASP A1309 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP A1309 " --> pdb=" O ARG A1281 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A1308 " --> pdb=" O LEU A1116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1116 " --> pdb=" O THR A1308 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1117 " --> pdb=" O TYR A1328 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A1328 " --> pdb=" O THR A1117 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 3.885A pdb=" N ARG A1274 " --> pdb=" O THR A1141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.730A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N VAL A1242 " --> pdb=" O TRP A1191 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP A1191 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A1149 " --> pdb=" O GLU A1196 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR A1154 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU I 42 " --> pdb=" O TYR A1154 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1290 through 1292 Processing sheet with id=AC2, first strand: chain 'A' and resid 1442 through 1445 removed outlier: 3.707A pdb=" N ASP A1442 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL F 133 " --> pdb=" O MET A1444 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 109 through 111 removed outlier: 5.490A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS B 99 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N SER B 125 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER B 126 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG B 169 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 128 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 109 through 111 removed outlier: 4.564A pdb=" N ILE B 70 " --> pdb=" O LYS Q 333 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS Q 333 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC6, first strand: chain 'B' and resid 215 through 218 Processing sheet with id=AC7, first strand: chain 'B' and resid 224 through 227 removed outlier: 7.071A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 497 through 499 Processing sheet with id=AC9, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AD1, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.504A pdb=" N CYS B 741 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.449A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 624 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.798A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.798A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 954 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU L 56 " --> pdb=" O VAL B 954 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.749A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.041A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.744A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD9, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AE1, first strand: chain 'B' and resid 1171 through 1174 Processing sheet with id=AE2, first strand: chain 'C' and resid 7 through 13 removed outlier: 3.723A pdb=" N GLN C 7 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 119 through 120 removed outlier: 3.722A pdb=" N VAL C 119 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 100 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 48 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.730A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AE6, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.841A pdb=" N LEU D 50 " --> pdb=" O PHE G 2 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.841A pdb=" N LEU D 50 " --> pdb=" O PHE G 2 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE G 2 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 60 through 62 removed outlier: 4.037A pdb=" N TRP E 79 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AF1, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AF2, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.098A pdb=" N ILE G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER G 162 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS G 107 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY G 161 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL G 110 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER G 93 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLN G 102 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL G 91 " --> pdb=" O GLN G 102 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AF4, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF5, first strand: chain 'I' and resid 83 through 86 Processing sheet with id=AF6, first strand: chain 'K' and resid 19 through 24 removed outlier: 4.583A pdb=" N ALA K 30 " --> pdb=" O ASP K 24 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 34 through 37 removed outlier: 6.290A pdb=" N VAL M 43 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 92 through 95 removed outlier: 4.752A pdb=" N ASN O 95 " --> pdb=" O ALA O 101 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALA O 101 " --> pdb=" O ASN O 95 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE O 106 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR O 111 " --> pdb=" O ILE O 106 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL O 161 " --> pdb=" O GLN O 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE O 70 " --> pdb=" O ASN O 159 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN O 159 " --> pdb=" O ILE O 70 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA O 72 " --> pdb=" O ILE O 157 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE O 157 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL O 74 " --> pdb=" O PHE O 155 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE O 155 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE