Starting phenix.real_space_refine on Mon Mar 18 01:15:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt7_33441/03_2024/7xt7_33441.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt7_33441/03_2024/7xt7_33441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt7_33441/03_2024/7xt7_33441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt7_33441/03_2024/7xt7_33441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt7_33441/03_2024/7xt7_33441.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xt7_33441/03_2024/7xt7_33441.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 260 5.49 5 Mg 1 5.21 5 S 317 5.16 5 C 51005 2.51 5 N 14417 2.21 5 O 16069 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 82079 Number of models: 1 Model: "" Number of chains: 43 Chain: "A" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1404, 11064 Classifications: {'peptide': 1404} Link IDs: {'PCIS': 3, 'PTRANS': 63, 'TRANS': 1337} Chain breaks: 5 Chain: "B" Number of atoms: 9284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9284 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 52, 'TRANS': 1111} Chain breaks: 4 Chain: "C" Number of atoms: 2098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2098 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 12, 'TRANS': 250} Chain: "D" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1349 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain breaks: 1 Chain: "E" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1741 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 202} Chain: "F" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1325 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 160} Chain: "H" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1053 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 917 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 554 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 932 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "M" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "N" Number of atoms: 2377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2377 Classifications: {'DNA': 115} Link IDs: {'rna3p': 114} Chain breaks: 1 Chain: "P" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna2p': 4, 'rna3p': 14} Chain: "T" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2570 Classifications: {'DNA': 126} Link IDs: {'rna3p': 125} Chain: "V" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "W" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4232 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Chain breaks: 2 Chain: "m" Number of atoms: 9730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9730 Classifications: {'peptide': 1187} Link IDs: {'PTRANS': 45, 'TRANS': 1141} Chain breaks: 3 Chain: "n" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "q" Number of atoms: 7552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7552 Classifications: {'peptide': 930} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 910} Chain: "r" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2139 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 259} Chain breaks: 2 Chain: "u" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1707 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "v" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2878 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 22, 'TRANS': 326} Chain breaks: 3 Chain: "x" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "a" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 746 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "b" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "d" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "e" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 757 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "h" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "j" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3754 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 449} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 14, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 94 Chain: "k" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3502 Classifications: {'peptide': 429} Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 409} Chain breaks: 2 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: "V" 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 527 SG CYS A 67 82.501 93.709 170.062 1.00 88.52 S ATOM 549 SG CYS A 70 85.813 92.267 171.267 1.00 80.61 S ATOM 594 SG CYS A 77 85.036 95.963 171.825 1.00 74.25 S ATOM 829 SG CYS A 107 94.787 117.816 129.868 1.00119.97 S ATOM 851 SG CYS A 110 96.607 114.580 129.024 1.00120.93 S ATOM 1157 SG CYS A 148 97.538 117.794 127.300 1.00130.56 S ATOM 1229 SG CYS A 168 94.017 116.276 126.654 1.00147.87 S ATOM 19880 SG CYS B1163 97.948 92.336 159.739 1.00 72.90 S ATOM 19898 SG CYS B1166 96.411 95.706 159.089 1.00 67.90 S ATOM 20021 SG CYS B1182 94.160 92.644 159.411 1.00 86.49 S ATOM 20044 SG CYS B1185 96.425 93.178 156.346 1.00 81.46 S ATOM 20989 SG CYS C 85 86.846 104.474 239.090 1.00 90.87 S ATOM 21002 SG CYS C 87 83.621 103.613 237.281 1.00 97.64 S ATOM 21037 SG CYS C 91 83.457 105.479 240.404 1.00 81.03 S ATOM 21060 SG CYS C 94 84.911 107.353 237.493 1.00 79.20 S ATOM 29206 SG CYS I 78 97.395 198.102 183.026 1.00230.27 S ATOM 29422 SG CYS I 103 97.784 193.672 182.528 1.00213.56 S ATOM 28659 SG CYS I 10 79.773 179.663 139.792 1.00179.72 S ATOM 28822 SG CYS I 29 84.082 179.729 138.314 1.00170.04 S ATOM 28847 SG CYS I 32 82.550 181.568 137.437 1.00176.35 S ATOM 29563 SG CYS J 7 92.756 137.533 228.544 1.00 51.40 S ATOM 29586 SG CYS J 10 94.891 136.439 231.579 1.00 53.77 S ATOM 29862 SG CYS J 44 95.968 139.386 229.303 1.00 51.15 S ATOM 29868 SG CYS J 45 93.186 139.569 231.832 1.00 53.74 S ATOM 31039 SG CYS L 33 53.777 127.162 210.328 1.00 96.95 S ATOM 31054 SG CYS L 36 51.423 127.872 213.254 1.00107.86 S ATOM 31164 SG CYS L 50 50.558 125.165 210.699 1.00114.52 S ATOM 31188 SG CYS L 53 50.624 128.826 209.640 1.00122.53 S ATOM 31445 SG CYS M 25 69.889 142.722 127.537 1.00236.78 S ATOM 31470 SG CYS M 28 69.653 138.992 127.680 1.00261.47 S ATOM 31628 SG CYS M 49 72.961 140.593 126.695 1.00240.45 S ATOM 31652 SG CYS M 52 69.829 140.602 124.350 1.00251.70 S ATOM 37246 SG CYS V 12 36.481 113.530 135.806 1.00262.86 S ATOM 37268 SG CYS V 15 38.136 116.485 134.283 1.00253.61 S ATOM 37370 SG CYS V 29 34.512 116.715 134.519 1.00249.01 S ATOM 37391 SG CYS V 32 36.027 114.329 132.024 1.00263.48 S Time building chain proxies: 32.81, per 1000 atoms: 0.40 Number of scatterers: 82079 At special positions: 0 Unit cell: (215.18, 227.052, 293.832, 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 317 16.00 P 260 15.00 Mg 1 11.99 O 16069 8.00 N 14417 7.00 C 51005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 27.78 Conformation dependent library (CDL) restraints added in 10.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 85 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 87 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 10 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 33 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 53 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 50 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 28 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 25 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 52 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 49 " pdb=" ZN V 300 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 15 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 29 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 32 " pdb="ZN ZN V 300 " - pdb=" SG CYS V 12 " Number of angles added : 45 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18118 Finding SS restraints... Secondary structure from input PDB file: 373 helices and 89 sheets defined 47.7% alpha, 15.1% beta 126 base pairs and 214 stacking pairs defined. Time for finding SS restraints: 22.93 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.723A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.495A pdb=" N THR A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 286 through 306 removed outlier: 3.701A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.711A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.526A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.890A pdb=" N SER A 477 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.678A pdb=" N ILE A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 536 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.505A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.769A pdb=" N ALA A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.582A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.725A pdb=" N ILE A 671 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.617A pdb=" N GLU A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.728A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 924 through 947 Processing helix chain 'A' and resid 961 through 974 Processing helix chain 'A' and resid 984 through 996 Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.683A pdb=" N THR A1017 " --> pdb=" O GLN A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1028 Processing helix chain 'A' and resid 1029 through 1036 Processing helix chain 'A' and resid 1040 through 1058 Processing helix chain 'A' and resid 1065 through 1079 Proline residue: A1077 - end of helix Processing helix chain 'A' and resid 1099 through 1109 Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 3.569A pdb=" N LEU A1128 " --> pdb=" O ARG A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1145 through 1148 No H-bonds generated for 'chain 'A' and resid 1145 through 1148' Processing helix chain 'A' and resid 1168 through 1177 Processing helix chain 'A' and resid 1200 through 1207 Processing helix chain 'A' and resid 1210 through 1223 Processing helix chain 'A' and resid 1259 through 1274 Processing helix chain 'A' and resid 1315 through 1321 removed outlier: 3.627A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.637A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 3.986A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1404 removed outlier: 3.514A pdb=" N SER A1404 " --> pdb=" O LEU A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.811A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1451 through 1455 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.662A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 299 through 314 Proline residue: B 308 - end of helix Processing helix chain 'B' and resid 318 through 329 removed outlier: 3.649A pdb=" N ARG B 329 " --> pdb=" O PHE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 351 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 401 through 430 removed outlier: 4.200A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.619A pdb=" N THR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.207A pdb=" N ARG B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.347A pdb=" N ALA B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 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 585 through 599 removed outlier: 3.574A pdb=" N LEU B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 658 Processing helix chain 'B' and resid 677 through 684 Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.621A pdb=" N ILE B 698 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 708 removed outlier: 3.620A pdb=" N GLN B 708 " --> pdb=" O GLU B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.745A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.553A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 removed outlier: 3.536A pdb=" N ASN B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 774 Processing helix chain 'B' and resid 775 through 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 806 through 811 removed outlier: 3.507A pdb=" N TYR B 811 " --> pdb=" O ALA B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 921 through 926 removed outlier: 4.145A pdb=" N GLU B 924 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY B 926 " --> pdb=" O GLU B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 removed outlier: 3.655A pdb=" N MET B 999 " --> pdb=" O HIS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.632A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.961A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.533A pdb=" N VAL 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 1152 Processing helix chain 'B' and resid 1198 through 1210 Processing helix chain 'C' and resid 25 through 39 Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.610A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.979A pdb=" N ARG C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 52 through 72 Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.996A pdb=" N THR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 112 Processing helix chain 'D' and resid 117 through 131 removed outlier: 3.606A pdb=" N SER D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 removed outlier: 3.670A pdb=" N VAL D 136 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.716A pdb=" N GLY D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 161 through 166 removed outlier: 4.195A pdb=" N ALA D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS D 166 " --> pdb=" O SER D 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 166' Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 64 through 71 Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 116 through 122 removed outlier: 3.588A pdb=" N MET E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 removed outlier: 3.586A pdb=" N VAL E 140 " --> pdb=" O SER E 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 137 through 140' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 156 through 168 Processing helix chain 'E' and resid 170 through 174 removed outlier: 3.643A pdb=" N LEU E 174 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.708A 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 Processing helix chain 'G' and resid 14 through 18 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 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.530A pdb=" N ASP H 91 " --> pdb=" O LEU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 133 through 135 No H-bonds generated for 'chain 'H' and resid 133 through 135' Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.574A pdb=" N ASP I 65 " --> pdb=" O ILE I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.892A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.817A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'M' and resid 65 through 78 Processing helix chain 'V' and resid 20 through 28 Processing helix chain 'V' and resid 31 through 35 removed outlier: 4.045A pdb=" N SER V 34 " --> pdb=" O ASN V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 49 Processing helix chain 'V' and resid 66 through 72 Processing helix chain 'V' and resid 91 through 101 Processing helix chain 'W' and resid 235 through 251 Processing helix chain 'W' and resid 278 through 287 Processing helix chain 'W' and resid 304 through 310 removed outlier: 4.207A pdb=" N ASP W 308 " --> pdb=" O VAL W 304 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU W 310 " --> pdb=" O TYR W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 395 through 403 Processing helix chain 'W' and resid 443 through 452 Processing helix chain 'W' and resid 453 through 455 No H-bonds generated for 'chain 'W' and resid 453 through 455' Processing helix chain 'W' and resid 461 through 475 Processing helix chain 'W' and resid 515 through 520 Processing helix chain 'W' and resid 692 through 695 Processing helix chain 'W' and resid 760 through 764 removed outlier: 4.298A pdb=" N TYR W 763 " --> pdb=" O GLN W 760 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS W 764 " --> pdb=" O GLY W 761 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 760 through 764' Processing helix chain 'W' and resid 792 through 794 No H-bonds generated for 'chain 'W' and resid 792 through 794' Processing helix chain 'm' and resid 230 through 242 Processing helix chain 'm' and resid 244 through 259 removed outlier: 4.414A pdb=" N TRP m 249 " --> pdb=" O THR m 245 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR m 250 " --> pdb=" O ASP m 246 " (cutoff:3.500A) Processing helix chain 'm' and resid 279 through 284 Processing helix chain 'm' and resid 285 through 293 Processing helix chain 'm' and resid 295 through 304 Processing helix chain 'm' and resid 307 through 314 Processing helix chain 'm' and resid 323 through 342 Processing helix chain 'm' and resid 342 through 353 Processing helix chain 'm' and resid 358 through 377 Processing helix chain 'm' and resid 380 through 388 Processing helix chain 'm' and resid 388 through 393 removed outlier: 3.934A pdb=" N ALA m 392 " --> pdb=" O ARG m 388 " (cutoff:3.500A) Processing helix chain 'm' and resid 410 through 442 removed outlier: 3.944A pdb=" N ASP m 429 " --> pdb=" O HIS m 425 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS m 430 " --> pdb=" O SER m 426 " (cutoff:3.500A) Processing helix chain 'm' and resid 447 through 456 removed outlier: 3.602A pdb=" N SER m 456 " --> pdb=" O GLU m 452 " (cutoff:3.500A) Processing helix chain 'm' and resid 459 through 474 Processing helix chain 'm' and resid 474 through 484 Processing helix chain 'm' and resid 518 through 527 Processing helix chain 'm' and resid 529 through 537 removed outlier: 4.044A pdb=" N ALA m 537 " --> pdb=" O VAL m 533 " (cutoff:3.500A) Processing helix chain 'm' and resid 538 through 549 Processing helix chain 'm' and resid 561 through 573 Processing helix chain 'm' and resid 581 through 599 Processing helix chain 'm' and resid 600 through 615 removed outlier: 3.503A pdb=" N ARG m 604 " --> pdb=" O GLU m 600 " (cutoff:3.500A) Processing helix chain 'm' and resid 622 through 629 removed outlier: 3.519A pdb=" N ILE m 629 " --> pdb=" O GLY m 625 " (cutoff:3.500A) Processing helix chain 'm' and resid 633 through 639 removed outlier: 3.718A pdb=" N ASP m 637 " --> pdb=" O PRO m 634 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS m 639 " --> pdb=" O PHE m 636 " (cutoff:3.500A) Processing helix chain 'm' and resid 648 through 651 Processing helix chain 'm' and resid 652 through 665 removed outlier: 3.909A pdb=" N TYR m 656 " --> pdb=" O THR m 652 " (cutoff:3.500A) Processing helix chain 'm' and resid 676 through 689 Processing helix chain 'm' and resid 694 through 748 Proline residue: m 717 - end of helix Processing helix chain 'm' and resid 802 through 815 removed outlier: 3.567A pdb=" N SER m 806 " --> pdb=" O SER m 802 " (cutoff:3.500A) Processing helix chain 'm' and resid 830 through 847 removed outlier: 4.060A pdb=" N LYS m 834 " --> pdb=" O ILE m 830 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU m 835 " --> pdb=" O HIS m 831 " (cutoff:3.500A) Processing helix chain 'm' and resid 878 through 887 removed outlier: 3.749A pdb=" N HIS m 886 " --> pdb=" O ARG m 882 " (cutoff:3.500A) Processing helix chain 'm' and resid 887 through 894 removed outlier: 3.689A pdb=" N SER m 891 " --> pdb=" O SER m 887 " (cutoff:3.500A) Processing helix chain 'm' and resid 898 through 913 Processing helix chain 'm' and resid 913 through 921 Processing helix chain 'm' and resid 922 through 928 removed outlier: 4.124A pdb=" N MET m 925 " --> pdb=" O ASP m 922 " (cutoff:3.500A) Processing helix chain 'm' and resid 938 through 958 Processing helix chain 'm' and resid 961 through 967 Processing helix chain 'm' and resid 967 through 972 Processing helix chain 'm' and resid 973 through 977 Processing helix chain 'm' and resid 981 through 996 Processing helix chain 'm' and resid 1003 through 1008 Processing helix chain 'm' and resid 1012 through 1020 Processing helix chain 'm' and resid 1030 through 1034 removed outlier: 3.952A pdb=" N ARG m1033 " --> pdb=" O ASP m1030 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN m1034 " --> pdb=" O VAL m1031 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 1030 through 1034' Processing helix chain 'm' and resid 1040 through 1045 Processing helix chain 'm' and resid 1048 through 1050 No H-bonds generated for 'chain 'm' and resid 1048 through 1050' Processing helix chain 'm' and resid 1051 through 1064 Processing helix chain 'm' and resid 1072 through 1085 Processing helix chain 'm' and resid 1097 through 1103 Processing helix chain 'm' and resid 1104 through 1117 removed outlier: 3.556A pdb=" N TYR m1108 " --> pdb=" O ILE m1104 " (cutoff:3.500A) Processing helix chain 'm' and resid 1120 through 1133 Processing helix chain 'm' and resid 1146 through 1156 Processing helix chain 'm' and resid 1194 through 1198 removed outlier: 4.375A pdb=" N LEU m1198 " --> pdb=" O ARG m1194 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 1194 through 1198' Processing helix chain 'm' and resid 1205 through 1210 Processing helix chain 'm' and resid 1235 through 1240 Processing helix chain 'm' and resid 1256 through 1273 Processing helix chain 'm' and resid 1290 through 1300 removed outlier: 3.706A pdb=" N ALA m1300 " --> pdb=" O ASP m1296 " (cutoff:3.500A) Processing helix chain 'm' and resid 1358 through 1380 removed outlier: 3.929A pdb=" N ASN m1368 " --> pdb=" O VAL m1364 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN m1369 " --> pdb=" O GLU m1365 " (cutoff:3.500A) Processing helix chain 'm' and resid 1387 through 1402 Processing helix chain 'm' and resid 1453 through 1469 Processing helix chain 'n' and resid 153 through 180 Processing helix chain 'n' and resid 185 through 200 Proline residue: n 192 - end of helix removed outlier: 3.549A pdb=" N ARG n 200 " --> pdb=" O ASP n 196 " (cutoff:3.500A) Processing helix chain 'n' and resid 203 through 211 Processing helix chain 'n' and resid 212 through 221 Processing helix chain 'n' and resid 230 through 244 Processing helix chain 'n' and resid 247 through 255 Processing helix chain 'n' and resid 255 through 266 removed outlier: 4.552A pdb=" N VAL n 259 " --> pdb=" O GLY n 255 " (cutoff:3.500A) Processing helix chain 'n' and resid 270 through 289 Proline residue: n 287 - end of helix Processing helix chain 'q' and resid 5 through 13 removed outlier: 3.879A pdb=" N TYR q 9 " --> pdb=" O ASP q 5 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 20 removed outlier: 3.751A pdb=" N GLU q 20 " --> pdb=" O ASP q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 21 through 23 No H-bonds generated for 'chain 'q' and resid 21 through 23' Processing helix chain 'q' and resid 46 through 58 Processing helix chain 'q' and resid 60 through 74 removed outlier: 3.663A pdb=" N TRP q 64 " --> pdb=" O ARG q 60 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 89 Processing helix chain 'q' and resid 90 through 96 Processing helix chain 'q' and resid 97 through 120 removed outlier: 3.873A pdb=" N THR q 101 " --> pdb=" O SER q 97 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR q 119 " --> pdb=" O GLU q 115 " (cutoff:3.500A) Processing helix chain 'q' and resid 122 through 141 Processing helix chain 'q' and resid 144 through 158 removed outlier: 3.689A pdb=" N GLY q 148 " --> pdb=" O LEU q 144 " (cutoff:3.500A) Processing helix chain 'q' and resid 160 through 175 Processing helix chain 'q' and resid 178 through 192 Processing helix chain 'q' and resid 194 through 209 removed outlier: 3.535A pdb=" N LEU q 201 " --> pdb=" O GLN q 197 " (cutoff:3.500A) Processing helix chain 'q' and resid 215 through 227 removed outlier: 4.131A pdb=" N GLY q 219 " --> pdb=" O ASP q 215 " (cutoff:3.500A) Processing helix chain 'q' and resid 229 through 244 Processing helix chain 'q' and resid 248 through 267 removed outlier: 3.877A pdb=" N LYS q 252 " --> pdb=" O ASN q 248 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER q 267 " --> pdb=" O CYS q 263 " (cutoff:3.500A) Processing helix chain 'q' and resid 269 through 289 Processing helix chain 'q' and resid 294 through 308 removed outlier: 3.601A pdb=" N SER q 303 " --> pdb=" O MET q 299 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR q 304 " --> pdb=" O VAL q 300 " (cutoff:3.500A) Processing helix chain 'q' and resid 310 through 325 Processing helix chain 'q' and resid 328 through 347 removed outlier: 3.553A pdb=" N VAL q 332 " --> pdb=" O ASN q 328 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS q 345 " --> pdb=" O ARG q 341 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS q 346 " --> pdb=" O VAL q 342 " (cutoff:3.500A) Processing helix chain 'q' and resid 348 through 363 Processing helix chain 'q' and resid 366 through 380 removed outlier: 3.545A pdb=" N LYS q 370 " --> pdb=" O ASN q 366 " (cutoff:3.500A) Processing helix chain 'q' and resid 382 through 397 Processing helix chain 'q' and resid 402 through 417 Processing helix chain 'q' and resid 419 through 438 Processing helix chain 'q' and resid 442 through 454 removed outlier: 3.802A pdb=" N TYR q 446 " --> pdb=" O LEU q 442 " (cutoff:3.500A) Processing helix chain 'q' and resid 457 through 473 Processing helix chain 'q' and resid 474 through 476 No H-bonds generated for 'chain 'q' and resid 474 through 476' Processing helix chain 'q' and resid 477 through 491 Processing helix chain 'q' and resid 493 through 508 Processing helix chain 'q' and resid 509 through 511 No H-bonds generated for 'chain 'q' and resid 509 through 511' Processing helix chain 'q' and resid 512 through 535 removed outlier: 4.233A pdb=" N GLU q 517 " --> pdb=" O PRO q 513 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA q 518 " --> pdb=" O GLN q 514 " (cutoff:3.500A) Processing helix chain 'q' and resid 535 through 550 removed outlier: 3.534A pdb=" N ALA q 539 " --> pdb=" O ASN q 535 " (cutoff:3.500A) Processing helix chain 'q' and resid 553 through 569 removed outlier: 4.099A pdb=" N LYS q 557 " --> pdb=" O TYR q 553 " (cutoff:3.500A) Processing helix chain 'q' and resid 572 through 583 Processing helix chain 'q' and resid 586 through 605 removed outlier: 6.249A pdb=" N ARG q 602 " --> pdb=" O LYS q 598 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS q 603 " --> pdb=" O ARG q 599 " (cutoff:3.500A) Processing helix chain 'q' and resid 609 through 622 Processing helix chain 'q' and resid 626 through 644 Processing helix chain 'q' and resid 648 through 673 Processing helix chain 'q' and resid 676 through 690 removed outlier: 3.546A pdb=" N ALA q 680 " --> pdb=" O ASN q 676 " (cutoff:3.500A) Processing helix chain 'q' and resid 692 through 707 Processing helix chain 'q' and resid 709 through 723 Processing helix chain 'q' and resid 725 through 740 Processing helix chain 'q' and resid 745 through 764 removed outlier: 3.789A pdb=" N LEU q 749 " --> pdb=" O ASP q 745 " (cutoff:3.500A) Processing helix chain 'q' and resid 765 through 784 removed outlier: 3.669A pdb=" N TYR q 769 " --> pdb=" O SER q 765 " (cutoff:3.500A) Processing helix chain 'q' and resid 785 through 806 Processing helix chain 'q' and resid 807 through 811 Processing helix chain 'q' and resid 812 through 835 Processing helix chain 'q' and resid 842 through 856 removed outlier: 3.534A pdb=" N THR q 856 " --> pdb=" O MET q 852 " (cutoff:3.500A) Processing helix chain 'q' and resid 856 through 930 removed outlier: 3.780A pdb=" N ARG q 883 " --> pdb=" O LEU q 879 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG q 884 " --> pdb=" O ARG q 880 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS q 885 " --> pdb=" O THR q 881 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU q 917 " --> pdb=" O ILE q 913 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU q 918 " --> pdb=" O LYS q 914 " (cutoff:3.500A) Processing helix chain 'r' and resid 197 through 204 removed outlier: 3.802A pdb=" N ILE r 204 " --> pdb=" O ASP r 200 " (cutoff:3.500A) Processing helix chain 'r' and resid 207 through 215 Processing helix chain 'r' and resid 219 through 225 Processing helix chain 'r' and resid 287 through 289 No H-bonds generated for 'chain 'r' and resid 287 through 289' Processing helix chain 'r' and resid 295 through 310 Processing helix chain 'r' and resid 315 through 332 Processing helix chain 'r' and resid 335 through 350 Processing helix chain 'r' and resid 353 through 374 Processing helix chain 'r' and resid 378 through 391 removed outlier: 3.610A pdb=" N ARG r 382 " --> pdb=" O GLU r 378 " (cutoff:3.500A) Processing helix chain 'r' and resid 398 through 433 removed outlier: 3.829A pdb=" N ARG r 420 " --> pdb=" O ASN r 416 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU r 428 " --> pdb=" O MET r 424 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS r 429 " --> pdb=" O ALA r 425 " (cutoff:3.500A) Processing helix chain 'r' and resid 486 through 490 Processing helix chain 'r' and resid 492 through 497 Processing helix chain 'r' and resid 498 through 505 Processing helix chain 'u' and resid 122 through 129 Processing helix chain 'u' and resid 135 through 149 Processing helix chain 'u' and resid 228 through 242 removed outlier: 3.625A pdb=" N GLN u 242 " --> pdb=" O LEU u 238 " (cutoff:3.500A) Processing helix chain 'u' and resid 258 through 282 Processing helix chain 'v' and resid 32 through 35 Processing helix chain 'v' and resid 36 through 45 Processing helix chain 'v' and resid 47 through 58 Processing helix chain 'v' and resid 64 through 71 removed outlier: 3.573A pdb=" N ASP v 68 " --> pdb=" O GLU v 65 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY v 69 " --> pdb=" O THR v 66 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP v 71 " --> pdb=" O ASP v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 73 through 77 removed outlier: 3.609A pdb=" N ILE v 77 " --> pdb=" O TYR v 74 " (cutoff:3.500A) Processing helix chain 'v' and resid 85 through 94 Processing helix chain 'v' and resid 103 through 109 Processing helix chain 'v' and resid 158 through 172 Processing helix chain 'v' and resid 178 through 185 Processing helix chain 'v' and resid 218 through 221 Processing helix chain 'v' and resid 225 through 233 Processing helix chain 'v' and resid 244 through 249 Processing helix chain 'v' and resid 271 through 284 Processing helix chain 'v' and resid 345 through 347 No H-bonds generated for 'chain 'v' and resid 345 through 347' Processing helix chain 'v' and resid 348 through 353 Processing helix chain 'v' and resid 368 through 380 Processing helix chain 'x' and resid 136 through 145 Processing helix chain 'x' and resid 153 through 157 removed outlier: 4.066A pdb=" N LEU x 156 " --> pdb=" O ASN x 153 " (cutoff:3.500A) Processing helix chain 'x' and resid 164 through 175 Processing helix chain 'x' and resid 224 through 230 Processing helix chain 'x' and resid 275 through 280 removed outlier: 3.547A pdb=" N TYR x 278 " --> pdb=" O LYS x 275 " (cutoff:3.500A) Processing helix chain 'x' and resid 290 through 295 removed outlier: 3.648A pdb=" N GLN x 293 " --> pdb=" O LYS x 290 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS x 295 " --> pdb=" O TRP x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 301 through 309 Processing helix chain 'x' and resid 322 through 327 Processing helix chain 'x' and resid 341 through 361 removed outlier: 4.390A pdb=" N GLN x 345 " --> pdb=" O PHE x 341 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 56 removed outlier: 3.713A pdb=" N LEU a 48 " --> pdb=" O GLY a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 76 Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 25 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.839A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.553A pdb=" N GLN b 93 " --> pdb=" O ALA b 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 17 through 21 removed outlier: 3.509A pdb=" N ALA c 21 " --> pdb=" O ARG c 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 17 through 21' Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.855A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.411A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 81 Processing helix chain 'd' and resid 87 through 99 Processing helix chain 'd' and resid 100 through 121 removed outlier: 3.537A pdb=" N ALA d 121 " --> pdb=" O LYS d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 76 Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 131 Processing helix chain 'f' and resid 25 through 29 removed outlier: 3.612A pdb=" N ILE f 29 " --> pdb=" O ILE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 Processing helix chain 'f' and resid 82 through 94 removed outlier: 3.637A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 46 through 73 removed outlier: 3.624A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 81 Processing helix chain 'h' and resid 87 through 99 Processing helix chain 'h' and resid 100 through 121 Processing helix chain 'j' and resid 483 through 511 Processing helix chain 'j' and resid 512 through 517 Processing helix chain 'j' and resid 534 through 538 Processing helix chain 'j' and resid 624 through 653 Processing helix chain 'j' and resid 780 through 806 Processing helix chain 'j' and resid 816 through 820 Processing helix chain 'j' and resid 890 through 892 No H-bonds generated for 'chain 'j' and resid 890 through 892' Processing helix chain 'j' and resid 893 through 904 Processing helix chain 'j' and resid 916 through 927 removed outlier: 3.862A pdb=" N LYS j 922 " --> pdb=" O GLY j 918 " (cutoff:3.500A) Processing helix chain 'j' and resid 927 through 935 removed outlier: 3.547A pdb=" N GLY j 935 " --> pdb=" O PHE j 931 " (cutoff:3.500A) Processing helix chain 'k' and resid 83 through 97 removed outlier: 4.392A pdb=" N GLN k 87 " --> pdb=" O GLN k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 202 through 213 Processing helix chain 'k' and resid 313 through 321 Processing helix chain 'k' and resid 334 through 347 Processing helix chain 'k' and resid 435 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.779A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N LYS A 88 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N ILE A 236 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 178 Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA5, first strand: chain 'A' and resid 344 through 346 removed outlier: 3.614A pdb=" N LYS A 344 " --> pdb=" O PHE B1130 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B1128 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.692A pdb=" N THR A 352 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 365 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.967A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALA A 403 " --> pdb=" O HIS A 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.328A pdb=" N VAL H 95 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE H 27 " --> pdb=" O GLN H 13 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LEU H 121 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS H 102 " --> pdb=" O TYR H 114 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER H 116 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL H 100 " --> pdb=" O SER H 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 589 through 591 removed outlier: 6.952A pdb=" N LEU A 607 " --> pdb=" O MET A 614 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 767 through 768 Processing sheet with id=AB3, first strand: chain 'A' and resid 850 through 851 removed outlier: 6.739A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 3.969A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A1118 " --> pdb=" O THR A1311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1143 through 1144 Processing sheet with id=AB7, first strand: chain 'A' and resid 1226 through 1230 removed outlier: 4.334A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR A1156 " --> pdb=" O LYS I 42 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS I 42 " --> pdb=" O TYR A1156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1444 through 1448 Processing sheet with id=AB9, first strand: chain 'B' and resid 55 through 62 removed outlier: 4.937A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE B 82 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL B 115 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AC2, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC3, first strand: chain 'B' and resid 397 through 400 Processing sheet with id=AC4, first strand: chain 'B' and resid 215 through 218 removed outlier: 3.950A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 538 removed outlier: 3.967A pdb=" N GLU B 644 " --> pdb=" O GLU B 634 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 644 through 645 current: chain 'B' and resid 740 through 741 Processing sheet with id=AC6, first strand: chain 'B' and resid 557 through 558 removed outlier: 5.659A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG B 572 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE B 619 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE B 574 " --> pdb=" O ILE B 619 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 792 through 796 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 853 through 862 current: chain 'B' and resid 947 through 956 removed outlier: 8.660A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 962 through 972 current: chain 'L' and resid 39 through 42 Processing sheet with id=AC8, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AC9, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 7.005A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 873 through 874 removed outlier: 7.424A pdb=" N LEU B 883 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.537A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD4, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id=AD5, first strand: chain 'C' and resid 6 through 12 removed outlier: 6.590A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.730A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ARG C 156 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILE C 50 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE C 158 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL C 48 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LYS C 160 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY C 162 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.671A pdb=" N GLU C 131 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.474A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 5 through 6 current: chain 'G' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 13 current: chain 'G' and resid 43 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 48 current: chain 'G' and resid 68 through 79 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE2, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.471A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.522A pdb=" N VAL E 87 " --> pdb=" O ASN E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.119A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 198 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 169 through 170 removed outlier: 5.589A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ASN G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY G 161 " --> pdb=" O PHE G 109 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE G 100 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 120 through 122 Processing sheet with id=AE7, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.735A pdb=" N ARG I 24 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE9, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF1, first strand: chain 'M' and resid 16 through 21 removed outlier: 3.902A pdb=" N VAL M 34 " --> pdb=" O THR M 21 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 18 through 19 Processing sheet with id=AF3, first strand: chain 'V' and resid 81 through 86 removed outlier: 6.968A pdb=" N GLY V 56 " --> pdb=" O VAL V 84 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 337 through 339 Processing sheet with id=AF5, first strand: chain 'W' and resid 349 through 354 removed outlier: 4.663A pdb=" N GLU W 420 " --> pdb=" O TYR W 427 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 522 through 526 removed outlier: 7.776A pdb=" N ILE W 506 " --> pdb=" O VAL W 501 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL W 501 " --> pdb=" O ILE W 506 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER W 508 " --> pdb=" O SER W 499 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 572 through 576 removed outlier: 6.041A pdb=" N ILE W 565 " --> pdb=" O ILE W 554 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE W 554 " --> pdb=" O ILE W 565 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 601 through 603 removed outlier: 6.872A pdb=" N ASP W 621 " --> pdb=" O ILE W 613 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 650 through 651 removed outlier: 3.558A pdb=" N ALA W 650 " --> pdb=" O VAL W 658 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 697 through 701 removed outlier: 6.908A pdb=" N PHE W 683 " --> pdb=" O VAL W 679 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL W 679 " --> pdb=" O PHE W 683 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE W 685 " --> pdb=" O LEU W 677 