Starting phenix.real_space_refine on Mon Feb 19 21:27:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsx_33436/02_2024/7xsx_33436.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsx_33436/02_2024/7xsx_33436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsx_33436/02_2024/7xsx_33436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsx_33436/02_2024/7xsx_33436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsx_33436/02_2024/7xsx_33436.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsx_33436/02_2024/7xsx_33436.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 224 5.49 5 Mg 1 5.21 5 S 317 5.16 5 C 50532 2.51 5 N 14233 2.21 5 O 15817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "v TYR 61": "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-5238/modules/chem_data/mon_lib" Total number of atoms: 81134 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: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2007 Classifications: {'DNA': 97} Link IDs: {'rna3p': 96} 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: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2202 Classifications: {'DNA': 108} Link IDs: {'rna3p': 107} 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: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 615 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "b" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "c" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "d" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 757 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} 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: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 544 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} 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: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3832 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 449} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 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 82.220 93.789 153.898 1.00 73.71 S ATOM 549 SG CYS A 70 85.524 92.327 155.104 1.00 62.33 S ATOM 594 SG CYS A 77 84.776 96.031 155.645 1.00 48.15 S ATOM 829 SG CYS A 107 94.610 117.607 113.564 1.00100.88 S ATOM 851 SG CYS A 110 96.403 114.353 112.732 1.00100.66 S ATOM 1157 SG CYS A 148 97.356 117.551 110.991 1.00143.83 S ATOM 1229 SG CYS A 168 93.822 116.056 110.360 1.00154.59 S ATOM 19880 SG CYS B1163 97.636 92.248 143.553 1.00 51.39 S ATOM 19898 SG CYS B1166 96.123 95.626 142.888 1.00 45.59 S ATOM 20021 SG CYS B1182 93.850 92.583 143.230 1.00 60.97 S ATOM 20044 SG CYS B1185 96.113 93.085 140.158 1.00 59.25 S ATOM 20989 SG CYS C 85 86.782 104.854 222.865 1.00 76.72 S ATOM 21002 SG CYS C 87 83.546 104.009 221.066 1.00 83.18 S ATOM 21037 SG CYS C 91 83.403 105.891 224.181 1.00 62.87 S ATOM 21060 SG CYS C 94 84.866 107.740 221.257 1.00 61.96 S ATOM 29206 SG CYS I 78 97.930 198.127 166.327 1.00242.53 S ATOM 29422 SG CYS I 103 98.285 193.692 165.850 1.00219.08 S ATOM 28659 SG CYS I 10 80.084 179.613 123.217 1.00185.16 S ATOM 28822 SG CYS I 29 84.391 179.640 121.729 1.00169.40 S ATOM 28847 SG CYS I 32 82.871 181.485 120.847 1.00172.29 S ATOM 29563 SG CYS J 7 92.922 137.816 212.147 1.00 25.03 S ATOM 29586 SG CYS J 10 95.054 136.720 215.183 1.00 27.11 S ATOM 29862 SG CYS J 44 96.149 139.648 212.890 1.00 26.87 S ATOM 29868 SG CYS J 45 93.373 139.864 215.425 1.00 30.09 S ATOM 31039 SG CYS L 33 53.830 127.653 194.057 1.00 78.20 S ATOM 31054 SG CYS L 36 51.487 128.395 196.983 1.00 95.22 S ATOM 31164 SG CYS L 50 50.596 125.682 194.443 1.00 97.21 S ATOM 31188 SG CYS L 53 50.688 129.338 193.366 1.00106.74 S ATOM 31445 SG CYS M 25 69.898 142.690 111.159 1.00217.03 S ATOM 31470 SG CYS M 28 69.633 138.962 111.322 1.00237.69 S ATOM 31628 SG CYS M 49 72.951 140.533 110.323 1.00240.31 S ATOM 31652 SG CYS M 52 69.815 140.555 107.983 1.00246.39 S ATOM 36508 SG CYS V 12 36.285 113.792 119.634 1.00255.10 S ATOM 36530 SG CYS V 15 37.959 116.728 118.094 1.00251.36 S ATOM 36632 SG CYS V 29 34.337 116.986 118.336 1.00242.76 S ATOM 36653 SG CYS V 32 35.828 114.576 115.850 1.00255.31 S Time building chain proxies: 31.75, per 1000 atoms: 0.39 Number of scatterers: 81134 At special positions: 0 Unit cell: (215.18, 225.568, 277.508, 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 224 15.00 Mg 1 11.99 O 15817 8.00 N 14233 7.00 C 50532 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: 26.48 Conformation dependent library (CDL) restraints added in 10.3 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 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " 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 10 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " 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 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18048 Finding SS restraints... Secondary structure from input PDB file: 370 helices and 88 sheets defined 47.7% alpha, 15.1% beta 107 base pairs and 187 stacking pairs defined. Time for finding SS restraints: 22.82 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: 4.527A 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: 3.664A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.525A 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: 3.891A 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: 3.722A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.724A 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: 3.757A 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: 3.625A pdb=" N ALA A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1334 through 1343 removed outlier: 3.636A 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: 3.987A 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: 3.810A 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: 4.199A pdb=" N GLU B 430 " --> pdb=" O GLN B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.618A 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: 4.208A 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: 3.573A 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: 3.620A 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: 3.744A 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: 4.146A pdb=" N GLU B 924 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 926 " --> pdb=" O GLU B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 removed outlier: 3.654A 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: 4.131A 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: 3.532A 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: 3.609A 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: 3.997A 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: 3.605A pdb=" N SER D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 removed outlier: 3.671A 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: 3.794A 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: 3.663A pdb=" N MET E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 removed outlier: 3.585A 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: 3.573A 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: 4.046A 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: 3.856A 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: 4.415A 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: 3.603A 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: 3.502A pdb=" N ARG m 604 " --> pdb=" O GLU m 600 " (cutoff:3.500A) Processing helix chain 'm' and resid 622 through 629 removed outlier: 3.520A pdb=" N ILE m 629 " --> pdb=" O GLY m 625 " (cutoff:3.500A) Processing helix chain 'm' and resid 633 through 639 removed outlier: 3.720A pdb=" N ASP m 637 " --> pdb=" O PRO m 634 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.907A 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: 4.125A 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: 3.951A pdb=" N ARG m1033 " --> pdb=" O ASP m1030 " (cutoff:3.500A) removed outlier: 3.999A 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: 3.557A 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: 3.550A 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: 4.551A 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: 3.878A 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: 3.664A 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: 3.690A 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: 4.130A 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: 3.589A 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: 3.600A 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: 3.552A 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: 4.232A 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: 3.533A pdb=" N ALA q 539 " --> pdb=" O ASN q 535 " (cutoff:3.500A) Processing helix chain 'q' and resid 553 through 569 removed outlier: 4.098A 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: 6.250A 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: 3.790A pdb=" N LEU q 749 " --> pdb=" O ASP q 745 " (cutoff:3.500A) Processing helix chain 'q' and resid 765 through 784 removed outlier: 3.671A 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: 3.535A 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: 3.870A 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: 3.771A pdb=" N LEU q 918 " --> pdb=" O LYS q 914 " (cutoff:3.500A) Processing helix chain 'r' and resid 197 through 204 removed outlier: 3.804A 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: 3.611A pdb=" N ARG r 382 " --> pdb=" O GLU r 378 " (cutoff:3.500A) Processing helix chain 'r' and resid 398 through 433 removed outlier: 3.830A 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: 3.624A 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: 3.574A pdb=" N ASP v 68 " --> pdb=" O GLU v 65 " (cutoff:3.500A) removed outlier: 4.095A 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: 3.607A 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: 3.647A 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 