O 160 " --> pdb=" O GLY O 216 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY O 216 " --> pdb=" O ILE O 160 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU O 186 " --> pdb=" O PHE O 190 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 138 through 141 removed outlier: 4.708A pdb=" N TRP Q 350 " --> pdb=" O GLY Q 363 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY Q 363 " --> pdb=" O TRP Q 350 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR Q 360 " --> pdb=" O ARG Q 398 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR Q 393 " --> pdb=" O THR Q 116 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU Q 118 " --> pdb=" O TYR Q 393 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE Q 395 " --> pdb=" O LEU Q 118 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS Q 120 " --> pdb=" O PHE Q 395 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 120 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLU R 132 " --> pdb=" O THR R 217 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR R 217 " --> pdb=" O GLU R 132 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL R 134 " --> pdb=" O VAL R 215 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS R 211 " --> pdb=" O GLN R 138 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU R 221 " --> pdb=" O THR R 125 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE R 104 " --> pdb=" O LEU R 122 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N PHE Q 384 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N MET Q 386 " --> pdb=" O PRO Q 102 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG Q 104 " --> pdb=" O MET Q 386 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN R 67 " --> pdb=" O VAL Q 378 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASP R 60 " --> pdb=" O LYS R 211 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ALA R 213 " --> pdb=" O ASP R 60 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU R 62 " --> pdb=" O ALA R 213 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL R 215 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ARG R 66 " --> pdb=" O THR R 217 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS R 219 " --> pdb=" O ARG R 66 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL R 68 " --> pdb=" O CYS R 219 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU R 221 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU R 70 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN R 223 " --> pdb=" O LEU R 70 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 313 through 314 removed outlier: 3.985A pdb=" N TRP R 313 " --> pdb=" O TYR R 349 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 243 through 254 removed outlier: 6.401A pdb=" N LEU U 243 " --> pdb=" O VAL U 267 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL U 267 " --> pdb=" O LEU U 243 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU U 245 " --> pdb=" O GLY U 265 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY U 265 " --> pdb=" O LEU U 245 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER U 261 " --> pdb=" O ASP U 249 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL U 251 " --> pdb=" O LYS U 259 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS U 259 " --> pdb=" O VAL U 251 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG U 253 " --> pdb=" O ARG U 257 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG U 257 " --> pdb=" O ARG U 253 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ARG U 257 " --> pdb=" O GLU U 284 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU U 284 " --> pdb=" O ARG U 257 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS U 259 " --> pdb=" O GLU U 282 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU U 282 " --> pdb=" O LYS U 259 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER U 261 " --> pdb=" O GLN U 280 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLN U 280 " --> pdb=" O SER U 261 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS U 263 " --> pdb=" O LYS U 278 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS U 278 " --> pdb=" O LYS U 263 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N SER V 58 " --> pdb=" O TYR U 274 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE U 276 " --> pdb=" O SER V 58 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU V 60 " --> pdb=" O PHE U 276 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS U 278 " --> pdb=" O LEU V 60 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL V 62 " --> pdb=" O LYS U 278 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLN U 280 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLY V 64 " --> pdb=" O GLN U 280 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU U 282 " --> pdb=" O GLY V 64 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU V 66 " --> pdb=" O GLU U 282 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLU U 284 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR V 68 " --> pdb=" O GLU U 284 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS V 59 " --> pdb=" O VAL V 87 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL V 87 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N THR V 61 " --> pdb=" O VAL V 85 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL V 85 " --> pdb=" O THR V 61 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS V 63 " --> pdb=" O CYS V 83 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N CYS V 83 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE V 79 " --> pdb=" O ASP V 67 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR V 69 " --> pdb=" O THR V 77 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR V 77 " --> pdb=" O TYR V 69 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE V 71 " --> pdb=" O