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 787 through 791 removed outlier: 4.574A pdb=" N LYS W 787 " --> pdb=" O LEU W 782 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'm' and resid 396 through 397 Processing sheet with id=AG4, first strand: chain 'm' and resid 644 through 645 Processing sheet with id=AG5, first strand: chain 'm' and resid 790 through 796 removed outlier: 3.833A pdb=" N SER m 792 " --> pdb=" O PHE m 783 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU m 766 " --> pdb=" O GLY m 824 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'm' and resid 959 through 960 removed outlier: 6.878A pdb=" N VAL m 959 " --> pdb=" O TYR m1024 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'm' and resid 1167 through 1175 removed outlier: 6.712A pdb=" N SER m1181 " --> pdb=" O ARG m1173 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VAL m1175 " --> pdb=" O TYR m1179 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N TYR m1179 " --> pdb=" O VAL m1175 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS m1230 " --> pdb=" O ALA m1189 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLN m1193 " --> pdb=" O LEU m1232 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N SER m1233 " --> pdb=" O ILE m1220 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE m1220 " --> pdb=" O SER m1233 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'm' and resid 1306 through 1310 removed outlier: 6.746A pdb=" N LEU m1328 " --> pdb=" O VAL m1324 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'm' and resid 1407 through 1412 Processing sheet with id=AH1, first strand: chain 'q' and resid 25 through 29 Processing sheet with id=AH2, first strand: chain 'r' and resid 228 through 232 removed outlier: 4.021A pdb=" N LEU r 229 " --> pdb=" O VAL r 246 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL r 246 " --> pdb=" O LEU r 229 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL r 248 " --> pdb=" O ALA r 275 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA r 275 " --> pdb=" O VAL r 248 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'r' and resid 259 through 260 Processing sheet with id=AH4, first strand: chain 'u' and resid 87 through 91 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 87 through 91 current: chain 'u' and resid 178 through 182 removed outlier: 4.925A pdb=" N TYR u 178 " --> pdb=" O MET u 189 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 185 through 193 current: chain 'u' and resid 208 through 223 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 208 through 223 current: chain 'v' and resid 263 through 268 removed outlier: 6.449A pdb=" N ILE v 264 " --> pdb=" O ASP v 302 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP v 302 " --> pdb=" O ILE v 264 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU v 266 " --> pdb=" O ILE v 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'v' and resid 295 through 309 current: chain 'v' and resid 327 through 333 Processing sheet with id=AH5, first strand: chain 'u' and resid 116 through 120 removed outlier: 4.466A pdb=" N TRP u 152 " --> pdb=" O ASN u 117 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU u 119 " --> pdb=" O TRP u 152 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N TYR u 154 " --> pdb=" O GLU u 119 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'v' and resid 29 through 30 Processing sheet with id=AH7, first strand: chain 'x' and resid 247 through 252 removed outlier: 5.934A pdb=" N ILE x 210 " --> pdb=" O VAL x 266 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE x 209 " --> pdb=" O VAL x 283 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE x 285 " --> pdb=" O ILE x 209 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL x 211 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE x 312 " --> pdb=" O VAL x 283 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE x 285 " --> pdb=" O PHE x 312 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE x 314 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY x 311 " --> pdb=" O LYS x 331 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU x 333 " --> pdb=" O GLY x 311 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR x 313 " --> pdb=" O LEU x 333 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE x 335 " --> pdb=" O TYR x 313 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS x 315 " --> pdb=" O ILE x 335 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.930A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AI1, first strand: chain 'b' and resid 96 through 98 removed outlier: 6.609A pdb=" N THR b 96 " --> pdb=" O THR g 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.627A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AI4, first strand: chain 'c' and resid 101 through 102 removed outlier: 7.020A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.593A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AI7, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.381A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AI9, first strand: chain 'j' and resid 548 through 550 Processing sheet with id=AJ1, first strand: chain 'j' and resid 572 through 580 removed outlier: 5.601A pdb=" N ARG j 616 " --> pdb=" O PHE j 590 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU k 122 " --> pdb=" O GLU k 133 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU k 133 " --> pdb=" O LEU k 122 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE k 124 " --> pdb=" O ALA k 131 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 129 through 135 current: chain 'k' and resid 149 through 154 removed outlier: 5.568A pdb=" N VAL k 172 " --> pdb=" O LEU k 154 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'j' and resid 707 through 711 removed outlier: 6.519A pdb=" N LEU j 689 " --> pdb=" O GLU j 672 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU j 672 " --> pdb=" O LEU j 689 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE j 691 " --> pdb=" O LYS j 670 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS j 670 " --> pdb=" O ILE j 691 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N ASN j 673 " --> pdb=" O GLU j 754 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU j 754 " --> pdb=" O ASN j 673 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N LYS j 745 " --> pdb=" O THR j 737 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N THR j 737 " --> pdb=" O LYS j 745 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE j 747 " --> pdb=" O LEU j 735 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE j 730 " --> pdb=" O PHE j 720 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE j 720 " --> pdb=" O ILE j 730 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N HIS j 732 " --> pdb=" O LEU j 718 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU j 718 " --> pdb=" O HIS j 732 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N HIS j 734 " --> pdb=" O LYS j 716 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'j' and resid 821 through 823 Processing sheet with id=AJ4, first strand: chain 'j' and resid 884 through 889 removed outlier: 5.885A pdb=" N PHE j 870 " --> pdb=" O THR j 888 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP j 871 " --> pdb=" O LEU j 860 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU j 860 " --> pdb=" O ASP j 871 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL j 873 " --> pdb=" O ALA j 858 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA j 858 " --> pdb=" O VAL j 873 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL j 875 " --> pdb=" O GLU j 856 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'k' and resid 44 through 47 removed outlier: 5.377A pdb=" N GLY k 18 " --> pdb=" O THR k 8 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL k 4 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 10.284A pdb=" N THR k 8 " --> pdb=" O PHE k 80 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N PHE k 80 " --> pdb=" O THR k 8 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TRP k 63 " --> pdb=" O GLY k 79 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'k' and resid 253 through 258 removed outlier: 3.591A pdb=" N TYR k 253 " --> pdb=" O GLY k 250 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY k 235 " --> pdb=" O LEU k 229 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU k 229 " --> pdb=" O GLY k 235 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N PHE k 237 " --> pdb=" O ASP k 227 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP k 227 " --> pdb=" O PHE k 237 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL k 223 " --> pdb=" O MET k 241 " (cutoff:3.500A) removed outlier: 13.055A pdb=" N ASP k 227 " --> pdb=" O ASP k 301 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N ASP k 301 " --> pdb=" O ASP k 227 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU k 229 " --> pdb=" O GLN k 299 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL k 297 " --> pdb=" O LEU k 231 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N ARG k 292 " --> pdb=" O PRO k 284 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG k 264 " --> pdb=" O GLN k 281 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP k 283 " --> pdb=" O VAL k 262 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL k 262 " --> pdb=" O ASP k 283 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N ILE k 351 " --> pdb=" O LEU k 263 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE k 265 " --> pdb=" O ILE k 351 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'k' and resid 305 through 309 removed outlier: 5.420A pdb=" N LEU k 306 " --> pdb=" O THR k 331 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR k 331 " --> pdb=" O LEU k 306 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'k' and resid 391 through 394 removed outlier: 8.440A pdb=" N ASN k 366 " --> pdb=" O ILE k 431 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE k 431 " --> pdb=" O ASN k 366 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN k 430 " --> pdb=" O PHE k 415 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N PHE k 415 " --> pdb=" O ASN k 430 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LYS k 451 " --> pdb=" O ILE k 399 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL k 401 " --> pdb=" O LYS k 451 " (cutoff:3.500A) 3757 hydrogen bonds defined for protein. 10692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 321 hydrogen bonds 642 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 214 stacking parallelities Total time for adding SS restraints: 42.77 Time building geometry restraints manager: 30.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 18394 1.33 - 1.45: 18942 1.45 - 1.58: 45750 1.58 - 1.70: 517 1.70 - 1.82: 517 Bond restraints: 84120 Sorted by residual: bond pdb=" C1' DA T -33 " pdb=" N9 DA T -33 " ideal model delta sigma weight residual 1.460 1.358 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C1' DG T -53 " pdb=" N9 DG T -53 " ideal model delta sigma weight residual 1.460 1.360 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C1' DG N 50 " pdb=" N9 DG N 50 " ideal model delta sigma weight residual 1.460 1.361 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C1' DG T -37 " pdb=" N9 DG T -37 " ideal model delta sigma weight residual 1.460 1.363 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C1' DG T -34 " pdb=" N9 DG T -34 " ideal model delta sigma weight residual 1.460 1.363 0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 84115 not shown) Histogram of bond angle deviations from ideal: 97.04 - 104.70: 2040 104.70 - 112.35: 43183 112.35 - 120.01: 32550 120.01 - 127.67: 35824 127.67 - 135.32: 1071 Bond angle restraints: 114668 Sorted by residual: angle pdb=" N PRO j 964 " pdb=" CA PRO j 964 " pdb=" CB PRO j 964 " ideal model delta sigma weight residual 103.25 110.90 -7.65 1.05e+00 9.07e-01 5.30e+01 angle pdb=" N VAL A1001 " pdb=" CA VAL A1001 " pdb=" C VAL A1001 " ideal model delta sigma weight residual 112.96 107.17 5.79 1.00e+00 1.00e+00 3.35e+01 angle pdb=" O3' DG T -1 " pdb=" C3' DG T -1 " pdb=" C2' DG T -1 " ideal model delta sigma weight residual 111.50 104.20 7.30 1.50e+00 4.44e-01 2.37e+01 angle pdb=" CA GLY k 59 " pdb=" C GLY k 59 " pdb=" N TYR k 60 " ideal model delta sigma weight residual 114.80 118.98 -4.18 1.04e+00 9.25e-01 1.61e+01 angle pdb=" OE1 GLN k 288 " pdb=" CD GLN k 288 " pdb=" NE2 GLN k 288 " ideal model delta sigma weight residual 122.60 118.61 3.99 1.00e+00 1.00e+00 1.60e+01 ... (remaining 114663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 46977 23.47 - 46.95: 3071 46.95 - 70.42: 736 70.42 - 93.90: 75 93.90 - 117.37: 3 Dihedral angle restraints: 50862 sinusoidal: 22907 harmonic: 27955 Sorted by residual: dihedral pdb=" O4' C P -4 " pdb=" C1' C P -4 " pdb=" N1 C P -4 " pdb=" C2 C P -4 " ideal model delta sinusoidal sigma weight residual 232.00 116.89 115.11 1 1.70e+01 3.46e-03 4.73e+01 dihedral pdb=" CA TYR A 466 " pdb=" C TYR A 466 " pdb=" N SER A 467 " pdb=" CA SER A 467 " ideal model delta harmonic sigma weight residual -180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" O4' C P -5 " pdb=" C1' C P -5 " pdb=" N1 C P -5 " pdb=" C2 C P -5 " ideal model delta sinusoidal sigma weight residual -128.00 -58.99 -69.01 1 1.70e+01 3.46e-03 2.13e+01 ... (remaining 50859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 10752 0.064 - 0.128: 1812 0.128 - 0.191: 177 0.191 - 0.255: 25 0.255 - 0.319: 4 Chirality restraints: 12770 Sorted by residual: chirality pdb=" CA ASP k 72 " pdb=" N ASP k 72 " pdb=" C ASP k 72 " pdb=" CB ASP k 72 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB THR k 115 " pdb=" CA THR k 115 " pdb=" OG1 THR k 