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: 3.507A 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: 3.853A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.412A 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 'c' and resid 112 through 116 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: 3.536A 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 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: 3.625A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) 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 477 through 511 removed outlier: 3.928A pdb=" N THR j 481 " --> pdb=" O LEU j 477 " (cutoff:3.500A) Processing helix chain 'j' and resid 512 through 518 Processing helix chain 'j' and resid 534 through 538 Processing helix chain 'j' and resid 624 through 654 removed outlier: 4.346A pdb=" N ASP j 654 " --> pdb=" O LYS j 650 " (cutoff:3.500A) Processing helix chain 'j' and resid 773 through 806 removed outlier: 3.547A pdb=" N GLU j 777 " --> pdb=" O GLY j 773 " (cutoff:3.500A) Processing helix chain 'j' and resid 816 through 820 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 'j' and resid 936 through 941 removed outlier: 4.104A pdb=" N PHE j 939 " --> pdb=" O GLY j 936 " (cutoff:3.500A) Processing helix chain 'k' and resid 83 through 97 removed outlier: 4.393A pdb=" N GLN k 87 " --> pdb=" O GLN k 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 202 through 214 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: 6.780A pdb=" N THR A 238 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 10.601A 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: 3.613A 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: 3.691A 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: 5.435A 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: 3.966A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.173A 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: 3.502A pdb=" N ILE H 29 " --> pdb=" O THR H 11 " (cutoff:3.500A) removed outlier: 6.663A 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: 6.395A 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: 3.636A 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: 5.780A 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: 6.953A 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: 6.740A 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: 4.335A 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: 6.441A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR A1156 " --> pdb=" O LYS I 42 " (cutoff:3.500A) removed outlier: 6.505A 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: 4.938A pdb=" N ASP B 118 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 4.431A 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: 4.416A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.862A 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: 5.658A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.700A 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: 8.016A pdb=" N ILE B 619 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 6.408A 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: 5.333A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 6.050A 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: 6.226A 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: 4.703A pdb=" N ALA C 12 " --> pdb=" O GLU C 16 " (cutoff:3.500A) removed outlier: 6.786A 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: 4.234A 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: 6.731A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.077A 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: 7.254A pdb=" N ILE C 158 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL C 48 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 7.209A 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: 6.676A 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: 6.476A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.711A 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: 3.521A 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: 4.118A 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: 4.847A 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: 3.901A 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: 6.471A pdb=" N VAL V 86 " --> pdb=" O PHE V 54 " (cutoff:3.500A) removed outlier: 6.640A 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: 7.775A pdb=" N ILE W 506 " --> pdb=" O VAL W 501 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL W 501 " --> pdb=" O ILE W 506 " (cutoff:3.500A) removed outlier: 6.937A 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: 5.911A 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: 3.559A 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: 4.573A pdb=" N LYS W 787 " --> pdb=" O LEU W 782 " (cutoff:3.500A) removed outlier: 6.493A 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: 6.877A 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: 5.370A pdb=" N VAL m1175 " --> pdb=" O TYR m1179 " (cutoff:3.500A) removed outlier: 7.188A 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: 5.749A 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: 6.747A 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: 4.020A pdb=" N LEU r 229 " --> pdb=" O VAL r 246 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL r 246 " --> pdb=" O LEU r 229 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL r 248 " --> pdb=" O ALA r 275 " (cutoff:3.500A) removed outlier: 6.880A 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: 5.935A 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: 6.347A 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: 6.337A 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: 6.908A 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: 6.347A pdb=" N TYR x 313 " --> pdb=" O LEU x 333 " (cutoff:3.500A) removed outlier: 7.605A 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: 6.931A 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 '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=AI1 Processing sheet with id=AI2, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AI3, first strand: chain 'c' and resid 101 through 102 removed outlier: 7.019A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, 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=AI4 Processing sheet with id=AI5, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AI6, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.383A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AI8, first strand: chain 'j' and resid 548 through 550 Processing sheet with id=AI9, 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: 6.426A 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: 5.885A pdb=" N VAL k 172 " --> pdb=" O LEU k 154 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'j' and resid 707 through 711 removed outlier: 6.518A pdb=" N LEU j 689 " --> pdb=" O GLU j 672 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU j 672 " --> pdb=" O LEU j 689 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE j 691 " --> pdb=" O LYS j 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS j 670 " --> pdb=" O ILE j 691 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N ASN j 673 " --> pdb=" O GLU j 754 " (cutoff:3.500A) removed outlier: 6.227A 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: 6.119A 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: 4.663A pdb=" N PHE j 720 " --> pdb=" O ILE j 730 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N HIS j 732 " --> pdb=" O LEU j 718 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU j 718 " --> pdb=" O HIS j 732 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS j 734 " --> pdb=" O LYS j 716 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'j' and resid 821 through 823 Processing sheet with id=AJ3, first strand: chain 'j' and resid 884 through 890 removed outlier: 5.884A 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: 4.375A pdb=" N ALA j 858 " --> pdb=" O VAL j 873 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL j 875 " --> pdb=" O GLU j 856 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'k' and resid 44 through 47 removed outlier: 5.284A 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: 10.298A pdb=" N THR k 8 " --> pdb=" O PHE k 80 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N PHE k 80 " --> pdb=" O THR k 8 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TRP k 63 " --> pdb=" O GLY k 79 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'k' and resid 255 through 258 removed outlier: 6.101A pdb=" N GLY k 235 " --> pdb=" O LEU k 229 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU k 229 " --> pdb=" O GLY k 235 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N PHE k 237 " --> pdb=" O ASP k 227 " (cutoff:3.500A) removed outlier: 3.865A 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: 13.056A 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: 4.392A pdb=" N LEU k 229 " --> pdb=" O GLN k 299 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL k 297 " --> pdb=" O LEU k 231 " (cutoff:3.500A) removed outlier: 9.820A 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: 6.739A 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: 8.782A 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=AJ6, first strand: chain 'k' and resid 305 through 309 removed outlier: 5.418A 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=AJ7, first strand: chain 'k' and resid 391 through 394 removed outlier: 8.441A 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: 3.784A 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: 8.084A pdb=" N LYS k 451 " --> pdb=" O ILE k 399 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL k 401 " --> pdb=" O LYS k 451 " (cutoff:3.500A) 3752 hydrogen bonds defined for protein. 