VAL V 75 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL V 75 " --> pdb=" O PHE V 71 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP V 109 " --> pdb=" O ASN V 82 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLN V 84 " --> pdb=" O SER V 107 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N SER V 107 " --> pdb=" O GLN V 84 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR V 86 " --> pdb=" O VAL V 105 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL V 105 " --> pdb=" O THR V 86 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS V 116 " --> pdb=" O CYS U 246 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 67 through 72 Processing sheet with id=AG4, first strand: chain 'W' and resid 130 through 131 removed outlier: 3.664A pdb=" N TYR W 131 " --> pdb=" O TYR W 122 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 169 through 172 removed outlier: 4.319A pdb=" N THR X 177 " --> pdb=" O ASP X 172 " (cutoff:3.500A) 1814 hydrogen bonds defined for protein. 5097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 248 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 23.91 Time building geometry restraints manager: 19.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 43733 1.54 - 1.87: 640 1.87 - 2.20: 0 2.20 - 2.53: 0 2.53 - 2.86: 1 Bond restraints: 44374 Sorted by residual: bond pdb=" C LEU X 181 " pdb=" N THR X 183 " ideal model delta sigma weight residual 1.332 2.864 -1.531 1.40e-02 5.10e+03 1.20e+04 bond pdb=" C THR B1213 " pdb=" N PRO B1214 " ideal model delta sigma weight residual 1.334 1.423 -0.089 2.34e-02 1.83e+03 1.44e+01 bond pdb=" C THR Q 403 " pdb=" N LEU Q 404 " ideal model delta sigma weight residual 1.332 1.368 -0.035 1.40e-02 5.10e+03 6.42e+00 bond pdb=" C LEU Q 404 " pdb=" N THR Q 405 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.40e-02 5.10e+03 4.79e+00 bond pdb=" C ALA A1434 " pdb=" N PRO A1435 " ideal model delta sigma weight residual 1.334 1.384 -0.050 2.34e-02 1.83e+03 4.53e+00 ... (remaining 44369 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.70: 1406 105.70 - 112.78: 24046 112.78 - 119.86: 14115 119.86 - 126.94: 20134 126.94 - 134.01: 674 Bond angle restraints: 60375 Sorted by residual: angle pdb=" O LEU X 181 " pdb=" C LEU X 181 " pdb=" N THR X 183 " ideal model delta sigma weight residual 122.59 99.65 22.94 1.33e+00 5.65e-01 2.98e+02 angle pdb=" C ILE E 127 " pdb=" N PRO E 128 " pdb=" CA PRO E 128 " ideal model delta sigma weight residual 119.66 124.37 -4.71 7.20e-01 1.93e+00 4.29e+01 angle pdb=" C VAL A1146 " pdb=" N THR A1147 " pdb=" CA THR A1147 " ideal model delta sigma weight residual 122.77 114.35 8.42 1.33e+00 5.65e-01 4.01e+01 angle pdb=" N CYS I 29 " pdb=" CA CYS I 29 " pdb=" C CYS I 29 " ideal model delta sigma weight residual 108.34 100.58 7.76 1.64e+00 3.72e-01 2.24e+01 angle pdb=" O PRO E 128 " pdb=" C PRO E 128 " pdb=" N PRO E 129 " ideal model delta sigma weight residual 121.15 123.12 -1.97 4.70e-01 4.53e+00 1.75e+01 ... (remaining 60370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 25328 17.83 - 35.67: 904 35.67 - 53.50: 425 53.50 - 71.34: 83 71.34 - 89.17: 20 Dihedral angle restraints: 26760 sinusoidal: 11495 harmonic: 15265 Sorted by residual: dihedral pdb=" CA LEU X 181 " pdb=" C LEU X 181 " pdb=" N THR X 183 " pdb=" CA THR X 183 " ideal model delta harmonic sigma weight residual 180.00 -96.10 -83.90 0 5.00e+00 4.00e-02 2.82e+02 dihedral pdb=" CA LYS Q 333 " pdb=" C LYS Q 333 " pdb=" N VAL Q 334 " pdb=" CA VAL Q 334 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA ASP O 81 " pdb=" C ASP O 81 " pdb=" N LEU O 82 " pdb=" CA LEU O 82 " ideal model delta harmonic sigma weight residual -180.00 -158.29 -21.71 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 26757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 5798 0.050 - 0.101: 813 0.101 - 0.151: 238 0.151 - 0.202: 3 0.202 - 0.252: 4 Chirality restraints: 6856 Sorted by residual: chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA CYS I 29 " pdb=" N CYS I 29 " pdb=" C CYS I 29 " pdb=" CB CYS I 29 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA PRO W 77 " pdb=" N PRO W 77 " pdb=" C PRO W 77 " pdb=" CB PRO W 77 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 6853 not shown) Planarity restraints: 7399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU X 181 " 0.125 2.00e-02 2.50e+03 1.84e-01 3.37e+02 pdb=" C LEU X 181 " -0.312 2.00e-02 2.50e+03 pdb=" O LEU X 181 " 0.140 2.00e-02 2.50e+03 pdb=" N THR X 183 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 73 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.10e+00 pdb=" N PRO R 74 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO R 74 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO R 74 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS Q 333 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.94e+00 pdb=" C LYS Q 333 " 0.046 2.00e-02 2.50e+03 pdb=" O LYS Q 333 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL Q 334 " -0.015 2.00e-02 2.50e+03 ... (remaining 7396 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.67: 11 1.67 - 2.48: 231 2.48 - 3.28: 46043 3.28 - 4.09: 105489 4.09 - 4.90: 191496 Warning: very small nonbonded interaction distances. Nonbonded interactions: 343270 Sorted by model distance: nonbonded pdb=" C LYS M 272 " pdb=" OP1 DG T 66 " model vdw 0.860 3.270 nonbonded pdb=" OP1 DG T 41 " pdb=" CB SER W 81 " model vdw 1.064 3.440 nonbonded pdb=" CA LYS M 272 " pdb=" OP1 DG T 66 " model vdw 1.078 3.470 nonbonded pdb=" NE ARG O 98 " pdb=" OP1 DA T 58 " model vdw 1.217 2.520 nonbonded pdb=" CB LYS M 272 " pdb=" P DG T 66 " model vdw 1.365 3.800 ... (remaining 343265 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.940 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 130.780 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0004 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.531 44374 Z= 0.549 Angle : 0.474 22.944 60375 Z= 0.283 Chirality : 0.039 0.252 6856 Planarity : 0.004 0.184 7399 Dihedral : 11.675 89.170 16846 Min Nonbonded Distance : 0.860 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 1.03 % Allowed : 6.21 % Favored : 92.76 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.10), residues: 5154 helix: -2.28 (0.09), residues: 1947 sheet: -1.62 (0.16), residues: 931 loop : -2.26 (0.11), residues: 2276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10308 Ramachandran restraints generated. 