115 " pdb=" CG2 THR k 115 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA TYR j 908 " pdb=" N TYR j 908 " pdb=" C TYR j 908 " pdb=" CB TYR j 908 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 12767 not shown) Planarity restraints: 13944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG T 11 " -0.276 2.00e-02 2.50e+03 1.20e-01 4.31e+02 pdb=" N9 DG T 11 " 0.009 2.00e-02 2.50e+03 pdb=" C8 DG T 11 " 0.155 2.00e-02 2.50e+03 pdb=" N7 DG T 11 " 0.127 2.00e-02 2.50e+03 pdb=" C5 DG T 11 " 0.037 2.00e-02 2.50e+03 pdb=" C6 DG T 11 " -0.059 2.00e-02 2.50e+03 pdb=" O6 DG T 11 " -0.195 2.00e-02 2.50e+03 pdb=" N1 DG T 11 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DG T 11 " 0.039 2.00e-02 2.50e+03 pdb=" N2 DG T 11 " 0.082 2.00e-02 2.50e+03 pdb=" N3 DG T 11 " 0.048 2.00e-02 2.50e+03 pdb=" C4 DG T 11 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC N -9 " 0.197 2.00e-02 2.50e+03 8.92e-02 1.79e+02 pdb=" N1 DC N -9 " -0.099 2.00e-02 2.50e+03 pdb=" C2 DC N -9 " -0.044 2.00e-02 2.50e+03 pdb=" O2 DC N -9 " -0.056 2.00e-02 2.50e+03 pdb=" N3 DC N -9 " 0.014 2.00e-02 2.50e+03 pdb=" C4 DC N -9 " 0.025 2.00e-02 2.50e+03 pdb=" N4 DC N -9 " 0.088 2.00e-02 2.50e+03 pdb=" C5 DC N -9 " -0.035 2.00e-02 2.50e+03 pdb=" C6 DC N -9 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT N -17 " 0.136 2.00e-02 2.50e+03 7.68e-02 1.48e+02 pdb=" N1 DT N -17 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT N -17 " -0.026 2.00e-02 2.50e+03 pdb=" O2 DT N -17 " -0.130 2.00e-02 2.50e+03 pdb=" N3 DT N -17 " 0.015 2.00e-02 2.50e+03 pdb=" C4 DT N -17 " 0.030 2.00e-02 2.50e+03 pdb=" O4 DT N -17 " 0.110 2.00e-02 2.50e+03 pdb=" C5 DT N -17 " -0.036 2.00e-02 2.50e+03 pdb=" C7 DT N -17 " -0.080 2.00e-02 2.50e+03 pdb=" C6 DT N -17 " -0.039 2.00e-02 2.50e+03 ... (remaining 13941 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 599 2.59 - 3.17: 67236 3.17 - 3.75: 128988 3.75 - 4.32: 179153 4.32 - 4.90: 292360 Nonbonded interactions: 668336 Sorted by model distance: nonbonded pdb=" OD1 ASP A 484 " pdb="MG MG A1803 " model vdw 2.018 2.170 nonbonded pdb=" OG1 THR K 57 " pdb=" OE1 GLN K 76 " model vdw 2.167 2.440 nonbonded pdb=" OP1 A P 11 " pdb="MG MG A1803 " model vdw 2.170 2.170 nonbonded pdb=" O ILE u 145 " pdb=" OG1 THR u 149 " model vdw 2.173 2.440 nonbonded pdb=" OD2 ASP E 47 " pdb=" NE2 GLN E 53 " model vdw 2.191 2.520 ... (remaining 668331 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'a' selection = (chain 'e' and resid 43 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 16 through 111) } ncs_group { reference = (chain 'd' and resid 31 through 121) selection = (chain 'h' and resid 31 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 6.880 Check model and map are aligned: 0.970 Set scattering table: 0.600 Process input model: 212.410 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 226.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 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 : 0.006 0.102 84120 Z= 0.383 Angle : 0.720 9.664 114668 Z= 0.450 Chirality : 0.048 0.319 12770 Planarity : 0.006 0.247 13944 Dihedral : 15.808 117.373 32744 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.49 % Favored : 97.43 % Rotamer: Outliers : 0.05 % Allowed : 0.27 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 1.23 (0.09), residues: 9441 helix: 1.90 (0.08), residues: 4115 sheet: 0.33 (0.14), residues: 1388 loop : -0.09 (0.10), residues: 3938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.003 TRP k 56 HIS 0.027 0.001 HIS j 692 PHE 0.069 0.003 PHE k 300 TYR 0.081 0.002 TYR k 60 ARG 0.022 0.001 ARG j 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 906 time to evaluate : 7.462 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: A 535 MET cc_start: 0.8690 (ttt) cc_final: 0.8480 (ttp) REVERT: A 548 MET cc_start: 0.8751 (mtm) cc_final: 0.8482 (mtp) REVERT: A 635 MET cc_start: 0.8079 (tpt) cc_final: 0.7874 (tpp) REVERT: A 903 MET cc_start: 0.8471 (mmt) cc_final: 0.8160 (mmp) REVERT: A 1266 ILE cc_start: 0.9594 (mt) cc_final: 0.9308 (tp) REVERT: A 1314 ILE cc_start: 0.8560 (pt) cc_final: 0.8232 (pt) REVERT: A 1371 MET cc_start: 0.8571 (mtm) cc_final: 0.8202 (mtm) REVERT: A 1385 MET cc_start: 0.8962 (tmm) cc_final: 0.8717 (ttm) REVERT: B 349 LEU cc_start: 0.9077 (tp) cc_final: 0.8739 (tt) REVERT: B 379 LEU cc_start: 0.9651 (mt) cc_final: 0.9356 (pp) REVERT: B 789 MET cc_start: 0.8658 (mmt) cc_final: 0.8181 (mmt) REVERT: B 839 MET cc_start: 0.8578 (ptp) cc_final: 0.8366 (ptp) REVERT: B 1082 MET cc_start: 0.8283 (tpp) cc_final: 0.8031 (mmm) REVERT: B 1098 MET cc_start: 0.8510 (mtt) cc_final: 0.8277 (mtt) REVERT: B 1152 MET cc_start: 0.8649 (mmm) cc_final: 0.8115 (mmm) REVERT: C 32 LEU cc_start: 0.9274 (tp) cc_final: 0.8767 (tt) REVERT: C 36 MET cc_start: 0.8264 (mtm) cc_final: 0.7794 (mtm) REVERT: E 138 ASP cc_start: 0.8565 (p0) cc_final: 0.8339 (p0) REVERT: G 44 TYR cc_start: 0.7687 (m-80) cc_final: 0.7377 (m-10) REVERT: G 158 TYR cc_start: 0.7981 (m-80) cc_final: 0.7189 (m-80) REVERT: I 20 LYS cc_start: 0.7383 (mttt) cc_final: 0.6831 (ttpt) REVERT: J 35 LEU cc_start: 0.9194 (mt) cc_final: 0.8960 (mp) REVERT: K 36 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7139 (mm-30) REVERT: M 53 ASN cc_start: 0.7490 (m-40) cc_final: 0.6722 (t0) REVERT: V 42 ASP cc_start: 0.7571 (p0) cc_final: 0.7368 (p0) REVERT: W 782 LEU cc_start: 0.8985 (mt) cc_final: 0.8618 (mp) REVERT: m 513 ARG cc_start: 0.6048 (mmt180) cc_final: 0.5650 (ppt170) REVERT: m 943 ILE cc_start: 0.8743 (mt) cc_final: 0.8299 (mt) REVERT: m 966 ARG cc_start: 0.5074 (mtm-85) cc_final: 0.4424 (tpm170) REVERT: m 1098 PHE cc_start: 0.8026 (t80) cc_final: 0.7721 (m-10) REVERT: q 299 MET cc_start: 0.3879 (mmp) cc_final: 0.3640 (tpp) REVERT: q 405 MET cc_start: 0.7076 (ttp) cc_final: 0.6721 (tmm) REVERT: q 547 MET cc_start: 0.1938 (ttm) cc_final: 0.1117 (tpp) REVERT: q 744 MET cc_start: 0.8287 (mmm) cc_final: 0.7964 (ppp) REVERT: q 773 LEU cc_start: 0.8597 (tp) cc_final: 0.8108 (tp) REVERT: q 852 MET cc_start: 0.4793 (tmm) cc_final: 0.4523 (mtm) REVERT: q 906 LYS cc_start: 0.9635 (mttt) cc_final: 0.9359 (mttt) REVERT: r 282 MET cc_start: 0.5734 (mtt) cc_final: 0.4987 (mmt) REVERT: r 363 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8594 (tm-30) REVERT: r 404 MET cc_start: 0.8483 (mtt) cc_final: 0.8276 (mtm) REVERT: r 424 MET cc_start: 0.7700 (mtt) cc_final: 0.7420 (mtt) REVERT: u 124 ARG cc_start: 0.8551 (mpp80) cc_final: 0.8052 (tpp-160) REVERT: u 195 ASP cc_start: 0.7705 (m-30) cc_final: 0.7182 (t70) REVERT: v 304 ASP cc_start: 0.6197 (t70) cc_final: 0.5961 (p0) REVERT: x 288 THR cc_start: 0.8688 (p) cc_final: 0.8471 (t) REVERT: x 291 ASP cc_start: 0.7957 (t0) cc_final: 0.7599 (p0) REVERT: e 83 ARG cc_start: 0.6505 (mtt180) cc_final: 0.6275 (ttp80) REVERT: j 487 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5993 (mm-30) REVERT: j 534 ARG cc_start: 0.2494 (mtt180) cc_final: 0.2061 (tpt170) REVERT: j 595 MET cc_start: 0.0238 (ttp) cc_final: -0.0206 (tpt) REVERT: j 652 MET cc_start: -0.1638 (mmt) cc_final: -0.2432 (tmm) REVERT: j 740 MET cc_start: 0.1599 (mmm) cc_final: 0.0633 (mtm) REVERT: j 752 TYR cc_start: 0.3454 (p90) cc_final: 0.1937 (p90) REVERT: k 32 SER cc_start: 0.5276 (t) cc_final: 0.5063 (p) REVERT: k 361 MET cc_start: 0.2591 (mmm) cc_final: 0.1869 (ttt) outliers start: 4 outliers final: 0 residues processed: 910 average time/residue: 0.7902 time to fit residues: 1217.5370 Evaluate side-chains 426 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 7.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 814 optimal weight: 6.9990 chunk 731 optimal weight: 40.0000 chunk 405 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 493 optimal weight: 40.0000 chunk 390 optimal weight: 40.0000 chunk 756 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 459 optimal weight: 9.9990 chunk 562 optimal weight: 40.0000 chunk 876 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1112 ASN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 GLN ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN D 172 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 ASN I 46 HIS ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 HIS ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 425 HIS m 661 GLN m 816 ASN m1004 HIS ** n 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 105 HIS q 319 ASN ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 855 ASN ** u 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 296 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 68 GLN e 93 GLN j 498 GLN j 578 ASN ** j 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 885 HIS k 127 ASN k 446 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 84120 Z= 0.393 Angle : 0.632 9.871 114668 Z= 0.337 Chirality : 0.043 0.235 12770 Planarity : 0.005 0.047 13944 Dihedral : 16.252 116.838 13389 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 1.34 (0.09), residues: 9441 helix: 1.98 (0.08), residues: 4159 sheet: 0.30 (0.13), residues: 1399 loop : -0.01 (0.10), residues: 3883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP n 284 HIS 0.013 0.001 HIS j 706 PHE 0.044 0.002 PHE j 939 TYR 0.023 0.002 TYR B 479 ARG 0.009 0.001 ARG q 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 500 time to evaluate : 7.387 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: A 548 MET cc_start: 0.8863 (mtm) cc_final: 0.8183 (mtp) REVERT: A 606 MET cc_start: 0.8595 (tpp) cc_final: 0.8289 (tpp) REVERT: A 709 MET cc_start: 0.8204 (ttp) cc_final: 0.7775 (ttm) REVERT: A 791 ASP cc_start: 0.7388 (m-30) cc_final: 0.7187 (m-30) REVERT: A 903 MET cc_start: 0.8713 (mmt) cc_final: 0.8187 (mmm) REVERT: A 1065 MET cc_start: 0.8837 (mmm) cc_final: 0.8589 (mmm) REVERT: A 1266 ILE cc_start: 0.9614 (mt) cc_final: 0.9199 (tp) REVERT: A 1371 MET cc_start: 0.8554 (mtm) cc_final: 0.8081 (mtm) REVERT: A 1447 MET cc_start: 0.8831 (mmm) cc_final: 0.8338 (mmm) REVERT: B 302 MET cc_start: 0.7852 (ptt) cc_final: 0.7334 (ptt) REVERT: B 305 MET cc_start: 0.8319 (mmm) cc_final: 0.8049 (mmm) REVERT: B 349 LEU cc_start: 0.9332 (tp) cc_final: 0.9072 (tt) REVERT: B 789 MET cc_start: 0.8757 (mmt) cc_final: 0.8508 (mmt) REVERT: B 839 MET cc_start: 0.8459 (ptp) cc_final: 0.8207 (ptp) REVERT: B 1152 MET cc_start: 0.8945 (mmm) cc_final: 0.8352 (mmm) REVERT: C 36 MET cc_start: 0.8584 (mtm) cc_final: 0.8133 (mtp) REVERT: C 60 GLU cc_start: 0.7484 (pm20) cc_final: 0.7076 (pm20) REVERT: E 57 MET cc_start: 0.8947 (mtm) cc_final: 0.8545 (mtm) REVERT: E 138 ASP cc_start: 0.8812 (p0) cc_final: 0.8500 (p0) REVERT: G 44 TYR cc_start: 0.7816 (m-80) cc_final: 0.7511 (m-10) REVERT: I 20 LYS cc_start: 0.7658 (mttt) cc_final: 0.7089 (ttpt) REVERT: I 33 ASP cc_start: 0.8553 (t0) cc_final: 0.8333 (t0) REVERT: I 94 ASP cc_start: 0.8517 (t0) cc_final: 0.8017 (p0) REVERT: m 513 ARG cc_start: 0.6028 (mmt180) cc_final: 0.5251 (ppt170) REVERT: m 966 ARG cc_start: 0.5003 (mtm-85) cc_final: 0.4482 (tpm170) REVERT: m 1098 PHE cc_start: 0.7995 (t80) cc_final: 0.7601 (m-10) REVERT: m 1180 MET cc_start: 0.6716 (ppp) cc_final: 0.6459 (mmt) REVERT: q 547 MET cc_start: 0.1644 (ttm) cc_final: 0.1048 (tpp) REVERT: q 744 MET cc_start: 0.8259 (mmm) cc_final: 0.7803 (ppp) REVERT: q 766 MET cc_start: 0.9115 (pmm) cc_final: 0.8760 (pmm) REVERT: q 852 MET cc_start: 0.5389 (tmm) cc_final: 0.5188 (mtt) REVERT: r 282 MET cc_start: 0.5857 (mtt) cc_final: 0.4860 (mmt) REVERT: r 424 MET cc_start: 0.7412 (mtt) cc_final: 0.7146 (mtt) REVERT: u 124 ARG cc_start: 0.8647 (mpp80) cc_final: 0.8022 (tpp-160) REVERT: v 362 MET cc_start: 0.7528 (mmp) cc_final: 0.6944 (ttm) REVERT: x 339 GLU cc_start: 0.7838 (mp0) cc_final: 0.7629 (mp0) REVERT: j 487 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6458 (mm-30) REVERT: j 534 ARG cc_start: 0.2886 (mtt180) cc_final: 0.2350 (tpt170) REVERT: j 595 MET cc_start: 0.0389 (ttp) cc_final: -0.0351 (tpt) REVERT: j 652 MET cc_start: -0.1518 (mmt) cc_final: -0.2389 (tmm) REVERT: j 740 MET cc_start: 0.1603 (mmm) cc_final: 0.0466 (mtm) REVERT: j 921 MET cc_start: 0.2146 (tpt) cc_final: 0.1305 (ptm) REVERT: k 32 SER cc_start: 0.4763 (t) cc_final: 0.4549 (p) REVERT: k 361 MET cc_start: 0.2756 (mmm) cc_final: 0.2036 (ttt) outliers start: 5 outliers final: 3 residues processed: 504 average time/residue: 0.7587 time to fit residues: 661.7974 Evaluate side-chains 348 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 345 time to evaluate : 7.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 487 optimal weight: 30.0000 chunk 271 optimal weight: 3.9990 chunk 729 optimal weight: 30.0000 chunk 596 optimal weight: 8.9990 chunk 241 optimal weight: 0.8980 chunk 877 optimal weight: 40.0000 chunk 948 optimal weight: 0.9980 chunk 781 optimal weight: 7.9990 chunk 870 optimal weight: 50.0000 chunk 299 optimal weight: 5.9990 chunk 704 optimal weight: 20.