10665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 272 hydrogen bonds 544 hydrogen bond angles 0 basepair planarities 107 basepair parallelities 187 stacking parallelities Total time for adding SS restraints: 46.42 Time building geometry restraints manager: 29.09 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: 20323 1.33 - 1.45: 16831 1.45 - 1.58: 44970 1.58 - 1.70: 444 1.70 - 1.82: 517 Bond restraints: 83085 Sorted by residual: bond pdb=" C1' DG N -18 " pdb=" N9 DG N -18 " ideal model delta sigma weight residual 1.460 1.381 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C1' DG N -19 " pdb=" N9 DG N -19 " ideal model delta sigma weight residual 1.460 1.385 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C1' DA N -21 " pdb=" N9 DA N -21 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1' DG T 28 " pdb=" N9 DG T 28 " ideal model delta sigma weight residual 1.460 1.387 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" O3' DC N 1 " pdb=" P DG N 2 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.32e+01 ... (remaining 83080 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.68: 1942 104.68 - 112.28: 42230 112.28 - 119.89: 31142 119.89 - 127.49: 36790 127.49 - 135.10: 1000 Bond angle restraints: 113104 Sorted by residual: 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=" O5' DC T 4 " pdb=" C5' DC T 4 " pdb=" C4' DC T 4 " ideal model delta sigma weight residual 110.80 118.23 -7.43 1.50e+00 4.44e-01 2.45e+01 angle pdb=" N LEU k 231 " pdb=" CA LEU k 231 " pdb=" C LEU k 231 " ideal model delta sigma weight residual 114.04 108.06 5.98 1.24e+00 6.50e-01 2.32e+01 angle pdb=" C3' DG N -8 " pdb=" O3' DG N -8 " pdb=" P DG N -7 " ideal model delta sigma weight residual 120.20 126.74 -6.54 1.50e+00 4.44e-01 1.90e+01 angle pdb=" C3' DT T 15 " pdb=" O3' DT T 15 " pdb=" P DA T 16 " ideal model delta sigma weight residual 120.20 126.66 -6.46 1.50e+00 4.44e-01 1.85e+01 ... (remaining 113099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.26: 48447 32.26 - 64.53: 1795 64.53 - 96.79: 104 96.79 - 129.05: 3 129.05 - 161.31: 1 Dihedral angle restraints: 50350 sinusoidal: 22501 harmonic: 27849 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 232.00 116.86 115.14 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 -155.89 -24.11 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 -59.00 -69.00 1 1.70e+01 3.46e-03 2.13e+01 ... (remaining 50347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 11220 0.077 - 0.153: 1273 0.153 - 0.230: 80 0.230 - 0.306: 9 0.306 - 0.383: 4 Chirality restraints: 12586 Sorted by residual: chirality pdb=" CA THR k 8 " pdb=" N THR k 8 " pdb=" C THR k 8 " pdb=" CB THR k 8 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" P DA T -54 " pdb=" OP1 DA T -54 " pdb=" OP2 DA T -54 " pdb=" O5' DA T -54 " both_signs ideal model delta sigma weight residual True 2.35 -2.71 -0.36 2.00e-01 2.50e+01 3.28e+00 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 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 12583 not shown) Planarity restraints: 13869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG T -53 " 0.187 2.00e-02 2.50e+03 1.10e-01 3.66e+02 pdb=" N9 DG T -53 " 0.005 2.00e-02 2.50e+03 pdb=" C8 DG T -53 " -0.164 2.00e-02 2.50e+03 pdb=" N7 DG T -53 " -0.136 2.00e-02 2.50e+03 pdb=" C5 DG T -53 " -0.021 2.00e-02 2.50e+03 pdb=" C6 DG T -53 " 0.044 2.00e-02 2.50e+03 pdb=" O6 DG T -53 " 0.170 2.00e-02 2.50e+03 pdb=" N1 DG T -53 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG T -53 " 0.019 2.00e-02 2.50e+03 pdb=" N2 DG T -53 " -0.176 2.00e-02 2.50e+03 pdb=" N3 DG T -53 " 0.057 2.00e-02 2.50e+03 pdb=" C4 DG T -53 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC T 7 " 0.214 2.00e-02 2.50e+03 1.11e-01 2.78e+02 pdb=" N1 DC T 7 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DC T 7 " -0.035 2.00e-02 2.50e+03 pdb=" O2 DC T 7 " -0.124 2.00e-02 2.50e+03 pdb=" N3 DC T 7 " 0.018 2.00e-02 2.50e+03 pdb=" C4 DC T 7 " 0.010 2.00e-02 2.50e+03 pdb=" N4 DC T 7 " 0.151 2.00e-02 2.50e+03 pdb=" C5 DC T 7 " -0.113 2.00e-02 2.50e+03 pdb=" C6 DC T 7 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT T 13 " -0.209 2.00e-02 2.50e+03 1.03e-01 2.64e+02 pdb=" N1 DT T 13 " 0.010 2.00e-02 2.50e+03 pdb=" C2 DT T 13 " 0.048 2.00e-02 2.50e+03 pdb=" O2 DT T 13 " 0.141 2.00e-02 2.50e+03 pdb=" N3 DT T 13 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DT T 13 " -0.040 2.00e-02 2.50e+03 pdb=" O4 DT T 13 " -0.152 2.00e-02 2.50e+03 pdb=" C5 DT T 13 " 0.049 2.00e-02 2.50e+03 pdb=" C7 DT T 13 " 0.081 2.00e-02 2.50e+03 pdb=" C6 DT T 13 " 0.076 2.00e-02 2.50e+03 ... (remaining 13866 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 605 2.59 - 3.17: 66441 3.17 - 3.75: 127264 3.75 - 4.32: 176481 4.32 - 4.90: 288849 Nonbonded interactions: 659640 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 2.168 2.440 nonbonded pdb=" OP1 A P 11 " pdb="MG MG A1803 " model vdw 2.168 2.170 nonbonded pdb=" O ILE u 145 " pdb=" OG1 THR u 149 " model vdw 2.172 2.440 nonbonded pdb=" OD2 ASP E 47 " pdb=" NE2 GLN E 53 " model vdw 2.191 2.520 ... (remaining 659635 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 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = (chain 'd' and resid 29 through 121) selection = chain 'h' } 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 6.540 Check model and map are aligned: 0.890 Set scattering table: 0.550 Process input model: 209.660 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.280 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 223.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 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 0.079 83085 Z= 0.374 Angle : 0.726 9.670 113104 Z= 0.453 Chirality : 0.047 0.383 12586 Planarity : 0.007 0.248 13869 Dihedral : 15.418 161.314 32302 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.30 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.89 % 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: 1.28 (0.09), residues: 9406 helix: 1.92 (0.08), residues: 4099 sheet: 0.35 (0.14), residues: 1382 loop : -0.03 (0.10), residues: 3925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.116 0.004 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 0.021 0.001 ARG j 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 913 time to evaluate : 7.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 306 ASP cc_start: 0.8371 (t0) cc_final: 0.8168 (t0) REVERT: A 548 MET cc_start: 0.8601 (mtm) cc_final: 0.7910 (mtp) REVERT: A 903 MET cc_start: 0.8007 (mmt) cc_final: 0.7555 (mmm) REVERT: A 1065 MET cc_start: 0.9045 (mmm) cc_final: 0.8747 (mmt) REVERT: B 326 ILE cc_start: 0.9074 (mm) cc_final: 0.8844 (mt) REVERT: B 349 LEU cc_start: 0.9558 (tp) cc_final: 0.9348 (tp) REVERT: B 506 GLN cc_start: 0.7862 (mt0) cc_final: 0.7648 (mt0) REVERT: B 556 MET cc_start: 0.9032 (ttt) cc_final: 0.8825 (ptm) REVERT: B 839 MET cc_start: 0.8271 (ptp) cc_final: 0.7886 (ptp) REVERT: B 944 THR cc_start: 0.8980 (p) cc_final: 0.8777 (p) REVERT: B 1125 ASP cc_start: 0.8065 (t0) cc_final: 0.7849 (t0) REVERT: E 49 MET cc_start: 0.8704 (pmm) cc_final: 0.8429 (pmm) REVERT: E 60 LEU cc_start: 0.8551 (mt) cc_final: 0.8162 (tt) REVERT: G 158 TYR cc_start: 0.7976 (m-80) cc_final: 0.7669 (m-80) REVERT: H 38 LEU cc_start: 0.8934 (tp) cc_final: 0.8568 (tt) REVERT: I 8 LEU cc_start: 0.8677 (mt) cc_final: 0.8434 (tp) REVERT: J 22 LEU cc_start: 0.9314 (mt) cc_final: 0.8794 (mm) REVERT: m 291 GLU cc_start: 0.7618 (tt0) cc_final: 0.7366 (mt-10) REVERT: m 479 LYS cc_start: 0.4588 (tttt) cc_final: 0.4377 (mmtm) REVERT: m 480 ASN cc_start: 0.7255 (m-40) cc_final: 0.6937 (t0) REVERT: m 542 MET cc_start: 0.6869 (mtm) cc_final: 0.5869 (mmt) REVERT: m 563 MET cc_start: 0.3197 (tpp) cc_final: 0.2364 (ptm) REVERT: m 661 GLN cc_start: 0.8183 (mm110) cc_final: 0.7944 (pt0) REVERT: m 1031 VAL cc_start: 0.5723 (t) cc_final: 0.5486 (p) REVERT: m 1069 ASP cc_start: 0.4631 (m-30) cc_final: 0.4100 (m-30) REVERT: n 153 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7879 (mp0) REVERT: n 275 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7411 (ttp80) REVERT: q 405 MET cc_start: 0.1858 (ttp) cc_final: 0.0999 (tmm) REVERT: q 466 MET cc_start: 0.3668 (mtp) cc_final: 0.3203 (ttm) REVERT: q 928 MET cc_start: 0.5479 (mtt) cc_final: 0.5173 (tmm) REVERT: r 314 MET cc_start: -0.1253 (ttm) cc_final: -0.2981 (mmm) REVERT: r 315 ASP cc_start: 0.6167 (m-30) cc_final: 0.5842 (m-30) REVERT: r 329 MET cc_start: 0.4205 (tmm) cc_final: 0.2834 (tpt) REVERT: u 124 ARG cc_start: 0.7516 (mpp80) cc_final: 0.6893 (tpm170) REVERT: u 189 MET cc_start: 0.8076 (mtt) cc_final: 0.7441 (mtp) REVERT: v 344 ILE cc_start: 0.4532 (pt) cc_final: 0.3830 (mp) REVERT: v 362 MET cc_start: 0.6663 (mmm) cc_final: 0.5979 (tpp) REVERT: v 366 ASN cc_start: 0.5261 (m-40) cc_final: 0.4984 (p0) REVERT: v 371 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6043 (tt0) REVERT: x 287 THR cc_start: 0.8776 (t) cc_final: 0.7607 (t) REVERT: x 329 ASN cc_start: 0.8208 (t0) cc_final: 0.7472 (p0) REVERT: x 364 LYS cc_start: 0.6624 (mttt) cc_final: 0.6357 (tmtt) REVERT: a 129 ARG cc_start: 0.6215 (ttt180) cc_final: 0.5677 (mmp80) REVERT: j 595 MET cc_start: 0.1625 (ttp) cc_final: 0.1166 (tpp) REVERT: k 11 LEU cc_start: 0.2234 (tp) cc_final: 0.1844 (tp) outliers start: 0 outliers final: 0 residues processed: 913 average time/residue: 0.8457 time to fit residues: 1265.6332 Evaluate side-chains 430 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 7.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 808 optimal weight: 50.0000 chunk 726 optimal weight: 30.0000 chunk 402 optimal weight: 40.0000 chunk 248 optimal weight: 2.9990 chunk 489 optimal weight: 50.0000 chunk 387 optimal weight: 10.0000 chunk 750 optimal weight: 20.0000 chunk 290 optimal weight: 30.0000 chunk 456 optimal weight: 40.0000 chunk 558 optimal weight: 20.0000 chunk 869 optimal weight: 50.0000 overall best weight: 16.