5154 Oldfield, 0 Emsley, 5154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 676 time to evaluate : 4.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 681 average time/residue: 0.6221 time to fit residues: 662.2850 Evaluate side-chains 380 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 377 time to evaluate : 4.652 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3720 time to fit residues: 8.9937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 40.0000 chunk 400 optimal weight: 10.0000 chunk 222 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 269 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 413 optimal weight: 40.0000 chunk 160 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 chunk 479 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 45 GLN A 64 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 ASN A 213 HIS ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS A 490 HIS A 525 GLN A 548 ASN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN A 660 ASN A 698 GLN A 723 ASN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 968 GLN A1040 GLN ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1130 GLN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 363 HIS B 415 GLN B 433 GLN ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS B 538 ASN B 573 GLN ** B 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 667 GLN B 686 ASN B 763 GLN ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 GLN B 986 GLN B1025 HIS ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN C 135 GLN C 224 GLN C 231 ASN C 242 GLN C 264 GLN ** D 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 179 GLN E 8 ASN E 54 GLN E 146 HIS G 102 GLN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN M 90 ASN M 124 ASN M 158 HIS ** M 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 179 HIS U 33 GLN U 280 GLN V 84 GLN ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 216 GLN ** X 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 267 GLN X 279 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1177 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.187 44374 Z= 0.519 Angle : 1.091 16.896 60375 Z= 0.565 Chirality : 0.056 0.342 6856 Planarity : 0.009 0.107 7399 Dihedral : 14.106 83.049 6767 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 27.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.85 % Favored : 94.76 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.60 (0.10), residues: 5156 helix: -1.33 (0.10), residues: 1977 sheet: -1.20 (0.17), residues: 850 loop : -2.23 (0.11), residues: 2329 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 521 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 10 residues processed: 553 average time/residue: 0.5868 time to fit residues: 523.8288 Evaluate side-chains 373 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 363 time to evaluate : 4.721 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4362 time to fit residues: 14.7874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 399 optimal weight: 7.9990 chunk 326 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 480 optimal weight: 20.0000 chunk 518 optimal weight: 0.0060 chunk 427 optimal weight: 3.9990 chunk 476 optimal weight: 40.0000 chunk 163 optimal weight: 6.9990 chunk 385 optimal weight: 0.9980 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 68 GLN A 253 ASN A 299 HIS A 311 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 700 ASN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B 395 GLN B 518 HIS B 822 ASN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS G 97 HIS ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN I 60 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 208 ASN O 91 ASN ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0967 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.101 44374 Z= 0.207 Angle : 0.640 12.426 60375 Z= 0.332 Chirality : 0.044 0.216 6856 Planarity : 0.005 0.116 7399 Dihedral : 13.826 76.912 6767 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.71 % Favored : 94.94 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.11), residues: 5156 helix: -0.43 (0.11), residues: 1985 sheet: -1.01 (0.17), residues: 852 loop : -2.01 (0.12), residues: 2319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 438 time to evaluate : 4.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 440 average time/residue: 0.5973 time to fit residues: 427.2593 Evaluate side-chains 349 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 5.488 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 20.0000 chunk 361 optimal weight: 20.0000 chunk 249 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 229 optimal weight: 10.0000 chunk 322 optimal weight: 0.7980 chunk 482 optimal weight: 6.9990 chunk 510 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 456 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN ** A 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 GLN B 975 GLN ** B1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN E 8 ASN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS ** G 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 ASN ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1201 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.100 44374 Z= 0.270 Angle : 0.710 12.486 60375 Z= 0.367 Chirality : 0.045 0.260 6856 Planarity : 0.006 0.095 7399 Dihedral : 13.906 80.145 6767 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.53 % Favored : 94.10 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.11), residues: 5156 helix: -0.12 (0.11), residues: 1972 sheet: -0.88 (0.17), residues: 827 loop : -2.01 (0.12), residues: 2357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 416 time to evaluate : 4.