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 HIS ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 283 ASN ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 512 HIS W 694 ASN m 553 HIS m 661 GLN m 819 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 615 HIS ** u 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 209 GLN ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 658 GLN k 102 HIS k 127 ASN ** k 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 84120 Z= 0.216 Angle : 0.508 9.162 114668 Z= 0.275 Chirality : 0.040 0.168 12770 Planarity : 0.004 0.075 13944 Dihedral : 16.159 117.720 13389 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 1.49 (0.09), residues: 9441 helix: 2.14 (0.08), residues: 4164 sheet: 0.29 (0.13), residues: 1388 loop : 0.07 (0.10), residues: 3889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP k 56 HIS 0.009 0.001 HIS d 79 PHE 0.030 0.001 PHE B 278 TYR 0.024 0.001 TYR k 253 ARG 0.023 0.000 ARG V 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 460 time to evaluate : 7.484 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: A 122 MET cc_start: 0.7899 (ttm) cc_final: 0.7679 (ttm) REVERT: A 548 MET cc_start: 0.8898 (mtm) cc_final: 0.8206 (mtp) REVERT: A 709 MET cc_start: 0.8142 (ttp) cc_final: 0.7882 (ttm) REVERT: A 839 GLN cc_start: 0.8861 (tt0) cc_final: 0.8628 (tp40) REVERT: A 903 MET cc_start: 0.8715 (mmt) cc_final: 0.8216 (mmm) REVERT: A 1112 ASN cc_start: 0.8639 (p0) cc_final: 0.8357 (p0) REVERT: A 1209 LEU cc_start: 0.8343 (mt) cc_final: 0.8009 (mt) REVERT: A 1266 ILE cc_start: 0.9561 (mt) cc_final: 0.9278 (tp) REVERT: A 1270 MET cc_start: 0.8217 (mmp) cc_final: 0.8016 (mmp) REVERT: A 1371 MET cc_start: 0.8360 (mtm) cc_final: 0.8018 (mtm) REVERT: A 1447 MET cc_start: 0.8770 (mmm) cc_final: 0.8357 (mmm) REVERT: B 302 MET cc_start: 0.7492 (ptt) cc_final: 0.7076 (ptt) REVERT: B 349 LEU cc_start: 0.9347 (tp) cc_final: 0.9105 (tt) REVERT: B 789 MET cc_start: 0.8714 (mmt) cc_final: 0.8412 (mmt) REVERT: B 999 MET cc_start: 0.8864 (mmm) cc_final: 0.8645 (mmm) REVERT: B 1082 MET cc_start: 0.8520 (mmm) cc_final: 0.7985 (tpp) REVERT: C 36 MET cc_start: 0.8635 (mtm) cc_final: 0.8371 (mtm) REVERT: C 52 MET cc_start: 0.8867 (ppp) cc_final: 0.8485 (ppp) REVERT: E 57 MET cc_start: 0.9005 (mtm) cc_final: 0.8735 (mtm) REVERT: E 138 ASP cc_start: 0.8810 (p0) cc_final: 0.8469 (p0) REVERT: H 40 LEU cc_start: 0.8826 (tp) cc_final: 0.8391 (tp) REVERT: I 20 LYS cc_start: 0.7645 (mttt) cc_final: 0.7099 (ttpt) REVERT: I 33 ASP cc_start: 0.8509 (t0) cc_final: 0.8274 (t0) REVERT: I 97 MET cc_start: 0.8620 (mpp) cc_final: 0.8408 (mpp) REVERT: J 26 GLU cc_start: 0.8712 (pt0) cc_final: 0.8469 (pt0) REVERT: W 781 GLU cc_start: 0.8008 (pp20) cc_final: 0.7791 (pp20) REVERT: m 966 ARG cc_start: 0.4876 (mtm-85) cc_final: 0.4449 (tpm170) REVERT: m 1098 PHE cc_start: 0.7994 (t80) cc_final: 0.7532 (m-10) REVERT: m 1166 MET cc_start: 0.5005 (mtm) cc_final: 0.4599 (tpt) REVERT: q 405 MET cc_start: 0.6383 (tmm) cc_final: 0.6112 (tmm) REVERT: q 547 MET cc_start: 0.1543 (ttm) cc_final: 0.0968 (tpp) REVERT: q 744 MET cc_start: 0.8196 (mmm) cc_final: 0.7759 (ppp) REVERT: q 766 MET cc_start: 0.9111 (pmm) cc_final: 0.8773 (pmm) REVERT: q 873 MET cc_start: 0.8256 (mpp) cc_final: 0.7943 (mmt) REVERT: r 216 TYR cc_start: 0.5288 (p90) cc_final: 0.4909 (p90) REVERT: r 282 MET cc_start: 0.6408 (mtt) cc_final: 0.5395 (mmt) REVERT: r 424 MET cc_start: 0.7392 (mtt) cc_final: 0.7154 (mtt) REVERT: u 124 ARG cc_start: 0.8646 (mpp80) cc_final: 0.7862 (tpp-160) REVERT: v 351 MET cc_start: -0.1513 (ppp) cc_final: -0.1858 (tmm) REVERT: v 362 MET cc_start: 0.7531 (mmp) cc_final: 0.6879 (ttm) REVERT: x 209 ILE cc_start: 0.8970 (mm) cc_final: 0.8723 (mt) REVERT: x 293 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7924 (mp10) REVERT: j 487 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6464 (mm-30) REVERT: j 534 ARG cc_start: 0.2880 (mtt180) cc_final: 0.2338 (tpt170) REVERT: j 595 MET cc_start: 0.0015 (ttp) cc_final: -0.0653 (tpt) REVERT: j 652 MET cc_start: -0.1459 (mmt) cc_final: -0.2389 (tmm) REVERT: j 740 MET cc_start: 0.1593 (mmm) cc_final: 0.0488 (mtm) REVERT: j 921 MET cc_start: 0.2662 (tpt) cc_final: 0.1947 (ptm) REVERT: k 361 MET cc_start: 0.2584 (mmm) cc_final: 0.1914 (ttt) outliers start: 0 outliers final: 0 residues processed: 460 average time/residue: 0.7477 time to fit residues: 602.3177 Evaluate side-chains 349 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 7.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 867 optimal weight: 50.0000 chunk 660 optimal weight: 40.0000 chunk 455 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 418 optimal weight: 6.9990 chunk 589 optimal weight: 50.0000 chunk 881 optimal weight: 9.9990 chunk 932 optimal weight: 7.9990 chunk 460 optimal weight: 40.0000 chunk 835 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 HIS ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 HIS ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 HIS C 150 HIS D 126 GLN D 172 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 HIS I 11 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 283 ASN ** W 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 433 GLN ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 661 GLN m 831 HIS m 970 HIS ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 105 HIS q 187 GLN q 363 GLN ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 133 HIS u 203 HIS ** u 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 127 ASN ** k 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 84120 Z= 0.413 Angle : 0.644 9.565 114668 Z= 0.340 Chirality : 0.043 0.193 12770 Planarity : 0.005 0.062 13944 Dihedral : 16.197 118.483 13389 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 0.01 % Allowed : 3.19 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 1.10 (0.09), residues: 9441 helix: 1.78 (0.08), residues: 4174 sheet: 0.10 (0.13), residues: 1403 loop : -0.10 (0.10), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP n 284 HIS 0.014 0.002 HIS L 55 PHE 0.032 0.002 PHE C 191 TYR 0.029 0.002 TYR B 797 ARG 0.013 0.001 ARG J 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 420 time to evaluate : 7.498 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: A 84 MET cc_start: 0.8606 (ttm) cc_final: 0.8369 (ttp) REVERT: A 548 MET cc_start: 0.8949 (mtm) cc_final: 0.8154 (mtp) REVERT: A 709 MET cc_start: 0.8304 (ttp) cc_final: 0.8006 (ttm) REVERT: A 903 MET cc_start: 0.8761 (mmt) cc_final: 0.8481 (mmt) REVERT: A 1112 ASN cc_start: 0.8825 (p0) cc_final: 0.8573 (p0) REVERT: A 1266 ILE cc_start: 0.9487 (mt) cc_final: 0.9048 (tp) REVERT: A 1270 MET cc_start: 0.8281 (mmp) cc_final: 0.8030 (mmm) REVERT: A 1371 MET cc_start: 0.8452 (mtm) cc_final: 0.8114 (mtm) REVERT: A 1447 MET cc_start: 0.8719 (mmm) cc_final: 0.8263 (mmm) REVERT: B 302 MET cc_start: 0.7829 (ptt) cc_final: 0.7404 (ptt) REVERT: B 699 MET cc_start: 0.8827 (tpt) cc_final: 0.8432 (tpp) REVERT: B 789 MET cc_start: 0.8681 (mmt) cc_final: 0.8305 (mmt) REVERT: B 1082 MET cc_start: 0.8423 (mmm) cc_final: 0.7825 (tpp) REVERT: B 1152 MET cc_start: 0.8975 (tpt) cc_final: 0.8741 (tpt) REVERT: C 36 MET cc_start: 0.8735 (mtm) cc_final: 0.8526 (mtp) REVERT: C 52 MET cc_start: 0.8734 (ppp) cc_final: 0.8088 (ppp) REVERT: D 167 LYS cc_start: 0.6150 (mmpt) cc_final: 0.5891 (mmpt) REVERT: E 122 MET cc_start: 0.7922 (ptm) cc_final: 0.7526 (tmm) REVERT: G 107 ASN cc_start: 0.9127 (p0) cc_final: 0.8754 (t0) REVERT: I 20 LYS cc_start: 0.7757 (mttt) cc_final: 0.7192 (mtpt) REVERT: I 97 MET cc_start: 0.8608 (mpp) cc_final: 0.8369 (mpp) REVERT: W 781 GLU cc_start: 0.7998 (pp20) cc_final: 0.7731 (pp20) REVERT: m 944 ASP cc_start: 0.8234 (t0) cc_final: 0.8019 (t70) REVERT: m 1098 PHE cc_start: 0.8055 (t80) cc_final: 0.7471 (m-10) REVERT: m 1166 MET cc_start: 0.5302 (mtm) cc_final: 0.4590 (tpt) REVERT: n 260 MET cc_start: 0.7777 (mtp) cc_final: 0.7576 (mtp) REVERT: q 405 MET cc_start: 0.6100 (tmm) cc_final: 0.5718 (tmm) REVERT: q 547 MET cc_start: 0.1575 (ttm) cc_final: 0.0958 (tpp) REVERT: q 744 MET cc_start: 0.8209 (mmm) cc_final: 0.7874 (tmm) REVERT: q 748 LEU cc_start: 0.7889 (tp) cc_final: 0.7678 (tp) REVERT: q 766 MET cc_start: 0.9169 (pmm) cc_final: 0.8827 (pmm) REVERT: q 873 MET cc_start: 0.8014 (mpp) cc_final: 0.7576 (mpp) REVERT: r 216 TYR cc_start: 0.5260 (p90) cc_final: 0.4833 (p90) REVERT: r 227 MET cc_start: 0.4891 (tmm) cc_final: 0.4615 (tmm) REVERT: r 282 MET cc_start: 0.6661 (mtt) cc_final: 0.5665 (mmt) REVERT: r 424 MET cc_start: 0.7369 (mtt) cc_final: 0.7099 (mtt) REVERT: u 124 ARG cc_start: 0.8479 (mpp80) cc_final: 0.7873 (tpp-160) REVERT: v 263 TRP cc_start: 0.4126 (p90) cc_final: 0.3816 (p90) REVERT: v 351 MET cc_start: -0.1360 (ppp) cc_final: -0.1566 (tmm) REVERT: v 362 MET cc_start: 0.7585 (mmp) cc_final: 0.7046 (ttm) REVERT: x 209 ILE cc_start: 0.8953 (mm) cc_final: 0.8611 (mt) REVERT: x 293 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8038 (mp10) REVERT: e 72 ARG cc_start: 0.3006 (pmt-80) cc_final: 0.2402 (tpt-90) REVERT: j 487 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6591 (mm-30) REVERT: j 534 ARG cc_start: 0.2699 (mtt180) cc_final: 0.2240 (tpt170) REVERT: j 595 MET cc_start: 0.0049 (ttp) cc_final: -0.0657 (tpt) REVERT: j 652 MET cc_start: -0.1512 (mmt) cc_final: -0.2362 (tmm) REVERT: j 740 MET cc_start: 0.1226 (mmm) cc_final: 0.0221 (mtm) REVERT: j 921 MET cc_start: 0.2681 (tpt) cc_final: 0.1938 (ptm) REVERT: k 361 MET cc_start: 0.2619 (mmm) cc_final: 0.1961 (ttt) outliers start: 1 outliers final: 0 residues processed: 421 average time/residue: 0.7742 time to fit residues: 576.7763 Evaluate side-chains 322 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 7.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 776 optimal weight: 30.0000 chunk 529 optimal weight: 40.0000 chunk 13 optimal weight: 0.9990 chunk 694 optimal weight: 50.0000 chunk 384 optimal weight: 0.9990 chunk 795 optimal weight: 30.0000 chunk 644 optimal weight: 50.0000 chunk 1 optimal weight: 2.9990 chunk 476 optimal weight: 8.9990 chunk 837 optimal weight: 8.9990 chunk 235 optimal weight: 0.0270 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 283 ASN W 433 GLN W 567 ASN W 694 ASN m 661 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 483 ASN ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 808 ASN ** q 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 261 GLN ** v 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 244 ASN v 359 HIS ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 84120 Z= 0.172 Angle : 0.496 9.758 114668 Z= 0.267 Chirality : 0.040 0.182 12770 Planarity : 0.003 0.042 13944 Dihedral : 16.105 119.411 13389 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 (0.09), residues: 9441 helix: 2.07 (0.08), residues: 4168 sheet: 0.12 (0.13), residues: 1429 loop : 0.06 (0.11), residues: 3844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP n 284 HIS 0.010 0.001 HIS q 105 PHE 0.023 0.001 PHE B1047 TYR 0.027 0.001 TYR n 263 ARG 0.008 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 7.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8602 (ttm) cc_final: 0.8311 (ttp) REVERT: A 122 MET cc_start: 0.7485 (ttm) cc_final: 0.7118 (ttm) REVERT: A 305 MET cc_start: 0.9182 (mmt) cc_final: 0.8864 (mmm) REVERT: A 548 MET cc_start: 0.8915 (mtm) cc_final: 0.8214 (mtp) REVERT: A 709 MET cc_start: 0.8273 (ttp) cc_final: 0.8009 (ttm) REVERT: A 839 GLN cc_start: 0.8794 (tt0) cc_final: 0.8586 (tp40) REVERT: A 903 MET cc_start: 0.8715 (mmt) cc_final: 0.8419 (mmt) REVERT: A 1266 ILE cc_start: 0.9495 (mt) cc_final: 0.9222 (tp) REVERT: A 1371 MET cc_start: 0.8279 (mtm) cc_final: 0.7886 (mtm) REVERT: A 1447 MET cc_start: 0.8759 (mmm) cc_final: 0.8318 (mmm) REVERT: B 302 MET cc_start: 0.7595 (ptt) cc_final: 0.7237 (ptt) REVERT: B 789 MET cc_start: 0.8470 (mmt) cc_final: 0.8116 (mmt) REVERT: B 1082 MET cc_start: 0.8455 (mmm) cc_final: 0.7846 (tpp) REVERT: C 32 LEU cc_start: 0.9280 (tt) cc_final: 0.8986 (tt) REVERT: C 36 MET cc_start: 0.8738 (mtm) cc_final: 0.8296 (mtm) REVERT: C 52 MET cc_start: 0.8860 (ppp) cc_final: 0.8399 (ppp) REVERT: D 167 LYS cc_start: 0.6134 (mmpt) cc_final: 0.5890 (mmpt) REVERT: E 122 MET cc_start: 0.7790 (ptm) cc_final: 0.7419 (tmm) REVERT: E 138 ASP cc_start: 0.8908 (p0) cc_final: 0.8562 (p0) REVERT: G 107 ASN cc_start: 0.9161 (p0) cc_final: 0.8755 (t0) REVERT: I 20 LYS cc_start: 0.7757 (mttt) cc_final: 0.7211 (mtpt) REVERT: I 61 ASP cc_start: 0.8941 (t0) cc_final: 0.8712 (t0) REVERT: J 26 GLU cc_start: 0.8729 (pt0) cc_final: 0.8450 (pt0) REVERT: L 70 ASP cc_start: 0.8592 (t0) cc_final: 0.7989 (t0) REVERT: W 422 TYR cc_start: 0.7187 (t80) cc_final: 0.6578 (t80) REVERT: m 1098 PHE cc_start: 0.8053 (t80) cc_final: 0.7455 (m-10) REVERT: q 405 MET cc_start: 0.6011 (tmm) cc_final: 0.5738 (tmm) REVERT: q 547 MET cc_start: 0.1732 (ttm) cc_final: 0.1141 (tpp) REVERT: q 744 MET cc_start: 0.8336 (mmm) cc_final: 0.7897 (ppp) REVERT: q 748 LEU cc_start: 0.7872 (tp) cc_final: 0.7632 (tp) REVERT: q 766 MET cc_start: 0.9110 (pmm) cc_final: 0.8746 (pmm) REVERT: q 873 MET cc_start: 0.8125 (mpp) cc_final: 0.7847 (mmt) REVERT: r 216 TYR cc_start: 0.5292 (p90) cc_final: 0.4738 (p90) REVERT: r 282 MET cc_start: 0.6502 (mtt) cc_final: 0.5572 (mmt) REVERT: u 124 ARG cc_start: 0.8511 (mpp80) cc_final: 0.8239 (mmm160) REVERT: u 195 ASP cc_start: 0.7719 (m-30) cc_final: 0.7314 (t70) REVERT: v 263 TRP cc_start: 0.4097 (p90) cc_final: 0.3795 (p90) REVERT: v 351 MET cc_start: -0.1528 (ppp) cc_final: -0.1881 (tmm) REVERT: x 209 ILE cc_start: 0.8887 (mm) cc_final: 0.8547 (mt) REVERT: x 293 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8026 (mp10) REVERT: e 72 ARG cc_start: 0.2917 (pmt-80) cc_final: 0.2472 (ttt180) REVERT: j 487 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6698 (mm-30) REVERT: j 534 ARG cc_start: 0.2662 (mtt180) cc_final: 0.2217 (tpt170) REVERT: j 595 MET cc_start: -0.0050 (ttp) cc_final: -0.0567 (tpt) REVERT: j 652 MET cc_start: -0.1473 (mmt) cc_final: -0.2356 (tmm) REVERT: j 683 LYS cc_start: -0.0706 (tptt) cc_final: -0.0932 (mmtt) REVERT: j 740 MET cc_start: 0.1198 (mmm) cc_final: 0.0200 (mtm) REVERT: j 921 MET cc_start: 0.2635 (tpt) cc_final: 0.1920 (ptm) REVERT: k 361 MET cc_start: 0.2799 (mmm) cc_final: 0.2131 (ttt) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.7543 time to fit residues: 577.2467 Evaluate side-chains 334 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 7.