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN A 359 ASN ** A 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN B 531 ASN B 887 HIS B 958 GLN B1084 GLN B1195 HIS C 25 ASN C 150 HIS ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 HIS ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 52 HIS W 402 HIS ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 438 ASN ** W 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 358 HIS m 386 ASN m 480 ASN m 587 GLN m 896 ASN ** m 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 962 ASN m1004 HIS m1271 GLN n 156 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 340 ASN ** v 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 251 GLN x 293 GLN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 60 ASN f 27 GLN ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 GLN h 92 GLN ** j 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 864 GLN k 127 ASN k 143 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.182 83085 Z= 0.884 Angle : 0.933 13.729 113104 Z= 0.483 Chirality : 0.053 0.269 12586 Planarity : 0.007 0.058 13869 Dihedral : 15.589 163.865 12963 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.60 % Rotamer: Outliers : 1.49 % Allowed : 7.70 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 0.58 (0.09), residues: 9406 helix: 1.27 (0.08), residues: 4141 sheet: -0.02 (0.14), residues: 1361 loop : -0.33 (0.10), residues: 3904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP x 292 HIS 0.023 0.003 HIS A 459 PHE 0.033 0.003 PHE C 191 TYR 0.034 0.003 TYR C 81 ARG 0.017 0.001 ARG D 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 399 time to evaluate : 7.139 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: A 548 MET cc_start: 0.8910 (mtm) cc_final: 0.8428 (mtp) REVERT: A 903 MET cc_start: 0.8599 (mmt) cc_final: 0.8127 (mmt) REVERT: A 1145 LEU cc_start: 0.9621 (tp) cc_final: 0.9361 (tp) REVERT: A 1262 MET cc_start: 0.7972 (tpp) cc_final: 0.7303 (tpp) REVERT: A 1302 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8427 (pttm) REVERT: B 99 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8192 (ttp) REVERT: B 190 MET cc_start: 0.8088 (pmm) cc_final: 0.7872 (pmm) REVERT: B 968 MET cc_start: 0.8178 (ttp) cc_final: 0.7900 (ppp) REVERT: B 1136 ASP cc_start: 0.8070 (m-30) cc_final: 0.7809 (m-30) REVERT: E 49 MET cc_start: 0.9116 (pmm) cc_final: 0.8714 (pmm) REVERT: G 52 MET cc_start: 0.7869 (pmm) cc_final: 0.7505 (pmm) REVERT: G 131 MET cc_start: 0.6005 (ptp) cc_final: 0.5582 (ptp) REVERT: I 97 MET cc_start: 0.8576 (mtm) cc_final: 0.8346 (mtm) REVERT: J 57 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7292 (mm-30) REVERT: K 8 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8034 (mm-30) REVERT: L 70 ASP cc_start: 0.8522 (t0) cc_final: 0.8316 (t0) REVERT: W 549 ASP cc_start: 0.7775 (m-30) cc_final: 0.7377 (t0) REVERT: m 479 LYS cc_start: 0.4621 (tttt) cc_final: 0.4408 (mmtm) REVERT: m 542 MET cc_start: 0.6829 (mtm) cc_final: 0.5734 (mmt) REVERT: m 563 MET cc_start: 0.2581 (tpp) cc_final: 0.2098 (ptt) REVERT: m 661 GLN cc_start: 0.8240 (mm110) cc_final: 0.7995 (pt0) REVERT: m 1289 MET cc_start: 0.5372 (mmp) cc_final: 0.4624 (mtt) REVERT: n 153 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7552 (tm-30) REVERT: n 260 MET cc_start: 0.7976 (mmp) cc_final: 0.7761 (mmp) REVERT: n 275 ARG cc_start: 0.8309 (mtt180) cc_final: 0.7794 (ttp80) REVERT: n 289 MET cc_start: 0.7409 (mtp) cc_final: 0.6988 (mtt) REVERT: q 405 MET cc_start: 0.2041 (ttp) cc_final: 0.1495 (tmm) REVERT: q 466 MET cc_start: 0.3214 (mtp) cc_final: 0.2848 (ttm) REVERT: q 873 MET cc_start: 0.9357 (mmp) cc_final: 0.9013 (mmp) REVERT: r 318 ASP cc_start: 0.2657 (OUTLIER) cc_final: 0.2260 (m-30) REVERT: r 329 MET cc_start: 0.3344 (tmm) cc_final: 0.2169 (mmm) REVERT: u 124 ARG cc_start: 0.7193 (mpp80) cc_final: 0.6689 (tpm170) REVERT: v 351 MET cc_start: 0.5481 (tmm) cc_final: 0.5069 (ppp) REVERT: v 362 MET cc_start: 0.6926 (mmm) cc_final: 0.6376 (tpt) REVERT: v 366 ASN cc_start: 0.4934 (m-40) cc_final: 0.4040 (p0) REVERT: v 371 GLU cc_start: 0.6048 (mt-10) cc_final: 0.5710 (tt0) REVERT: x 297 TYR cc_start: 0.7434 (m-10) cc_final: 0.7198 (m-10) REVERT: x 329 ASN cc_start: 0.8408 (t0) cc_final: 0.7992 (p0) REVERT: x 364 LYS cc_start: 0.6791 (mttt) cc_final: 0.6426 (tmtt) REVERT: a 83 ARG cc_start: 0.0833 (mmt180) cc_final: 0.0379 (mmm160) REVERT: a 129 ARG cc_start: 0.5992 (ttt180) cc_final: 0.5509 (mmp80) REVERT: j 774 ASP cc_start: 0.2332 (OUTLIER) cc_final: 0.1173 (t0) REVERT: k 78 ASP cc_start: 0.1882 (OUTLIER) cc_final: 0.1594 (p0) outliers start: 126 outliers final: 82 residues processed: 501 average time/residue: 0.7521 time to fit residues: 654.4516 Evaluate side-chains 429 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 342 time to evaluate : 7.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1042 ASP Chi-restraints excluded: chain A residue 1097 THR Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1168 ASP Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1302 LYS Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1090 THR Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 64 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 72 LEU Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 781 GLU Chi-restraints excluded: chain m residue 318 LYS Chi-restraints excluded: chain m residue 468 ASP Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1277 GLU Chi-restraints excluded: chain m residue 1384 MET Chi-restraints excluded: chain n residue 194 VAL Chi-restraints excluded: chain n residue 272 ASN Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 460 VAL Chi-restraints excluded: chain r residue 197 THR Chi-restraints excluded: chain r residue 318 ASP Chi-restraints excluded: chain r residue 395 VAL Chi-restraints excluded: chain u residue 251 VAL Chi-restraints excluded: chain x residue 325 VAL Chi-restraints excluded: chain f residue 61 PHE Chi-restraints excluded: chain g residue 57 TYR Chi-restraints excluded: chain h residue 118 TYR Chi-restraints excluded: chain j residue 602 THR Chi-restraints excluded: chain j residue 774 ASP Chi-restraints excluded: chain k residue 78 ASP Chi-restraints excluded: chain k residue 166 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 483 optimal weight: 20.0000 chunk 270 optimal weight: 3.9990 chunk 724 optimal weight: 5.9990 chunk 592 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 871 optimal weight: 7.9990 chunk 941 optimal weight: 30.0000 chunk 776 optimal weight: 40.0000 chunk 864 optimal weight: 50.0000 chunk 297 optimal weight: 8.9990 chunk 699 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN A 436 HIS A 768 GLN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 144 GLN G 24 GLN H 44 ASN I 11 ASN I 31 ASN I 46 HIS K 85 GLN ** V 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 264 GLN ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 425 HIS ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 615 HIS q 758 HIS r 252 GLN r 340 ASN u 203 HIS v 132 GLN ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 305 GLN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 864 GLN k 13 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 83085 Z= 0.365 Angle : 0.582 11.353 113104 Z= 0.309 Chirality : 0.042 0.162 12586 Planarity : 0.004 0.053 13869 Dihedral : 15.438 158.267 12963 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.84 % Favored : 97.15 % Rotamer: Outliers : 1.29 % Allowed : 9.68 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 1.09 (0.09), residues: 9406 helix: 1.79 (0.08), residues: 4125 sheet: 0.06 (0.14), residues: 1366 loop : -0.11 (0.10), residues: 3915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP q 64 HIS 0.007 0.001 HIS C 64 PHE 0.019 0.002 PHE n 238 TYR 0.020 0.001 TYR j 929 ARG 0.008 0.000 ARG v 361 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 369 time to evaluate : 7.215 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 548 MET cc_start: 0.8852 (mtm) cc_final: 0.8210 (mtp) REVERT: A 903 MET cc_start: 0.8559 (mmt) cc_final: 0.7915 (mmm) REVERT: A 1145 LEU cc_start: 0.9526 (tp) cc_final: 0.9053 (pt) REVERT: A 1169 PHE cc_start: 0.8508 (m-80) cc_final: 0.8261 (m-10) REVERT: A 1262 MET cc_start: 0.7986 (tpp) cc_final: 0.7623 (tpp) REVERT: A 1302 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8488 (pttm) REVERT: B 99 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8152 (ttp) REVERT: B 190 MET cc_start: 0.8083 (pmm) cc_final: 0.7794 (pmm) REVERT: B 363 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7290 (t80) REVERT: B 968 MET cc_start: 0.8024 (ttp) cc_final: 0.7739 (ppp) REVERT: B 1152 MET cc_start: 0.8625 (mmm) cc_final: 0.8333 (mmm) REVERT: E 49 MET cc_start: 0.9001 (pmm) cc_final: 0.8612 (pmm) REVERT: G 52 MET cc_start: 0.7881 (pmm) cc_final: 0.7498 (pmm) REVERT: G 131 MET cc_start: 0.5957 (ptp) cc_final: 0.5504 (ptp) REVERT: H 9 ILE cc_start: 0.9706 (OUTLIER) cc_final: 0.9477 (tp) REVERT: K 55 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7304 (p0) REVERT: M 70 TYR cc_start: 0.8694 (t80) cc_final: 0.8463 (t80) REVERT: W 549 ASP cc_start: 0.7839 (m-30) cc_final: 0.7443 (t0) REVERT: W 578 ASN cc_start: 0.6435 (OUTLIER) cc_final: 0.6023 (p0) REVERT: W 771 LYS cc_start: 0.9061 (mmmm) cc_final: 0.8843 (mmmm) REVERT: m 542 MET cc_start: 0.6884 (mtm) cc_final: 0.5709 (mmt) REVERT: m 563 MET cc_start: 0.2573 (tpp) cc_final: 0.1858 (ptt) REVERT: m 661 GLN cc_start: 0.8237 (mm110) cc_final: 0.8001 (pt0) REVERT: m 1289 MET cc_start: 0.5385 (mmp) cc_final: 0.4646 (mtt) REVERT: n 153 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7506 (tm-30) REVERT: n 275 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8098 (ttp80) REVERT: n 289 MET cc_start: 0.7683 (mtp) cc_final: 0.7245 (mtt) REVERT: q 299 MET cc_start: 0.5107 (tmm) cc_final: 0.4136 (ptm) REVERT: q 405 MET cc_start: 0.1237 (ttp) cc_final: 0.0818 (tmm) REVERT: q 466 MET cc_start: 0.3258 (mtp) cc_final: 0.2747 (ttm) REVERT: q 721 MET cc_start: 0.6703 (mtp) cc_final: 0.6443 (mtp) REVERT: q 744 MET cc_start: 0.3180 (ptt) cc_final: 0.2917 (ptt) REVERT: q 766 MET cc_start: 0.9369 (pmm) cc_final: 0.8850 (tpt) REVERT: q 873 MET cc_start: 0.9324 (mmp) cc_final: 0.8999 (mmp) REVERT: r 211 MET cc_start: 0.5279 (mtt) cc_final: 0.5034 (ptp) REVERT: r 252 GLN cc_start: 0.5699 (OUTLIER) cc_final: 0.5423 (pm20) REVERT: r 329 MET cc_start: 0.3216 (tmm) cc_final: 0.2164 (tpt) REVERT: u 126 PHE cc_start: 0.5192 (t80) cc_final: 0.4931 (m-10) REVERT: v 351 MET cc_start: 0.5439 (tmm) cc_final: 0.4855 (ttm) REVERT: v 362 MET cc_start: 0.6855 (mmm) cc_final: 0.6379 (tmm) REVERT: v 366 ASN cc_start: 0.4751 (m-40) cc_final: 0.3946 (p0) REVERT: v 371 GLU cc_start: 0.6527 (mt-10) cc_final: 0.5862 (tt0) REVERT: x 364 LYS cc_start: 0.6744 (mttt) cc_final: 0.6351 (tmtt) REVERT: a 129 ARG cc_start: 0.6099 (ttt180) cc_final: 0.5730 (mmp80) REVERT: c 56 GLU cc_start: 0.4344 (pt0) cc_final: 0.3343 (tp30) outliers start: 109 outliers final: 56 residues processed: 448 average time/residue: 0.7152 time to fit residues: 567.9006 Evaluate side-chains 400 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 337 time to evaluate : 7.