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 419 average time/residue: 0.5894 time to fit residues: 403.2501 Evaluate side-chains 350 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 348 time to evaluate : 4.713 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3707 time to fit residues: 8.2061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 20.0000 chunk 289 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 chunk 380 optimal weight: 3.9990 chunk 210 optimal weight: 0.6980 chunk 435 optimal weight: 20.0000 chunk 352 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 260 optimal weight: 0.6980 chunk 458 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 GLN A 768 GLN A 881 GLN A1312 ASN B 215 GLN B 518 HIS B 538 ASN B 770 GLN ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1112 GLN ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 HIS ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS G 158 HIS H 33 GLN H 128 ASN H 131 ASN K 104 ASN ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 ASN ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 280 GLN ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1119 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 44374 Z= 0.194 Angle : 0.612 12.101 60375 Z= 0.317 Chirality : 0.043 0.250 6856 Planarity : 0.005 0.078 7399 Dihedral : 13.869 78.283 6767 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.14 % Favored : 94.57 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.11), residues: 5156 helix: 0.25 (0.12), residues: 1990 sheet: -0.78 (0.17), residues: 813 loop : -1.87 (0.12), residues: 2353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 406 time to evaluate : 4.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 407 average time/residue: 0.6141 time to fit residues: 407.3096 Evaluate side-chains 334 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 333 time to evaluate : 4.858 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3890 time to fit residues: 7.8177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.5980 chunk 459 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 510 optimal weight: 8.9990 chunk 424 optimal weight: 6.9990 chunk 236 optimal weight: 0.0170 chunk 42 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 268 optimal weight: 0.9990 overall best weight: 2.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN A 736 ASN ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1059 HIS A1390 ASN B 110 HIS B 518 HIS ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 HIS B1097 HIS ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1176 ASN ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 ASN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS G 71 ASN H 43 ASN ** J 53 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** K 104 ASN M 114 GLN ** R 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 65 ASN ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1389 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 44374 Z= 0.274 Angle : 0.728 11.955 60375 Z= 0.377 Chirality : 0.045 0.211 6856 Planarity : 0.006 0.079 7399 Dihedral : 14.084 80.151 6767 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.25 % Favored : 93.44 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.11), residues: 5156 helix: 0.21 (0.12), residues: 1978 sheet: -0.82 (0.17), residues: 839 loop : -1.98 (0.12), residues: 2339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 413 time to evaluate : 4.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 415 average time/residue: 0.6150 time to fit residues: 415.1430 Evaluate side-chains 342 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 341 time to evaluate : 4.563 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4939 time to fit residues: 7.5405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 20.0000 chunk 57 optimal weight: 5.9990 chunk 291 optimal weight: 7.9990 chunk 373 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 430 optimal weight: 0.6980 chunk 285 optimal weight: 6.9990 chunk 508 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 310 optimal weight: 20.0000 chunk 234 optimal weight: 0.5980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 HIS ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 994 GLN ** B 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1161 HIS B1176 ASN ** B1195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 HIS C 131 HIS C 184 ASN E 8 ASN E 99 HIS ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 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** K 104 ASN M 124 ASN O 88 HIS ** R 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 65 ASN ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1564 moved from start: 0.7848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 44374 Z= 0.322 Angle : 0.807 13.229 60375 Z= 0.419 Chirality : 0.048 0.265 6856 Planarity : 0.006 0.101 7399 Dihedral : 14.382 78.411 6767 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.79 % Favored : 92.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.11), residues: 5156 helix: -0.00 (0.12), residues: 1953 sheet: -1.00 (0.18), residues: 824 loop : -2.17 (0.12), residues: 2379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 4.