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 313 optimal weight: 0.9990 chunk 840 optimal weight: 50.0000 chunk 184 optimal weight: 4.9990 chunk 547 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 933 optimal weight: 10.0000 chunk 775 optimal weight: 50.0000 chunk 432 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 308 optimal weight: 10.0000 chunk 490 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 512 HIS m 661 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 359 HIS ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 84120 Z= 0.272 Angle : 0.533 9.368 114668 Z= 0.284 Chirality : 0.040 0.159 12770 Planarity : 0.004 0.052 13944 Dihedral : 16.037 118.442 13389 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 1.32 (0.09), residues: 9441 helix: 1.98 (0.08), residues: 4179 sheet: 0.13 (0.14), residues: 1394 loop : 0.02 (0.10), residues: 3868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP n 284 HIS 0.010 0.001 HIS q 105 PHE 0.020 0.001 PHE j 939 TYR 0.024 0.001 TYR B 797 ARG 0.011 0.000 ARG q 849 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 7.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8636 (mmt) cc_final: 0.8382 (mmt) REVERT: A 84 MET cc_start: 0.8601 (ttm) cc_final: 0.8326 (ttp) REVERT: A 122 MET cc_start: 0.7524 (ttm) cc_final: 0.7109 (ttm) REVERT: A 180 MET cc_start: 0.8718 (mtm) cc_final: 0.7815 (mpp) REVERT: A 305 MET cc_start: 0.9158 (mmt) cc_final: 0.8623 (mmm) REVERT: A 548 MET cc_start: 0.8927 (mtm) cc_final: 0.8206 (mtp) REVERT: A 709 MET cc_start: 0.8315 (ttp) cc_final: 0.8007 (ttm) REVERT: A 903 MET cc_start: 0.8772 (mmt) cc_final: 0.8477 (mmt) REVERT: A 1081 MET cc_start: 0.7708 (ptm) cc_final: 0.7208 (ptt) REVERT: A 1266 ILE cc_start: 0.9494 (mt) cc_final: 0.9147 (tp) REVERT: A 1371 MET cc_start: 0.8336 (mtm) cc_final: 0.7947 (mtm) REVERT: A 1447 MET cc_start: 0.8694 (mmm) cc_final: 0.8203 (mmm) REVERT: B 302 MET cc_start: 0.7614 (ptt) cc_final: 0.7140 (ptt) REVERT: B 789 MET cc_start: 0.8472 (mmt) cc_final: 0.8200 (mmt) REVERT: B 1082 MET cc_start: 0.8467 (mmm) cc_final: 0.7816 (tpp) REVERT: B 1136 ASP cc_start: 0.8345 (m-30) cc_final: 0.8098 (m-30) REVERT: C 32 LEU cc_start: 0.9330 (tt) cc_final: 0.9014 (tt) REVERT: C 36 MET cc_start: 0.8743 (mtm) cc_final: 0.8236 (mtm) REVERT: C 52 MET cc_start: 0.8819 (ppp) cc_final: 0.8293 (tmm) REVERT: C 244 PHE cc_start: 0.8107 (t80) cc_final: 0.7844 (t80) REVERT: D 167 LYS cc_start: 0.6257 (mmpt) cc_final: 0.5993 (mmpt) REVERT: E 122 MET cc_start: 0.7881 (ptm) cc_final: 0.7492 (tmm) REVERT: E 157 ASP cc_start: 0.7648 (p0) cc_final: 0.7434 (p0) REVERT: G 107 ASN cc_start: 0.9107 (p0) cc_final: 0.8704 (t0) REVERT: H 46 MET cc_start: 0.8614 (mmp) cc_final: 0.8327 (mmp) REVERT: I 20 LYS cc_start: 0.7816 (mttt) cc_final: 0.7228 (mtpt) REVERT: I 61 ASP cc_start: 0.9022 (t0) cc_final: 0.8756 (t0) REVERT: I 97 MET cc_start: 0.8685 (mpp) cc_final: 0.8356 (mpp) REVERT: J 26 GLU cc_start: 0.8934 (pt0) cc_final: 0.8636 (pt0) REVERT: W 781 GLU cc_start: 0.8432 (pp20) cc_final: 0.8195 (pp20) REVERT: m 1098 PHE cc_start: 0.8158 (t80) cc_final: 0.7536 (m-10) REVERT: m 1166 MET cc_start: 0.5127 (mpp) cc_final: 0.3297 (mmp) REVERT: q 405 MET cc_start: 0.6285 (tmm) cc_final: 0.6018 (tmm) REVERT: q 547 MET cc_start: 0.1808 (ttm) cc_final: 0.1199 (tpp) REVERT: q 744 MET cc_start: 0.8428 (mmm) cc_final: 0.7926 (ppp) REVERT: q 748 LEU cc_start: 0.7897 (tp) cc_final: 0.7681 (tp) REVERT: q 766 MET cc_start: 0.9089 (pmm) cc_final: 0.8765 (pmm) REVERT: q 873 MET cc_start: 0.7967 (mpp) cc_final: 0.7549 (mpp) REVERT: r 216 TYR cc_start: 0.5358 (p90) cc_final: 0.4696 (p90) REVERT: r 227 MET cc_start: 0.5033 (tmm) cc_final: 0.4774 (tmm) REVERT: r 282 MET cc_start: 0.6608 (mtt) cc_final: 0.5840 (mmt) REVERT: r 424 MET cc_start: 0.7163 (mtt) cc_final: 0.6925 (mtt) REVERT: u 124 ARG cc_start: 0.8571 (mpp80) cc_final: 0.8273 (mmm160) REVERT: u 195 ASP cc_start: 0.7757 (m-30) cc_final: 0.7337 (t70) REVERT: v 263 TRP cc_start: 0.4345 (p90) cc_final: 0.4059 (p90) REVERT: v 351 MET cc_start: -0.0926 (ppp) cc_final: -0.1242 (tmm) REVERT: x 209 ILE cc_start: 0.8884 (mm) cc_final: 0.8539 (mt) REVERT: x 293 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7995 (mp10) REVERT: j 487 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6705 (mm-30) REVERT: j 534 ARG cc_start: 0.2693 (mtt180) cc_final: 0.2237 (tpt170) REVERT: j 584 MET cc_start: 0.4638 (tpp) cc_final: 0.3336 (mmm) REVERT: j 595 MET cc_start: -0.0123 (ttp) cc_final: -0.0522 (tpt) REVERT: j 652 MET cc_start: -0.1497 (mmt) cc_final: -0.2335 (tmm) REVERT: j 683 LYS cc_start: -0.0586 (tptt) cc_final: -0.0824 (mmtt) REVERT: j 740 MET cc_start: 0.0899 (mmm) cc_final: -0.0652 (ptp) REVERT: j 921 MET cc_start: 0.3493 (tpt) cc_final: 0.2762 (ptm) REVERT: k 298 MET cc_start: 0.2320 (ttm) cc_final: 0.1677 (mpp) REVERT: k 361 MET cc_start: 0.2739 (mmm) cc_final: 0.2062 (ttt) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.7556 time to fit residues: 557.7645 Evaluate side-chains 327 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 7.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 900 optimal weight: 50.0000 chunk 105 optimal weight: 0.9990 chunk 531 optimal weight: 0.2980 chunk 681 optimal weight: 6.9990 chunk 528 optimal weight: 9.9990 chunk 785 optimal weight: 40.0000 chunk 521 optimal weight: 5.9990 chunk 930 optimal weight: 10.0000 chunk 582 optimal weight: 30.0000 chunk 567 optimal weight: 50.0000 chunk 429 optimal weight: 20.0000 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1211 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 512 HIS m 464 GLN m 661 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 359 HIS v 370 GLN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 84120 Z= 0.244 Angle : 0.517 9.254 114668 Z= 0.276 Chirality : 0.040 0.284 12770 Planarity : 0.003 0.041 13944 Dihedral : 15.993 117.877 13389 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 1.31 (0.09), residues: 9441 helix: 1.99 (0.08), residues: 4170 sheet: 0.14 (0.14), residues: 1375 loop : -0.01 (0.10), residues: 3896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP n 284 HIS 0.009 0.001 HIS u 231 PHE 0.032 0.001 PHE q 260 TYR 0.020 0.001 TYR B 797 ARG 0.007 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 7.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8610 (ttm) cc_final: 0.8313 (ttp) REVERT: A 305 MET cc_start: 0.8914 (mmt) cc_final: 0.8493 (mmm) REVERT: A 548 MET cc_start: 0.8924 (mtm) cc_final: 0.8223 (mtp) REVERT: A 709 MET cc_start: 0.8332 (ttp) cc_final: 0.8004 (ttm) REVERT: A 903 MET cc_start: 0.8783 (mmt) cc_final: 0.8528 (mmt) REVERT: A 1211 MET cc_start: 0.7242 (mtt) cc_final: 0.6889 (mtt) REVERT: A 1266 ILE cc_start: 0.9553 (mt) cc_final: 0.9229 (tp) REVERT: A 1371 MET cc_start: 0.8307 (mtm) cc_final: 0.7911 (mtm) REVERT: A 1447 MET cc_start: 0.8660 (mmm) cc_final: 0.8155 (mmm) REVERT: B 302 MET cc_start: 0.7634 (ptt) cc_final: 0.7214 (ptt) REVERT: B 789 MET cc_start: 0.8475 (mmt) cc_final: 0.8218 (mmt) REVERT: B 1082 MET cc_start: 0.8435 (mmm) cc_final: 0.7781 (tpp) REVERT: B 1136 ASP cc_start: 0.8326 (m-30) cc_final: 0.8115 (m-30) REVERT: B 1210 MET cc_start: 0.8920 (mmm) cc_final: 0.8677 (tpp) REVERT: C 32 LEU cc_start: 0.9304 (tt) cc_final: 0.8661 (tt) REVERT: C 36 MET cc_start: 0.8795 (mtm) cc_final: 0.8326 (mtm) REVERT: C 52 MET cc_start: 0.8803 (ppp) cc_final: 0.8395 (tmm) REVERT: D 167 LYS cc_start: 0.6323 (mmpt) cc_final: 0.6059 (mmpt) REVERT: E 57 MET cc_start: 0.8818 (mtm) cc_final: 0.8577 (mtm) REVERT: E 122 MET cc_start: 0.7819 (ptm) cc_final: 0.7515 (tmm) REVERT: G 107 ASN cc_start: 0.9068 (p0) cc_final: 0.8729 (t0) REVERT: H 46 MET cc_start: 0.8489 (mmp) cc_final: 0.8256 (mmp) REVERT: I 20 LYS cc_start: 0.7821 (mttt) cc_final: 0.7247 (mtpt) REVERT: I 61 ASP cc_start: 0.9049 (t0) cc_final: 0.8639 (t0) REVERT: I 97 MET cc_start: 0.8660 (mpp) cc_final: 0.8366 (mpp) REVERT: J 26 GLU cc_start: 0.8938 (pt0) cc_final: 0.8670 (pt0) REVERT: W 422 TYR cc_start: 0.7549 (t80) cc_final: 0.7093 (t80) REVERT: m 944 ASP cc_start: 0.8183 (t0) cc_final: 0.7933 (t0) REVERT: m 1166 MET cc_start: 0.4908 (mpp) cc_final: 0.2951 (mmp) REVERT: n 260 MET cc_start: 0.8371 (ttt) cc_final: 0.8071 (ttt) REVERT: q 405 MET cc_start: 0.6115 (tmm) cc_final: 0.5877 (tmm) REVERT: q 547 MET cc_start: 0.1877 (ttm) cc_final: 0.1278 (tpp) REVERT: q 744 MET cc_start: 0.8436 (mmm) cc_final: 0.7930 (ppp) REVERT: q 748 LEU cc_start: 0.7889 (tp) cc_final: 0.7672 (tp) REVERT: q 766 MET cc_start: 0.9105 (pmm) cc_final: 0.8765 (pmm) REVERT: r 216 TYR cc_start: 0.5407 (p90) cc_final: 0.4666 (p90) REVERT: r 227 MET cc_start: 0.5288 (tmm) cc_final: 0.5030 (tmm) REVERT: r 282 MET cc_start: 0.6491 (mtt) cc_final: 0.5665 (mmt) REVERT: r 424 MET cc_start: 0.7239 (mtt) cc_final: 0.7034 (mtt) REVERT: u 124 ARG cc_start: 0.8582 (mpp80) cc_final: 0.8265 (mmm160) REVERT: u 195 ASP cc_start: 0.7830 (m-30) cc_final: 0.7373 (t70) REVERT: v 263 TRP cc_start: 0.3811 (p90) cc_final: 0.3531 (p90) REVERT: x 209 ILE cc_start: 0.8960 (mm) cc_final: 0.8595 (mt) REVERT: x 293 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7961 (mp10) REVERT: e 72 ARG cc_start: 0.3097 (pmt-80) cc_final: 0.2682 (ttt180) REVERT: f 52 GLU cc_start: 0.2286 (pp20) cc_final: 0.1917 (mp0) REVERT: j 487 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6687 (mm-30) REVERT: j 534 ARG cc_start: 0.3082 (mtt180) cc_final: 0.2597 (tpt170) REVERT: j 595 MET cc_start: -0.0274 (ttp) cc_final: -0.0738 (tpt) REVERT: j 652 MET cc_start: -0.1433 (mmt) cc_final: -0.2304 (tmm) REVERT: j 683 LYS cc_start: -0.0194 (tptt) cc_final: -0.0404 (mmtt) REVERT: j 740 MET cc_start: 0.0878 (mmm) cc_final: -0.0670 (ptp) REVERT: j 921 MET cc_start: 0.3295 (tpt) cc_final: 0.2642 (ptm) REVERT: k 298 MET cc_start: 0.2373 (ttm) cc_final: 0.1736 (mpp) REVERT: k 361 MET cc_start: 0.2484 (mmm) cc_final: 0.1775 (ttt) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.7787 time to fit residues: 568.1367 Evaluate side-chains 330 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 7.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 575 optimal weight: 50.0000 chunk 371 optimal weight: 7.9990 chunk 555 optimal weight: 30.0000 chunk 280 optimal weight: 3.9990 chunk 182 optimal weight: 0.0870 chunk 180 optimal weight: 10.0000 chunk 591 optimal weight: 40.0000 chunk 633 optimal weight: 8.9990 chunk 459 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 731 optimal weight: 20.0000 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1211 ASN ** D 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 512 HIS m 661 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 ASN ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 294 HIS v 359 HIS ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 64 ASN ** j 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 84120 Z= 0.184 Angle : 0.492 13.006 114668 Z= 0.263 Chirality : 0.040 0.257 12770 Planarity : 0.003 0.040 13944 Dihedral : 15.935 116.901 13389 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 0.01 % Allowed : 0.47 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 1.41 (0.09), residues: 9441 helix: 2.07 (0.08), residues: 4175 sheet: 0.15 (0.14), residues: 1380 loop : 0.05 (0.10), residues: 3886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP n 284 HIS 0.010 0.001 HIS u 231 PHE 0.032 0.001 PHE q 224 TYR 0.014 0.001 TYR M 70 ARG 0.019 0.000 ARG v 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 413 time to evaluate : 7.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8602 (ttm) cc_final: 0.8270 (ttp) REVERT: A 180 MET cc_start: 0.8688 (mtm) cc_final: 0.8154 (mpp) REVERT: A 305 MET cc_start: 0.8895 (mmt) cc_final: 0.8548 (mmm) REVERT: A 548 MET cc_start: 0.8878 (mtm) cc_final: 0.8223 (mtp) REVERT: A 709 MET cc_start: 0.8315 (ttp) cc_final: 0.8002 (ttm) REVERT: A 903 MET cc_start: 0.8757 (mmt) cc_final: 0.8217 (mmm) REVERT: A 1211 MET cc_start: 0.7223 (mtt) cc_final: 0.6996 (ttm) REVERT: A 1266 ILE cc_start: 0.9498 (mt) cc_final: 0.9264 (tp) REVERT: A 1371 MET cc_start: 0.8272 (mtm) cc_final: 0.7843 (mtm) REVERT: A 1447 MET cc_start: 0.8649 (mmm) cc_final: 0.8156 (mmm) REVERT: B 183 MET cc_start: 0.8750 (mmm) cc_final: 0.8409 (mmp) REVERT: B 302 MET cc_start: 0.7561 (ptt) cc_final: 0.7167 (ptt) REVERT: B 789 MET cc_start: 0.8459 (mmt) cc_final: 0.8178 (mmt) REVERT: B 1082 MET cc_start: 0.8413 (mmm) cc_final: 0.7768 (tpp) REVERT: B 1152 MET cc_start: 0.8309 (tpt) cc_final: 0.8068 (tpt) REVERT: C 32 LEU cc_start: 0.9191 (tt) cc_final: 0.8940 (tt) REVERT: C 36 MET cc_start: 0.8781 (mtm) cc_final: 0.8555 (mtm) REVERT: C 52 MET cc_start: 0.8802 (ppp) cc_final: 0.8409 (tmm) REVERT: D 167 LYS cc_start: 0.6342 (mmpt) cc_final: 0.6078 (mmpt) REVERT: E 57 MET cc_start: 0.8931 (mtm) cc_final: 0.8728 (mtm) REVERT: E 122 MET cc_start: 0.7786 (ptm) cc_final: 0.7487 (tmm) REVERT: G 107 ASN cc_start: 0.9067 (p0) cc_final: 0.8725 (t0) REVERT: H 46 MET cc_start: 0.8457 (mmp) cc_final: 0.8226 (mmp) REVERT: I 20 LYS cc_start: 0.7765 (mttt) cc_final: 0.7200 (mtpt) REVERT: I 61 ASP cc_start: 0.9062 (t0) cc_final: 0.8613 (t0) REVERT: I 97 MET cc_start: 0.8608 (mpp) cc_final: 0.8288 (mpp) REVERT: V 40 ASP cc_start: 0.5302 (m-30) cc_final: 0.4595 (t0) REVERT: W 422 TYR cc_start: 0.7540 (t80) cc_final: 0.7080 (t80) REVERT: W 781 GLU cc_start: 0.8439 (pp20) cc_final: 0.8115 (pp20) REVERT: m 659 MET cc_start: 0.7376 (ptm) cc_final: 0.7013 (ptm) REVERT: m 944 ASP cc_start: 0.8167 (t0) cc_final: 0.7927 (t0) REVERT: m 1019 MET cc_start: 0.6680 (ptt) cc_final: 0.6083 (ptt) REVERT: m 1166 MET cc_start: 0.4856 (mpp) cc_final: 0.2937 (mmp) REVERT: n 260 MET cc_start: 0.8424 (ttt) cc_final: 0.7587 (ptt) REVERT: q 405 MET cc_start: 0.6037 (tmm) cc_final: 0.5814 (tmm) REVERT: q 744 MET cc_start: 0.8287 (mmm) cc_final: 0.7789 (ppp) REVERT: q 748 LEU cc_start: 0.7860 (tp) cc_final: 0.7644 (tp) REVERT: q 766 MET cc_start: 0.9101 (pmm) cc_final: 0.8787 (pmm) REVERT: q 873 MET cc_start: 0.8138 (mpp) cc_final: 0.7936 (mmt) REVERT: r 216 TYR cc_start: 0.5428 (p90) cc_final: 0.4667 (p90) REVERT: r 227 MET cc_start: 0.4851 (tmm) cc_final: 0.4594 (tmm) REVERT: r 282 MET cc_start: 0.6583 (mtt) cc_final: 0.6035 (mmt) REVERT: r 424 MET cc_start: 0.7240 (mtt) cc_final: 0.7011 (mtt) REVERT: u 124 ARG cc_start: 0.8601 (mpp80) cc_final: 0.8282 (mmm160) REVERT: u 195 ASP cc_start: 0.7833 (m-30) cc_final: 0.7373 (t70) REVERT: v 351 MET cc_start: 0.0552 (tmm) cc_final: -0.0125 (ppp) REVERT: x 209 ILE cc_start: 0.8922 (mm) cc_final: 0.8562 (mt) REVERT: x 293 GLN cc_start: 0.8343 (mm-40) cc_final: 0.7933 (mp10) REVERT: f 52 GLU cc_start: 0.2280 (pp20) cc_final: 0.1919 (mp0) REVERT: f 79 LYS cc_start: 0.4256 (pptt) cc_final: 0.3799 (ptpp) REVERT: j 487 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6710 (mm-30) REVERT: j 534 ARG cc_start: 0.2804 (mtt180) cc_final: 0.2397 (tpt170) REVERT: j 595 MET cc_start: -0.0264 (ttp) cc_final: -0.0734 (tpt) REVERT: j 652 MET cc_start: -0.1595 (mmt) cc_final: -0.2404 (tmm) REVERT: j 683 LYS cc_start: 0.0422 (tptt) cc_final: 0.0148 (mmtt) REVERT: j 740 MET cc_start: 0.0852 (mmm) cc_final: -0.0698 (ptp) REVERT: j 921 MET cc_start: 0.3268 (tpt) cc_final: 0.2629 (ptm) REVERT: k 298 MET cc_start: 0.2302 (ttm) cc_final: 0.1787 (mpp) REVERT: k 361 MET cc_start: 0.2676 (mmm) cc_final: 0.1881 (ttt) outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.7579 time to fit residues: 558.1251 Evaluate side-chains 336 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 7.