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1302 LYS Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain m residue 922 ASP Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1384 MET Chi-restraints excluded: chain n residue 194 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 460 VAL Chi-restraints excluded: chain q residue 859 ASN Chi-restraints excluded: chain r residue 252 GLN Chi-restraints excluded: chain r residue 395 VAL Chi-restraints excluded: chain v residue 374 ILE Chi-restraints excluded: chain x residue 325 VAL Chi-restraints excluded: chain d residue 56 MET Chi-restraints excluded: chain f residue 61 PHE Chi-restraints excluded: chain g residue 57 TYR Chi-restraints excluded: chain j residue 717 HIS Chi-restraints excluded: chain k residue 10 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 861 optimal weight: 10.0000 chunk 655 optimal weight: 7.9990 chunk 452 optimal weight: 0.6980 chunk 96 optimal weight: 7.9990 chunk 415 optimal weight: 20.0000 chunk 585 optimal weight: 50.0000 chunk 874 optimal weight: 40.0000 chunk 926 optimal weight: 40.0000 chunk 456 optimal weight: 5.9990 chunk 828 optimal weight: 50.0000 chunk 249 optimal weight: 0.6980 overall best weight: 4.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN H 13 GLN W 264 GLN ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 480 ASN ** m 962 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 319 ASN q 459 ASN ** q 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 864 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 83085 Z= 0.284 Angle : 0.534 10.524 113104 Z= 0.283 Chirality : 0.041 0.151 12586 Planarity : 0.004 0.052 13869 Dihedral : 15.312 158.105 12963 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.89 % Favored : 97.10 % Rotamer: Outliers : 1.50 % Allowed : 10.44 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 1.28 (0.09), residues: 9406 helix: 1.97 (0.08), residues: 4138 sheet: 0.08 (0.14), residues: 1376 loop : 0.01 (0.10), residues: 3892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP x 292 HIS 0.005 0.001 HIS A1269 PHE 0.055 0.001 PHE n 238 TYR 0.030 0.001 TYR m 976 ARG 0.006 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 357 time to evaluate : 8.229 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: A 108 MET cc_start: 0.8526 (mmp) cc_final: 0.8216 (mmp) REVERT: A 282 MET cc_start: 0.7532 (tmm) cc_final: 0.7219 (tmm) REVERT: A 337 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9084 (mm) REVERT: A 548 MET cc_start: 0.8807 (mtm) cc_final: 0.8198 (mtp) REVERT: A 903 MET cc_start: 0.8421 (mmt) cc_final: 0.7840 (mmm) REVERT: A 1229 MET cc_start: 0.7893 (mmm) cc_final: 0.7635 (mmm) REVERT: A 1262 MET cc_start: 0.7966 (tpp) cc_final: 0.7603 (tpp) REVERT: A 1302 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8440 (pttm) REVERT: B 190 MET cc_start: 0.8030 (pmm) cc_final: 0.7824 (pmm) REVERT: B 363 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7316 (t80) REVERT: B 968 MET cc_start: 0.7963 (ttp) cc_final: 0.7701 (ppp) REVERT: B 1152 MET cc_start: 0.8635 (mmm) cc_final: 0.8349 (mmm) REVERT: E 49 MET cc_start: 0.9044 (pmm) cc_final: 0.8586 (pmm) REVERT: E 83 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8076 (m-30) REVERT: G 52 MET cc_start: 0.7998 (pmm) cc_final: 0.7726 (pmm) REVERT: G 131 MET cc_start: 0.5924 (ptp) cc_final: 0.5462 (ptp) REVERT: J 57 GLU cc_start: 0.7077 (mm-30) cc_final: 0.6728 (mm-30) REVERT: M 70 TYR cc_start: 0.8717 (t80) cc_final: 0.8470 (t80) REVERT: V 25 MET cc_start: 0.7365 (tpp) cc_final: 0.7008 (tpp) REVERT: W 549 ASP cc_start: 0.7846 (m-30) cc_final: 0.7601 (t0) REVERT: W 771 LYS cc_start: 0.9087 (mmmm) cc_final: 0.8855 (mmmm) REVERT: m 511 MET cc_start: 0.1521 (ptm) cc_final: 0.0654 (tpt) REVERT: m 542 MET cc_start: 0.6903 (mtm) cc_final: 0.5700 (mmt) REVERT: m 563 MET cc_start: 0.2491 (tpp) cc_final: 0.2060 (ptm) REVERT: m 661 GLN cc_start: 0.8338 (mm110) cc_final: 0.8038 (pt0) REVERT: m 1289 MET cc_start: 0.5401 (mmp) cc_final: 0.4681 (mtt) REVERT: n 153 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7370 (tm-30) REVERT: n 167 MET cc_start: 0.7803 (ttt) cc_final: 0.7549 (ttt) REVERT: n 275 ARG cc_start: 0.8695 (mtt180) cc_final: 0.8192 (ttp80) REVERT: n 289 MET cc_start: 0.7695 (mtp) cc_final: 0.7270 (mtt) REVERT: q 299 MET cc_start: 0.5041 (tmm) cc_final: 0.4569 (ppp) REVERT: q 405 MET cc_start: 0.1277 (ttp) cc_final: 0.0816 (tmm) REVERT: q 466 MET cc_start: 0.3240 (mtp) cc_final: 0.2716 (ttm) REVERT: q 721 MET cc_start: 0.7191 (mtp) cc_final: 0.6907 (mtp) REVERT: q 744 MET cc_start: 0.3815 (ptt) cc_final: 0.3506 (ptt) REVERT: q 766 MET cc_start: 0.9380 (pmm) cc_final: 0.8851 (tpt) REVERT: q 873 MET cc_start: 0.9324 (mmp) cc_final: 0.9006 (mmp) REVERT: r 314 MET cc_start: -0.0929 (ttm) cc_final: -0.2342 (mmm) REVERT: r 329 MET cc_start: 0.3377 (tmm) cc_final: 0.2277 (tpt) REVERT: u 189 MET cc_start: 0.7467 (mtp) cc_final: 0.7099 (mtp) REVERT: u 210 MET cc_start: 0.4882 (tpt) cc_final: 0.4682 (tpp) REVERT: v 351 MET cc_start: 0.5482 (tmm) cc_final: 0.4949 (ttm) REVERT: v 362 MET cc_start: 0.6917 (mmm) cc_final: 0.6284 (tpt) REVERT: v 366 ASN cc_start: 0.4599 (m-40) cc_final: 0.3739 (p0) REVERT: v 371 GLU cc_start: 0.6497 (mt-10) cc_final: 0.5838 (tt0) REVERT: x 292 TRP cc_start: 0.6519 (p-90) cc_final: 0.6193 (p-90) REVERT: x 364 LYS cc_start: 0.6791 (mttt) cc_final: 0.6380 (tmtt) REVERT: a 120 MET cc_start: 0.1002 (mmm) cc_final: 0.0261 (mmm) REVERT: a 129 ARG cc_start: 0.6218 (ttt180) cc_final: 0.5662 (mmp80) REVERT: c 56 GLU cc_start: 0.4253 (pt0) cc_final: 0.3107 (tp30) REVERT: e 55 GLN cc_start: 0.5303 (mp10) cc_final: 0.4932 (mp10) REVERT: j 584 MET cc_start: -0.0295 (tpp) cc_final: -0.0669 (tpp) REVERT: j 774 ASP cc_start: 0.2298 (OUTLIER) cc_final: 0.1260 (t0) outliers start: 127 outliers final: 80 residues processed: 457 average time/residue: 0.7270 time to fit residues: 588.7569 Evaluate side-chains 417 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 332 time to evaluate : 7.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1302 LYS Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 436 ILE Chi-restraints excluded: chain W residue 781 GLU Chi-restraints excluded: chain m residue 611 PHE Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 922 ASP Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1384 MET Chi-restraints excluded: chain n residue 194 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 859 ASN Chi-restraints excluded: chain r residue 395 VAL Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain u residue 162 ILE Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 180 LEU Chi-restraints excluded: chain x residue 325 VAL Chi-restraints excluded: chain x residue 335 ILE Chi-restraints excluded: chain d residue 56 MET Chi-restraints excluded: chain f residue 61 PHE Chi-restraints excluded: chain j residue 717 HIS Chi-restraints excluded: chain j residue 774 ASP Chi-restraints excluded: chain k residue 10 PHE Chi-restraints excluded: chain k residue 60 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 771 optimal weight: 30.0000 chunk 525 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 689 optimal weight: 9.9990 chunk 382 optimal weight: 2.9990 chunk 790 optimal weight: 0.0870 chunk 640 optimal weight: 30.0000 chunk 1 optimal weight: 2.9990 chunk 472 optimal weight: 10.0000 chunk 831 optimal weight: 50.0000 chunk 233 optimal weight: 0.8980 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN A 768 GLN B 63 GLN ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 GLN C 25 ASN ** V 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 962 ASN m 998 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 349 GLN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 591 ASN j 864 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 83085 Z= 0.221 Angle : 0.498 10.912 113104 Z= 0.264 Chirality : 0.040 0.209 12586 Planarity : 0.003 0.055 13869 Dihedral : 15.215 157.971 12963 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.65 % Favored : 97.33 % Rotamer: Outliers : 1.39 % Allowed : 11.16 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 1.44 (0.09), residues: 9406 helix: 2.12 (0.08), residues: 4141 sheet: 0.12 (0.14), residues: 1371 loop : 0.08 (0.10), residues: 3894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 64 HIS 0.005 0.001 HIS v 164 PHE 0.024 0.001 PHE W 293 TYR 0.018 0.001 TYR m 976 ARG 0.010 0.000 ARG W 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 357 time to evaluate : 7.