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.6169 time to fit residues: 413.8994 Evaluate side-chains 337 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 4.462 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 303 optimal weight: 9.9990 chunk 153 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 323 optimal weight: 9.9990 chunk 346 optimal weight: 7.9990 chunk 251 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 400 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 394 ASN ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 757 ASN A1011 GLN B 110 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 GLN E 3 GLN E 99 HIS E 106 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** 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** K 104 ASN ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1462 moved from start: 0.8034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 44374 Z= 0.219 Angle : 0.680 11.308 60375 Z= 0.352 Chirality : 0.044 0.245 6856 Planarity : 0.005 0.081 7399 Dihedral : 14.272 77.227 6767 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.05 % Favored : 93.66 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.11), residues: 5156 helix: 0.29 (0.12), residues: 1950 sheet: -0.94 (0.17), residues: 876 loop : -1.96 (0.12), residues: 2330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 395 time to evaluate : 4.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 396 average time/residue: 0.6363 time to fit residues: 409.3139 Evaluate side-chains 336 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 335 time to evaluate : 5.045 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4830 time to fit residues: 7.6840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 6.9990 chunk 487 optimal weight: 9.9990 chunk 444 optimal weight: 0.9980 chunk 474 optimal weight: 10.0000 chunk 285 optimal weight: 0.0970 chunk 206 optimal weight: 0.6980 chunk 372 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 428 optimal weight: 4.9990 chunk 448 optimal weight: 7.9990 chunk 472 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN A 611 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 ASN ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 ASN ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 245 HIS ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1345 moved from start: 0.8038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 44374 Z= 0.174 Angle : 0.621 10.692 60375 Z= 0.322 Chirality : 0.043 0.253 6856 Planarity : 0.005 0.081 7399 Dihedral : 14.117 77.016 6767 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.39 % Favored : 94.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.12), residues: 5156 helix: 0.63 (0.12), residues: 1942 sheet: -0.68 (0.18), residues: 811 loop : -1.87 (0.12), residues: 2403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 4.666 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.6024 time to fit residues: 378.2011 Evaluate side-chains 330 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 4.707 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 5.9990 chunk 501 optimal weight: 20.0000 chunk 306 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 348 optimal weight: 0.0060 chunk 526 optimal weight: 4.9990 chunk 484 optimal weight: 50.0000 chunk 418 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 chunk 256 optimal weight: 0.8980 overall best weight: 3.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1128 GLN B 206 ASN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN E 8 ASN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1673 moved from start: 0.8888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.100 44374 Z= 0.308 Angle : 0.817 12.531 60375 Z= 0.423 Chirality : 0.048 0.231 6856 Planarity : 0.006 0.074 7399 Dihedral : 14.379 80.009 6767 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.76 % Favored : 91.93 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.11), residues: 5156 helix: 0.23 (0.12), residues: 1943 sheet: -0.84 (0.18), residues: 793 loop : -2.10 (0.12), residues: 2420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.5989 time to fit residues: 400.3688 Evaluate side-chains 340 residues out of total 4654 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 4.768 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 0.8980 chunk 446 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 386 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 419 optimal weight: 30.0000 chunk 175 optimal weight: 9.9990 chunk 430 optimal weight: 9.9990 chunk 53 optimal weight: 0.0970 chunk 77 optimal weight: 0.5980 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 GLN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN D 179 GLN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 93 HIS ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.170748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.154715 restraints weight = 157062.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.155479 restraints weight = 151380.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.155197 restraints weight = 111454.171| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1793 moved from start: 0.8958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 44374 Z= 0.206 Angle : 0.675 11.418 60375 Z= 0.350 Chirality : 0.044 0.241 6856 Planarity : 0.005 0.073 7399 Dihedral : 14.308 76.701 6767 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.01 % Favored : 93.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.11), residues: 5156 helix: 0.47 (0.12), residues: 1945 sheet: -0.66 (0.18), residues: 787 loop : -2.03 (0.12), residues: 2424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8384.51 seconds wall clock time: 154 minutes 25.68 seconds (9265.68 seconds total)