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 846 optimal weight: 40.0000 chunk 891 optimal weight: 50.0000 chunk 812 optimal weight: 50.0000 chunk 866 optimal weight: 50.0000 chunk 890 optimal weight: 30.0000 chunk 521 optimal weight: 10.0000 chunk 377 optimal weight: 0.9990 chunk 680 optimal weight: 40.0000 chunk 265 optimal weight: 10.0000 chunk 783 optimal weight: 10.0000 chunk 819 optimal weight: 40.0000 overall best weight: 12.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 140 GLN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** L 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 283 ASN ** W 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 433 GLN W 512 HIS W 547 HIS m 643 ASN m 661 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 ASN ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 310 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 64 ASN d 79 HIS ** e 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN ** j 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 84120 Z= 0.542 Angle : 0.743 12.426 114668 Z= 0.388 Chirality : 0.046 0.355 12770 Planarity : 0.005 0.079 13944 Dihedral : 16.150 115.933 13389 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.39 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.55 (0.09), residues: 9441 helix: 1.33 (0.08), residues: 4180 sheet: -0.21 (0.14), residues: 1388 loop : -0.39 (0.10), residues: 3873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP n 284 HIS 0.013 0.002 HIS A 852 PHE 0.036 0.002 PHE C 191 TYR 0.048 0.002 TYR B 797 ARG 0.013 0.001 ARG W 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 7.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8621 (ttm) cc_final: 0.8336 (ttp) REVERT: A 180 MET cc_start: 0.8850 (mtm) cc_final: 0.7970 (mpp) REVERT: A 548 MET cc_start: 0.9001 (mtm) cc_final: 0.8157 (mtp) REVERT: A 709 MET cc_start: 0.8304 (ttp) cc_final: 0.8035 (ttm) REVERT: A 1211 MET cc_start: 0.7183 (mtt) cc_final: 0.6853 (mtt) REVERT: A 1266 ILE cc_start: 0.9549 (mt) cc_final: 0.9229 (tp) REVERT: A 1371 MET cc_start: 0.8433 (mtm) cc_final: 0.8001 (mtm) REVERT: B 302 MET cc_start: 0.7839 (ptt) cc_final: 0.7448 (ptt) REVERT: B 789 MET cc_start: 0.8400 (mmt) cc_final: 0.8163 (mmt) REVERT: B 1082 MET cc_start: 0.8197 (mmm) cc_final: 0.7923 (tpt) REVERT: B 1136 ASP cc_start: 0.8448 (m-30) cc_final: 0.8181 (m-30) REVERT: B 1138 MET cc_start: 0.8791 (mmm) cc_final: 0.8469 (mmm) REVERT: B 1152 MET cc_start: 0.8569 (tpt) cc_final: 0.8281 (tpt) REVERT: C 52 MET cc_start: 0.8788 (ppp) cc_final: 0.8296 (tmm) REVERT: E 57 MET cc_start: 0.9082 (mtm) cc_final: 0.8798 (mtm) REVERT: E 122 MET cc_start: 0.8010 (ptm) cc_final: 0.7612 (tmm) REVERT: G 107 ASN cc_start: 0.8987 (p0) cc_final: 0.8711 (t0) REVERT: I 20 LYS cc_start: 0.8083 (mttt) cc_final: 0.7583 (mptt) REVERT: J 26 GLU cc_start: 0.8834 (pt0) cc_final: 0.8569 (pt0) REVERT: W 781 GLU cc_start: 0.8299 (pp20) cc_final: 0.7872 (pp20) REVERT: m 676 MET cc_start: 0.7046 (tmm) cc_final: 0.5872 (mtt) REVERT: m 944 ASP cc_start: 0.8239 (t0) cc_final: 0.8022 (t70) REVERT: m 983 ARG cc_start: 0.5507 (mtm-85) cc_final: 0.5275 (mtm-85) REVERT: m 1166 MET cc_start: 0.5071 (mpp) cc_final: 0.3134 (mmp) REVERT: m 1180 MET cc_start: 0.5054 (mmp) cc_final: 0.4658 (mmp) REVERT: n 260 MET cc_start: 0.8457 (ttt) cc_final: 0.7650 (ptt) REVERT: q 405 MET cc_start: 0.6042 (tmm) cc_final: 0.5756 (tmm) REVERT: q 744 MET cc_start: 0.8326 (mmm) cc_final: 0.7904 (ppp) REVERT: q 766 MET cc_start: 0.9140 (pmm) cc_final: 0.8787 (pmm) REVERT: r 216 TYR cc_start: 0.5375 (p90) cc_final: 0.4744 (p90) REVERT: r 227 MET cc_start: 0.4847 (tmm) cc_final: 0.4599 (tmm) REVERT: r 282 MET cc_start: 0.6845 (mtt) cc_final: 0.6093 (mmt) REVERT: r 424 MET cc_start: 0.7443 (mtt) cc_final: 0.7207 (mtt) REVERT: u 124 ARG cc_start: 0.8701 (mpp80) cc_final: 0.8361 (mmm160) REVERT: u 195 ASP cc_start: 0.7660 (m-30) cc_final: 0.7136 (t70) REVERT: x 209 ILE cc_start: 0.8923 (mm) cc_final: 0.8588 (mt) REVERT: x 293 GLN cc_start: 0.8496 (mm-40) cc_final: 0.7971 (mp10) REVERT: e 54 TYR cc_start: 0.5274 (m-10) cc_final: 0.5058 (m-10) REVERT: e 72 ARG cc_start: 0.3025 (pmt-80) cc_final: 0.2644 (ttt180) REVERT: j 487 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6744 (mm-30) REVERT: j 534 ARG cc_start: 0.3206 (mtt180) cc_final: 0.2681 (tpt170) REVERT: j 595 MET cc_start: 0.0118 (ttp) cc_final: -0.0450 (tpt) REVERT: j 652 MET cc_start: -0.1561 (mmt) cc_final: -0.2407 (tmm) REVERT: j 683 LYS cc_start: -0.0075 (tptt) cc_final: -0.0356 (mmtt) REVERT: j 740 MET cc_start: 0.0790 (mmm) cc_final: -0.1129 (ptp) REVERT: j 921 MET cc_start: 0.3296 (tpt) cc_final: 0.2612 (ptm) REVERT: k 298 MET cc_start: 0.2948 (ttm) cc_final: 0.2238 (mpp) REVERT: k 361 MET cc_start: 0.3275 (mmm) cc_final: 0.2244 (ttt) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.7300 time to fit residues: 481.2158 Evaluate side-chains 297 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 7.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 863 optimal weight: 40.0000 chunk 569 optimal weight: 50.0000 chunk 916 optimal weight: 30.0000 chunk 559 optimal weight: 50.0000 chunk 434 optimal weight: 30.0000 chunk 637 optimal weight: 50.0000 chunk 961 optimal weight: 30.0000 chunk 884 optimal weight: 0.9990 chunk 765 optimal weight: 30.0000 chunk 79 optimal weight: 1.9990 chunk 591 optimal weight: 6.9990 overall best weight: 13.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 ASN ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN ** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN A 895 HIS ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 986 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1211 ASN C 64 HIS G 107 ASN I 89 GLN W 402 HIS ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 661 GLN m1288 ASN ** m1407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m1449 ASN n 156 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 397 ASN ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 232 ASN u 129 ASN ** u 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 370 GLN x 296 ASN x 310 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN f 93 GLN k 275 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.120 84120 Z= 0.605 Angle : 0.819 20.429 114668 Z= 0.429 Chirality : 0.048 0.302 12770 Planarity : 0.006 0.208 13944 Dihedral : 16.537 114.380 13389 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 0.02 % Allowed : 0.35 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: -0.30 (0.08), residues: 9441 helix: 0.67 (0.08), residues: 4179 sheet: -0.61 (0.13), residues: 1368 loop : -0.90 (0.10), residues: 3894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP n 219 HIS 0.054 0.002 HIS B 887 PHE 0.028 0.003 PHE C 191 TYR 0.037 0.003 TYR B 797 ARG 0.023 0.001 ARG m1469 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18882 Ramachandran restraints generated. 9441 Oldfield, 0 Emsley, 9441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 360 time to evaluate : 7.514 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: A 57 LYS cc_start: 0.9358 (mttt) cc_final: 0.9104 (mtpp) REVERT: A 84 MET cc_start: 0.8520 (ttm) cc_final: 0.8254 (ttm) REVERT: A 305 MET cc_start: 0.8539 (mmm) cc_final: 0.7155 (mmm) REVERT: A 548 MET cc_start: 0.9067 (mtm) cc_final: 0.8358 (mtp) REVERT: A 677 MET cc_start: 0.8384 (mmp) cc_final: 0.8093 (mmp) REVERT: A 709 MET cc_start: 0.8404 (ttp) cc_final: 0.7895 (ttm) REVERT: A 1266 ILE cc_start: 0.9451 (mt) cc_final: 0.9233 (tp) REVERT: A 1371 MET cc_start: 0.8393 (mtm) cc_final: 0.7922 (mtm) REVERT: B 183 MET cc_start: 0.8708 (mmm) cc_final: 0.8477 (mmp) REVERT: B 789 MET cc_start: 0.8414 (mmt) cc_final: 0.8168 (mmt) REVERT: B 1082 MET cc_start: 0.8487 (mmm) cc_final: 0.8261 (tpp) REVERT: B 1136 ASP cc_start: 0.8526 (m-30) cc_final: 0.8239 (m-30) REVERT: B 1152 MET cc_start: 0.8468 (tpt) cc_final: 0.8262 (tpt) REVERT: B 1210 MET cc_start: 0.8348 (mmm) cc_final: 0.8113 (mmm) REVERT: C 52 MET cc_start: 0.8629 (ppp) cc_final: 0.8267 (tmm) REVERT: E 122 MET cc_start: 0.8186 (ptm) cc_final: 0.7690 (tmm) REVERT: W 422 TYR cc_start: 0.7630 (t80) cc_final: 0.7424 (t80) REVERT: W 781 GLU cc_start: 0.8042 (pp20) cc_final: 0.7723 (pp20) REVERT: m 676 MET cc_start: 0.6858 (tmm) cc_final: 0.5841 (mtt) REVERT: m 944 ASP cc_start: 0.8318 (t0) cc_final: 0.8090 (t0) REVERT: m 1166 MET cc_start: 0.5189 (mpp) cc_final: 0.3511 (mmp) REVERT: n 167 MET cc_start: 0.8278 (ttt) cc_final: 0.7967 (ptm) REVERT: n 260 MET cc_start: 0.8275 (ttt) cc_final: 0.7549 (ptt) REVERT: n 267 LYS cc_start: 0.8410 (mttt) cc_final: 0.7985 (ptpp) REVERT: q 405 MET cc_start: 0.5962 (tmm) cc_final: 0.5536 (tmm) REVERT: q 744 MET cc_start: 0.8351 (mmm) cc_final: 0.7968 (tmm) REVERT: q 766 MET cc_start: 0.9181 (pmm) cc_final: 0.8808 (pmm) REVERT: q 873 MET cc_start: 0.8609 (mpp) cc_final: 0.8177 (mpp) REVERT: r 211 MET cc_start: -0.0118 (mtp) cc_final: -0.0332 (mtm) REVERT: r 282 MET cc_start: 0.7288 (mtt) cc_final: 0.6691 (mmt) REVERT: u 124 ARG cc_start: 0.8781 (mpp80) cc_final: 0.8434 (mmm160) REVERT: u 195 ASP cc_start: 0.7863 (m-30) cc_final: 0.7272 (t70) REVERT: v 129 ARG cc_start: 0.8742 (mmm-85) cc_final: 0.8421 (mtp85) REVERT: v 224 LYS cc_start: 0.4732 (mttt) cc_final: 0.4241 (tmtt) REVERT: v 351 MET cc_start: 0.0846 (tmm) cc_final: 0.0547 (tmm) REVERT: x 209 ILE cc_start: 0.8974 (mm) cc_final: 0.8643 (mt) REVERT: x 293 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8296 (mp10) REVERT: x 349 GLN cc_start: 0.9348 (tt0) cc_final: 0.8806 (tm-30) REVERT: e 54 TYR cc_start: 0.5382 (m-10) cc_final: 0.5107 (m-10) REVERT: j 487 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6874 (mm-30) REVERT: j 534 ARG cc_start: 0.2893 (mtt180) cc_final: 0.2587 (tpt170) REVERT: j 555 THR cc_start: 0.1935 (m) cc_final: 0.1642 (m) REVERT: j 595 MET cc_start: -0.0672 (ttp) cc_final: -0.1027 (tpt) REVERT: j 652 MET cc_start: -0.1595 (mmt) cc_final: -0.2343 (tmm) REVERT: j 683 LYS cc_start: 0.0047 (tptt) cc_final: -0.0249 (mmtt) REVERT: j 740 MET cc_start: 0.1100 (mmm) cc_final: -0.0532 (ptp) REVERT: j 921 MET cc_start: 0.3089 (tpt) cc_final: 0.2609 (ptm) REVERT: k 298 MET cc_start: 0.2732 (ttm) cc_final: 0.1910 (mpp) REVERT: k 361 MET cc_start: 0.3710 (mmm) cc_final: 0.2396 (ttt) outliers start: 2 outliers final: 0 residues processed: 361 average time/residue: 0.7715 time to fit residues: 494.0158 Evaluate side-chains 285 residues out of total 8507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 7.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 965 random chunks: chunk 469 optimal weight: 0.3980 chunk 608 optimal weight: 8.9990 chunk 815 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 705 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 766 optimal weight: 20.0000 chunk 320 optimal weight: 0.0980 chunk 787 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN A 655 ASN ** B1174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1211 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 299 ASN m1407 HIS ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 147 ASN ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 578 ASN ** j 692 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 290 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.113231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.090153 restraints weight = 447521.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.089193 restraints weight = 520776.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.089364 restraints weight = 407249.108| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 84120 Z= 0.161 Angle : 0.547 10.216 114668 Z= 0.293 Chirality : 0.041 0.191 12770 Planarity : 0.004 0.057 13944 Dihedral : 16.265 113.227 13389 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.54 (0.09), residues: 9441 helix: 1.43 (0.08), residues: 4147 sheet: -0.41 (0.13), residues: 1395 loop : -0.43 (0.10), residues: 3899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP q 225 HIS 0.012 0.001 HIS q 758 PHE 0.017 0.001 PHE j 939 TYR 0.023 0.001 TYR q 116 ARG 0.010 0.000 ARG q 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12553.85 seconds wall clock time: 226 minutes 13.07 seconds (13573.07 seconds total)