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9110 (mm) REVERT: A 548 MET cc_start: 0.8623 (mtm) cc_final: 0.8118 (mtp) REVERT: A 903 MET cc_start: 0.8374 (mmt) cc_final: 0.7821 (mmm) REVERT: A 914 ILE cc_start: 0.9479 (OUTLIER) cc_final: 0.9230 (mt) REVERT: A 1169 PHE cc_start: 0.8636 (m-10) cc_final: 0.8429 (m-10) REVERT: A 1229 MET cc_start: 0.8205 (mmm) cc_final: 0.7940 (mmm) REVERT: A 1262 MET cc_start: 0.7999 (tpp) cc_final: 0.7519 (tpp) REVERT: A 1302 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8488 (pttm) REVERT: B 190 MET cc_start: 0.8117 (pmm) cc_final: 0.7900 (pmm) REVERT: B 363 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7624 (t80) REVERT: B 556 MET cc_start: 0.8718 (ttt) cc_final: 0.8045 (ttt) REVERT: B 968 MET cc_start: 0.7947 (ttp) cc_final: 0.7681 (ppp) REVERT: B 1152 MET cc_start: 0.8530 (mmm) cc_final: 0.8229 (mmm) REVERT: C 36 MET cc_start: 0.7987 (mtp) cc_final: 0.7729 (mtp) REVERT: E 49 MET cc_start: 0.9024 (pmm) cc_final: 0.8535 (pmm) REVERT: E 83 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: G 52 MET cc_start: 0.7622 (pmm) cc_final: 0.7412 (pmm) REVERT: H 9 ILE cc_start: 0.9709 (OUTLIER) cc_final: 0.9440 (tp) REVERT: H 45 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7736 (mm-30) REVERT: J 57 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6712 (mm-30) REVERT: M 70 TYR cc_start: 0.8625 (t80) cc_final: 0.8416 (t80) REVERT: V 25 MET cc_start: 0.7152 (tpp) cc_final: 0.6700 (tpt) REVERT: W 549 ASP cc_start: 0.7819 (m-30) cc_final: 0.7587 (t0) REVERT: W 771 LYS cc_start: 0.9141 (mmmm) cc_final: 0.8912 (mmmm) REVERT: m 511 MET cc_start: 0.1472 (ptm) cc_final: 0.0649 (tpt) REVERT: m 563 MET cc_start: 0.3841 (tpp) cc_final: 0.3092 (ptm) REVERT: m 661 GLN cc_start: 0.8337 (mm110) cc_final: 0.8034 (pt0) REVERT: m 1197 ILE cc_start: 0.6005 (OUTLIER) cc_final: 0.5428 (mm) REVERT: m 1289 MET cc_start: 0.5379 (mmp) cc_final: 0.4671 (mtp) REVERT: n 153 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7482 (tm-30) REVERT: n 178 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6900 (mm) REVERT: n 275 ARG cc_start: 0.8704 (mtt180) cc_final: 0.8189 (ttp80) REVERT: n 289 MET cc_start: 0.7559 (mtp) cc_final: 0.7105 (mtt) REVERT: q 299 MET cc_start: 0.4682 (tmm) cc_final: 0.4355 (ppp) REVERT: q 405 MET cc_start: 0.1116 (ttp) cc_final: 0.0626 (tmm) REVERT: q 466 MET cc_start: 0.3240 (mtp) cc_final: 0.2756 (ttm) REVERT: q 721 MET cc_start: 0.7222 (mtp) cc_final: 0.6958 (mtp) REVERT: q 744 MET cc_start: 0.4136 (ptt) cc_final: 0.3761 (ptt) REVERT: q 766 MET cc_start: 0.9388 (pmm) cc_final: 0.8853 (tpt) REVERT: q 873 MET cc_start: 0.9295 (mmp) cc_final: 0.8964 (mmp) REVERT: r 211 MET cc_start: 0.5272 (mtt) cc_final: 0.4960 (ptp) REVERT: r 282 MET cc_start: 0.0685 (ptp) cc_final: 0.0454 (ptp) REVERT: r 314 MET cc_start: -0.0930 (ttm) cc_final: -0.2375 (mmm) REVERT: r 329 MET cc_start: 0.3330 (tmm) cc_final: 0.2221 (tpt) REVERT: u 189 MET cc_start: 0.7431 (mtp) cc_final: 0.7170 (mtp) REVERT: u 210 MET cc_start: 0.4868 (tpt) cc_final: 0.4668 (tpp) REVERT: v 351 MET cc_start: 0.5589 (tmm) cc_final: 0.5073 (ttm) REVERT: v 362 MET cc_start: 0.6834 (mmm) cc_final: 0.6170 (tpt) REVERT: v 366 ASN cc_start: 0.4185 (m-40) cc_final: 0.3312 (p0) REVERT: v 371 GLU cc_start: 0.6547 (mt-10) cc_final: 0.5917 (tt0) REVERT: x 307 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.6959 (mt0) REVERT: x 364 LYS cc_start: 0.6763 (mttt) cc_final: 0.6363 (tmtt) REVERT: a 120 MET cc_start: 0.0919 (mmm) cc_final: 0.0268 (mmm) REVERT: a 129 ARG cc_start: 0.6109 (ttt180) cc_final: 0.5538 (mmp80) REVERT: a 134 ARG cc_start: 0.3701 (mpt-90) cc_final: 0.3416 (tmt170) REVERT: c 56 GLU cc_start: 0.4161 (pt0) cc_final: 0.2954 (tp30) REVERT: d 59 MET cc_start: 0.4372 (ttm) cc_final: 0.3641 (mmm) REVERT: j 900 TRP cc_start: 0.1391 (OUTLIER) cc_final: 0.0953 (t60) outliers start: 118 outliers final: 74 residues processed: 449 average time/residue: 0.7253 time to fit residues: 576.7222 Evaluate side-chains 416 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 332 time to evaluate : 7.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1302 LYS Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 436 ILE Chi-restraints excluded: chain W residue 689 ARG Chi-restraints excluded: chain W residue 781 GLU Chi-restraints excluded: chain m residue 611 PHE Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 922 ASP Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1197 ILE Chi-restraints excluded: chain m residue 1384 MET Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 194 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 460 VAL Chi-restraints excluded: chain r residue 395 VAL Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain u residue 180 LEU Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 325 VAL Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain d residue 56 MET Chi-restraints excluded: chain e residue 55 GLN Chi-restraints excluded: chain f residue 61 PHE Chi-restraints excluded: chain j residue 602 THR Chi-restraints excluded: chain j residue 717 HIS Chi-restraints excluded: chain j residue 900 TRP Chi-restraints excluded: chain k residue 10 PHE Chi-restraints excluded: chain k residue 60 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 311 optimal weight: 9.9990 chunk 833 optimal weight: 30.0000 chunk 183 optimal weight: 0.0670 chunk 543 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 926 optimal weight: 40.0000 chunk 769 optimal weight: 50.0000 chunk 429 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 306 optimal weight: 10.0000 chunk 486 optimal weight: 9.9990 overall best weight: 6.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN G 107 ASN H 44 ASN W 346 ASN ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 947 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 212 HIS ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 83085 Z= 0.372 Angle : 0.581 10.465 113104 Z= 0.304 Chirality : 0.042 0.233 12586 Planarity : 0.004 0.051 13869 Dihedral : 15.203 160.813 12963 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 2.07 % Allowed : 11.46 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 1.27 (0.09), residues: 9406 helix: 1.97 (0.08), residues: 4150 sheet: -0.02 (0.14), residues: 1374 loop : 0.02 (0.10), residues: 3882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP x 292 HIS 0.007 0.001 HIS A 459 PHE 0.025 0.002 PHE n 238 TYR 0.020 0.002 TYR m 521 ARG 0.010 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 352 time to evaluate : 7.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8511 (ttm) cc_final: 0.8283 (ttm) REVERT: A 399 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7642 (pt0) REVERT: A 548 MET cc_start: 0.8834 (mtm) cc_final: 0.8181 (mtp) REVERT: A 903 MET cc_start: 0.8508 (mmt) cc_final: 0.8062 (mmt) REVERT: A 914 ILE cc_start: 0.9479 (OUTLIER) cc_final: 0.9217 (mt) REVERT: A 1112 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7682 (p0) REVERT: A 1262 MET cc_start: 0.8007 (tpp) cc_final: 0.7534 (tpp) REVERT: A 1302 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8548 (pttm) REVERT: B 363 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7354 (t80) REVERT: B 773 MET cc_start: 0.8472 (mtm) cc_final: 0.8265 (mtm) REVERT: B 968 MET cc_start: 0.8057 (ttp) cc_final: 0.7820 (ppp) REVERT: B 1152 MET cc_start: 0.8634 (mmm) cc_final: 0.8329 (mmm) REVERT: E 30 SER cc_start: 0.8080 (OUTLIER) cc_final: 0.7876 (p) REVERT: E 49 MET cc_start: 0.9094 (pmm) cc_final: 0.8465 (pmm) REVERT: E 83 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: G 52 MET cc_start: 0.7788 (pmm) cc_final: 0.7490 (pmm) REVERT: H 125 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: I 52 ILE cc_start: 0.8184 (mt) cc_final: 0.7865 (pt) REVERT: I 97 MET cc_start: 0.8622 (mtm) cc_final: 0.8389 (mtm) REVERT: J 57 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6958 (mm-30) REVERT: K 55 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7280 (p0) REVERT: V 25 MET cc_start: 0.7477 (tpp) cc_final: 0.6768 (tpp) REVERT: W 549 ASP cc_start: 0.7838 (m-30) cc_final: 0.7601 (t0) REVERT: W 578 ASN cc_start: 0.6601 (OUTLIER) cc_final: 0.6352 (p0) REVERT: W 771 LYS cc_start: 0.9105 (mmmm) cc_final: 0.8876 (mmmm) REVERT: m 511 MET cc_start: 0.1204 (ptm) cc_final: 0.0587 (tpt) REVERT: m 563 MET cc_start: 0.3719 (tpp) cc_final: 0.2920 (ptm) REVERT: m 661 GLN cc_start: 0.8291 (mm110) cc_final: 0.8028 (pt0) REVERT: m 1197 ILE cc_start: 0.5797 (OUTLIER) cc_final: 0.5330 (mm) REVERT: m 1289 MET cc_start: 0.5739 (mmp) cc_final: 0.5052 (mtp) REVERT: m 1384 MET cc_start: 0.4673 (tmm) cc_final: 0.3297 (mmm) REVERT: n 153 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7367 (tm-30) REVERT: n 178 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6964 (mm) REVERT: n 275 ARG cc_start: 0.8700 (mtt180) cc_final: 0.8206 (ttp80) REVERT: n 289 MET cc_start: 0.7528 (mtp) cc_final: 0.7099 (mtt) REVERT: q 299 MET cc_start: 0.5071 (tmm) cc_final: 0.4601 (ppp) REVERT: q 405 MET cc_start: 0.1314 (ttp) cc_final: 0.0797 (tmm) REVERT: q 744 MET cc_start: 0.3048 (ptt) cc_final: 0.2793 (ptt) REVERT: q 873 MET cc_start: 0.9316 (mmp) cc_final: 0.8943 (mmp) REVERT: r 282 MET cc_start: 0.0593 (ptp) cc_final: 0.0311 (ptp) REVERT: r 314 MET cc_start: -0.0967 (ttm) cc_final: -0.2707 (mmm) REVERT: r 329 MET cc_start: 0.3256 (tmm) cc_final: 0.2181 (tpt) REVERT: u 189 MET cc_start: 0.7362 (mtp) cc_final: 0.7069 (mtp) REVERT: u 210 MET cc_start: 0.4961 (tpt) cc_final: 0.4454 (tpp) REVERT: u 261 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6694 (tp40) REVERT: v 351 MET cc_start: 0.5630 (tmm) cc_final: 0.5130 (ttm) REVERT: v 366 ASN cc_start: 0.3117 (m-40) cc_final: 0.2626 (p0) REVERT: v 371 GLU cc_start: 0.6182 (mt-10) cc_final: 0.5878 (tt0) REVERT: x 307 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6824 (mt0) REVERT: x 364 LYS cc_start: 0.6835 (mttt) cc_final: 0.6363 (tmtt) REVERT: a 129 ARG cc_start: 0.5871 (ttt180) cc_final: 0.5220 (mmp80) REVERT: a 134 ARG cc_start: 0.3916 (mpt-90) cc_final: 0.3524 (tmt170) REVERT: d 59 MET cc_start: 0.4443 (ttm) cc_final: 0.3648 (mmm) REVERT: j 774 ASP cc_start: 0.2355 (OUTLIER) cc_final: 0.1285 (t0) REVERT: j 900 TRP cc_start: 0.1453 (OUTLIER) cc_final: 0.0770 (t60) REVERT: k 84 ASP cc_start: 0.3961 (OUTLIER) cc_final: 0.2978 (t0) outliers start: 175 outliers final: 113 residues processed: 497 average time/residue: 0.7219 time to fit residues: 644.5590 Evaluate side-chains 461 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 331 time to evaluate : 7.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain A residue 1302 LYS Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 436 ILE Chi-restraints excluded: chain W residue 506 ILE Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 587 THR Chi-restraints excluded: chain W residue 689 ARG Chi-restraints excluded: chain W residue 781 GLU Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 611 PHE Chi-restraints excluded: chain m residue 725 GLU Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 922 ASP Chi-restraints excluded: chain m residue 1083 MET Chi-restraints excluded: chain m residue 1197 ILE Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 194 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 460 VAL Chi-restraints excluded: chain q residue 614 HIS Chi-restraints excluded: chain q residue 859 ASN Chi-restraints excluded: chain r residue 395 VAL Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 180 LEU Chi-restraints excluded: chain u residue 251 VAL Chi-restraints excluded: chain u residue 261 GLN Chi-restraints excluded: chain v residue 374 ILE Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 325 VAL Chi-restraints excluded: chain x residue 335 ILE Chi-restraints excluded: chain x residue 343 ASP Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain f residue 61 PHE Chi-restraints excluded: chain j residue 602 THR Chi-restraints excluded: chain j residue 717 HIS Chi-restraints excluded: chain j residue 774 ASP Chi-restraints excluded: chain j residue 900 TRP Chi-restraints excluded: chain k residue 10 PHE Chi-restraints excluded: chain k residue 84 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 893 optimal weight: 50.0000 chunk 104 optimal weight: 0.7980 chunk 528 optimal weight: 40.0000 chunk 676 optimal weight: 50.0000 chunk 524 optimal weight: 40.0000 chunk 780 optimal weight: 50.0000 chunk 517 optimal weight: 6.9990 chunk 923 optimal weight: 30.0000 chunk 577 optimal weight: 20.0000 chunk 562 optimal weight: 8.9990 chunk 426 optimal weight: 0.0010 overall best weight: 7.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 742 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1390 HIS ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 GLN ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 164 HIS v 231 GLN ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 89 ASN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 83085 Z= 0.407 Angle : 0.592 13.183 113104 Z= 0.311 Chirality : 0.042 0.262 12586 Planarity : 0.004 0.050 13869 Dihedral : 15.221 161.398 12963 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.39 % Favored : 96.59 % Rotamer: Outliers : 2.15 % Allowed : 12.09 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 1.11 (0.09), residues: 9406 helix: 1.87 (0.08), residues: 4132 sheet: -0.16 (0.14), residues: 1372 loop : -0.07 (0.10), residues: 3902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP x 292 HIS 0.007 0.001 HIS A 852 PHE 0.030 0.002 PHE n 238 TYR 0.020 0.002 TYR M 70 ARG 0.008 0.001 ARG I 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 353 time to evaluate : 7.242 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: A 337 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9050 (mm) REVERT: A 399 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: A 548 MET cc_start: 0.8630 (mtm) cc_final: 0.8131 (mtp) REVERT: A 903 MET cc_start: 0.8505 (mmt) cc_final: 0.7929 (mmm) REVERT: A 914 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9230 (mt) REVERT: A 1112 ASN cc_start: 0.8330 (OUTLIER) cc_final: 0.7682 (p0) REVERT: A 1229 MET cc_start: 0.7945 (mmm) cc_final: 0.7603 (mmm) REVERT: A 1262 MET cc_start: 0.8008 (tpp) cc_final: 0.7558 (tpp) REVERT: A 1274 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.9284 (mm) REVERT: A 1302 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8661 (pttm) REVERT: B 363 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7496 (t80) REVERT: B 864 LYS cc_start: 0.9141 (ptmt) cc_final: 0.8940 (ptmm) REVERT: B 968 MET cc_start: 0.8117 (ttp) cc_final: 0.7863 (ppp) REVERT: B 1152 MET cc_start: 0.8628 (mmm) cc_final: 0.8313 (mmm) REVERT: E 49 MET cc_start: 0.9048 (pmm) cc_final: 0.8191 (pmm) REVERT: G 52 MET cc_start: 0.7609 (pmm) cc_final: 0.7354 (pmm) REVERT: G 156 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8296 (mp0) REVERT: H 125 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7761 (mt-10) REVERT: I 52 ILE cc_start: 0.8174 (mt) cc_final: 0.7917 (pt) REVERT: J 57 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7037 (mm-30) REVERT: K 55 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7302 (p0) REVERT: V 25 MET cc_start: 0.7404 (tpp) cc_final: 0.6557 (tpp) REVERT: W 549 ASP cc_start: 0.7931 (m-30) cc_final: 0.7434 (t0) REVERT: W 771 LYS cc_start: 0.9103 (mmmm) cc_final: 0.8862 (mmmm) REVERT: m 511 MET cc_start: 0.1277 (ptm) cc_final: 0.0822 (tpt) REVERT: m 563 MET cc_start: 0.3214 (tpp) cc_final: 0.2562 (ppp) REVERT: m 661 GLN cc_start: 0.8303 (mm110) cc_final: 0.8056 (pt0) REVERT: m 925 MET cc_start: 0.8577 (mmm) cc_final: 0.8060 (mmm) REVERT: m 1197 ILE cc_start: 0.5778 (OUTLIER) cc_final: 0.5281 (mm) REVERT: m 1289 MET cc_start: 0.5769 (mmp) cc_final: 0.5046 (mtp) REVERT: m 1384 MET cc_start: 0.4873 (OUTLIER) cc_final: 0.4011 (mmm) REVERT: n 153 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7328 (tm-30) REVERT: n 178 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.6986 (mm) REVERT: n 275 ARG cc_start: 0.8659 (mtt180) cc_final: 0.8162 (ttp80) REVERT: n 289 MET cc_start: 0.7178 (mtp) cc_final: 0.6695 (mtt) REVERT: q 405 MET cc_start: 0.1313 (ttp) cc_final: 0.0768 (tmm) REVERT: q 644 MET cc_start: 0.0751 (tmm) cc_final: -0.1520 (tpp) REVERT: q 744 MET cc_start: 0.3465 (ptt) cc_final: 0.3220 (ptt) REVERT: q 873 MET cc_start: 0.9319 (mmp) cc_final: 0.8959 (mmp) REVERT: r 211 MET cc_start: 0.5460 (mtt) cc_final: 0.5003 (ptp) REVERT: r 282 MET cc_start: 0.0535 (ptp) cc_final: 0.0213 (ptp) REVERT: r 314 MET cc_start: -0.0980 (ttm) cc_final: -0.2759 (mmm) REVERT: r 329 MET cc_start: 0.3364 (tmm) cc_final: 0.2351 (tpt) REVERT: u 261 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6910 (tp40) REVERT: v 351 MET cc_start: 0.5466 (tmm) cc_final: 0.5195 (ttm) REVERT: v 366 ASN cc_start: 0.3187 (m-40) cc_final: 0.2658 (p0) REVERT: v 380 GLU cc_start: 0.7530 (pt0) cc_final: 0.6977 (mm-30) REVERT: x 307 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.6889 (mt0) REVERT: a 120 MET cc_start: 0.0244 (mmm) cc_final: -0.0342 (mmm) REVERT: a 129 ARG cc_start: 0.5882 (ttt180) cc_final: 0.5193 (mmt-90) REVERT: a 134 ARG cc_start: 0.4112 (mpt-90) cc_final: 0.3457 (tmm160) REVERT: d 59 MET cc_start: 0.4438 (ttm) cc_final: 0.3678 (mmm) REVERT: j 774 ASP cc_start: 0.2539 (OUTLIER) cc_final: 0.1459 (t70) REVERT: j 775 GLU cc_start: 0.7183 (tt0) cc_final: 0.6932 (mm-30) REVERT: j 900 TRP cc_start: 0.1839 (OUTLIER) cc_final: 0.0874 (t60) REVERT: k 84 ASP cc_start: 0.4426 (OUTLIER) cc_final: 0.3456 (t0) outliers start: 182 outliers final: 125 residues processed: 502 average time/residue: 0.7372 time to fit residues: 669.2470 Evaluate side-chains 474 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 332 time to evaluate : 7.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1208 GLN Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1302 LYS Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 536 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 815 ARG Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain B residue 1099 VAL Chi-restraints excluded: chain B residue 1101 ASP Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 436 ILE Chi-restraints excluded: chain W residue 506 ILE Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 689 ARG Chi-restraints excluded: chain W residue 781 GLU Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 611 PHE Chi-restraints excluded: chain m residue 725 GLU Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 922 ASP Chi-restraints excluded: chain m residue 1004 HIS Chi-restraints excluded: chain m residue 1197 ILE Chi-restraints excluded: chain m residue 1384 MET Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 194 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 460 VAL Chi-restraints excluded: chain q residue 614 HIS Chi-restraints excluded: chain q residue 859 ASN Chi-restraints excluded: chain r residue 395 VAL Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 180 LEU Chi-restraints excluded: chain u residue 251 VAL Chi-restraints excluded: chain u residue 261 GLN Chi-restraints excluded: chain v residue 103 HIS Chi-restraints excluded: chain v residue 174 ILE Chi-restraints excluded: chain v residue 374 ILE Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 335 ILE Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain f residue 61 PHE Chi-restraints excluded: chain j residue 602 THR Chi-restraints excluded: chain j residue 717 HIS Chi-restraints excluded: chain j residue 774 ASP Chi-restraints excluded: chain j residue 900 TRP Chi-restraints excluded: chain k residue 10 PHE Chi-restraints excluded: chain k residue 84 ASP Chi-restraints excluded: chain k residue 239 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 571 optimal weight: 40.0000 chunk 368 optimal weight: 8.9990 chunk 551 optimal weight: 40.0000 chunk 278 optimal weight: 0.1980 chunk 181 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 587 optimal weight: 10.0000 chunk 629 optimal weight: 30.0000 chunk 456 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 725 optimal weight: 30.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 65 GLN ** V 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 816 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 483 ASN ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 377 HIS u 172 GLN ** v 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 349 GLN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 HIS j 864 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 83085 Z= 0.201 Angle : 0.507 18.891 113104 Z= 0.268 Chirality : 0.040 0.291 12586 Planarity : 0.003 0.049 13869 Dihedral : 15.091 160.569 12963 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 1.36 % Allowed : 13.07 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 1.37 (0.09), residues: 9406 helix: 2.08 (0.08), residues: 4146 sheet: -0.01 (0.14), residues: 1340 loop : 0.06 (0.11), residues: 3920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP x 292 HIS 0.005 0.001 HIS A 660 PHE 0.034 0.001 PHE n 238 TYR 0.020 0.001 TYR M 70 ARG 0.006 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 351 time to evaluate : 7.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8577 (mmm) cc_final: 0.8293 (mmt) REVERT: A 337 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9051 (mm) REVERT: A 548 MET cc_start: 0.8522 (mtm) cc_final: 0.8128 (mtp) REVERT: A 709 MET cc_start: 0.8209 (mpp) cc_final: 0.7991 (mpp) REVERT: A 903 MET cc_start: 0.8391 (mmt) cc_final: 0.7835 (mmm) REVERT: A 914 ILE cc_start: 0.9457 (OUTLIER) cc_final: 0.9218 (mt) REVERT: A 1112 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7630 (p0) REVERT: A 1229 MET cc_start: 0.7961 (mmm) cc_final: 0.7541 (mmm) REVERT: A 1262 MET cc_start: 0.8121 (tpp) cc_final: 0.7646 (tpp) REVERT: B 363 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7413 (t80) REVERT: B 506 GLN cc_start: 0.7846 (mt0) cc_final: 0.7645 (mt0) REVERT: B 556 MET cc_start: 0.8687 (ttt) cc_final: 0.8072 (ttt) REVERT: B 864 LYS cc_start: 0.9090 (ptmt) cc_final: 0.8879 (ptmm) REVERT: B 1152 MET cc_start: 0.8513 (mmm) cc_final: 0.8231 (mmm) REVERT: C 36 MET cc_start: 0.7962 (mtp) cc_final: 0.7634 (mtp) REVERT: E 49 MET cc_start: 0.9006 (pmm) cc_final: 0.8335 (pmm) REVERT: E 83 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: G 156 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8249 (mp0) REVERT: H 45 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7561 (mm-30) REVERT: H 125 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: I 52 ILE cc_start: 0.7909 (mt) cc_final: 0.7657 (pt) REVERT: J 57 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6738 (mm-30) REVERT: K 38 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7554 (mm-30) REVERT: V 25 MET cc_start: 0.7390 (tpp) cc_final: 0.6879 (tpt) REVERT: W 771 LYS cc_start: 0.9127 (mmmm) cc_final: 0.8876 (mmmm) REVERT: m 563 MET cc_start: 0.3787 (tpp) cc_final: 0.3094 (ptm) REVERT: m 661 GLN cc_start: 0.8366 (mm110) cc_final: 0.8011 (pt0) REVERT: m 1197 ILE cc_start: 0.5821 (OUTLIER) cc_final: 0.5299 (mm) REVERT: m 1289 MET cc_start: 0.5883 (mmp) cc_final: 0.5226 (mtp) REVERT: m 1384 MET cc_start: 0.4549 (OUTLIER) cc_final: 0.3680 (mmm) REVERT: n 153 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7384 (tm-30) REVERT: n 178 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6930 (mm) REVERT: n 275 ARG cc_start: 0.8676 (mtt180) cc_final: 0.8169 (ttp80) REVERT: n 289 MET cc_start: 0.7176 (mtp) cc_final: 0.6719 (mtt) REVERT: q 405 MET cc_start: 0.1238 (ttp) cc_final: 0.0620 (tmm) REVERT: q 644 MET cc_start: 0.0710 (tmm) cc_final: -0.1572 (tpp) REVERT: q 744 MET cc_start: 0.3380 (ptt) cc_final: 0.3120 (ptt) REVERT: q 766 MET cc_start: 0.9334 (pmm) cc_final: 0.8943 (tpt) REVERT: q 873 MET cc_start: 0.9440 (mmp) cc_final: 0.9234 (mmp) REVERT: r 211 MET cc_start: 0.5405 (mtt) cc_final: 0.5019 (ptp) REVERT: r 282 MET cc_start: 0.1156 (ptp) cc_final: 0.0868 (ptp) REVERT: r 314 MET cc_start: -0.0885 (ttm) cc_final: -0.2387 (mmm) REVERT: r 329 MET cc_start: 0.3353 (tmm) cc_final: 0.2334 (tpt) REVERT: u 261 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6955 (tp40) REVERT: v 351 MET cc_start: 0.5434 (tmm) cc_final: 0.5172 (ttm) REVERT: v 366 ASN cc_start: 0.3144 (m-40) cc_final: 0.2667 (p0) REVERT: v 380 GLU cc_start: 0.7498 (pt0) cc_final: 0.6984 (mm-30) REVERT: x 307 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.6862 (mt0) REVERT: a 120 MET cc_start: 0.0287 (mmm) cc_final: -0.0311 (mmm) REVERT: a 129 ARG cc_start: 0.5881 (ttt180) cc_final: 0.5190 (mmt-90) REVERT: a 134 ARG cc_start: 0.4120 (mpt-90) cc_final: 0.3653 (tmt170) REVERT: d 59 MET cc_start: 0.4438 (ttm) cc_final: 0.3679 (mmm) REVERT: j 774 ASP cc_start: 0.2496 (OUTLIER) cc_final: 0.1471 (t70) REVERT: j 900 TRP cc_start: 0.1427 (OUTLIER) cc_final: 0.0653 (t60) outliers start: 115 outliers final: 87 residues processed: 442 average time/residue: 0.7043 time to fit residues: 558.8582 Evaluate side-chains 437 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 337 time to evaluate : 7.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 436 ILE Chi-restraints excluded: chain W residue 506 ILE Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 689 ARG Chi-restraints excluded: chain W residue 781 GLU Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 611 PHE Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 725 GLU Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 922 ASP Chi-restraints excluded: chain m residue 1197 ILE Chi-restraints excluded: chain m residue 1384 MET Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 194 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 460 VAL Chi-restraints excluded: chain q residue 859 ASN Chi-restraints excluded: chain r residue 369 GLU Chi-restraints excluded: chain r residue 395 VAL Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 180 LEU Chi-restraints excluded: chain u residue 261 GLN Chi-restraints excluded: chain v residue 103 HIS Chi-restraints excluded: chain v residue 174 ILE Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 343 ASP Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain f residue 61 PHE Chi-restraints excluded: chain j residue 602 THR Chi-restraints excluded: chain j residue 717 HIS Chi-restraints excluded: chain j residue 774 ASP Chi-restraints excluded: chain j residue 900 TRP Chi-restraints excluded: chain k residue 10 PHE Chi-restraints excluded: chain k residue 60 TYR Chi-restraints excluded: chain k residue 239 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 839 optimal weight: 0.6980 chunk 884 optimal weight: 30.0000 chunk 807 optimal weight: 50.0000 chunk 860 optimal weight: 20.0000 chunk 517 optimal weight: 1.9990 chunk 374 optimal weight: 8.9990 chunk 675 optimal weight: 40.0000 chunk 264 optimal weight: 6.9990 chunk 777 optimal weight: 50.0000 chunk 813 optimal weight: 7.9990 chunk 857 optimal weight: 5.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 556 ASN ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 864 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 83085 Z= 0.286 Angle : 0.539 13.705 113104 Z= 0.283 Chirality : 0.041 0.239 12586 Planarity : 0.004 0.058 13869 Dihedral : 15.053 161.759 12963 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.16 % Favored : 96.82 % Rotamer: Outliers : 1.59 % Allowed : 12.93 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 1.36 (0.09), residues: 9406 helix: 2.06 (0.08), residues: 4134 sheet: -0.01 (0.14), residues: 1372 loop : 0.07 (0.11), residues: 3900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP x 292 HIS 0.005 0.001 HIS u 93 PHE 0.040 0.001 PHE n 238 TYR 0.016 0.001 TYR M 70 ARG 0.008 0.000 ARG E 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 333 time to evaluate : 7.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9026 (mm) REVERT: A 548 MET cc_start: 0.8712 (mtm) cc_final: 0.8153 (mtp) REVERT: A 709 MET cc_start: 0.8063 (mpp) cc_final: 0.7843 (mpp) REVERT: A 903 MET cc_start: 0.8392 (mmt) cc_final: 0.7816 (mmm) REVERT: A 914 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9231 (mt) REVERT: A 1112 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7654 (p0) REVERT: A 1229 MET cc_start: 0.7819 (mmm) cc_final: 0.7409 (mmm) REVERT: A 1262 MET cc_start: 0.8120 (tpp) cc_final: 0.7845 (tpp) REVERT: B 363 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7489 (t80) REVERT: B 556 MET cc_start: 0.8761 (ttt) cc_final: 0.8169 (ttt) REVERT: B 864 LYS cc_start: 0.9121 (ptmt) cc_final: 0.8907 (ptmm) REVERT: B 1152 MET cc_start: 0.8538 (mmm) cc_final: 0.8228 (mmm) REVERT: E 49 MET cc_start: 0.9042 (pmm) cc_final: 0.8387 (pmm) REVERT: E 83 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: G 156 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8233 (mp0) REVERT: H 125 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: J 57 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6959 (mm-30) REVERT: V 25 MET cc_start: 0.7395 (tpp) cc_final: 0.6846 (tpt) REVERT: W 771 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8859 (mmmm) REVERT: m 511 MET cc_start: 0.2980 (tpt) cc_final: 0.2268 (tmm) REVERT: m 563 MET cc_start: 0.3803 (tpp) cc_final: 0.3092 (ptm) REVERT: m 661 GLN cc_start: 0.8323 (mm110) cc_final: 0.7958 (pt0) REVERT: m 1197 ILE cc_start: 0.5805 (OUTLIER) cc_final: 0.5299 (mm) REVERT: m 1289 MET cc_start: 0.5889 (mmp) cc_final: 0.5165 (mtp) REVERT: n 153 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7358 (tm-30) REVERT: n 178 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.6969 (mm) REVERT: n 275 ARG cc_start: 0.8689 (mtt180) cc_final: 0.8177 (ttp80) REVERT: n 289 MET cc_start: 0.7193 (mtp) cc_final: 0.6738 (mtt) REVERT: q 406 MET cc_start: 0.3220 (ttt) cc_final: 0.2970 (ttp) REVERT: q 644 MET cc_start: 0.0739 (tmm) cc_final: -0.1482 (tpp) REVERT: q 744 MET cc_start: 0.3411 (ptt) cc_final: 0.3167 (ptt) REVERT: q 766 MET cc_start: 0.9365 (pmm) cc_final: 0.8945 (tpt) REVERT: q 873 MET cc_start: 0.9429 (mmp) cc_final: 0.9215 (mmp) REVERT: r 211 MET cc_start: 0.5460 (mtt) cc_final: 0.5064 (ptp) REVERT: r 282 MET cc_start: 0.1046 (ptp) cc_final: 0.0725 (ptp) REVERT: r 314 MET cc_start: -0.0796 (ttm) cc_final: -0.2626 (mmm) REVERT: r 329 MET cc_start: 0.3355 (tmm) cc_final: 0.2362 (tpt) REVERT: u 261 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6885 (tp40) REVERT: v 351 MET cc_start: 0.5460 (tmm) cc_final: 0.5101 (ttp) REVERT: v 366 ASN cc_start: 0.3166 (m-40) cc_final: 0.2686 (p0) REVERT: v 380 GLU cc_start: 0.7569 (pt0) cc_final: 0.7074 (mm-30) REVERT: x 307 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.6878 (mt0) REVERT: a 120 MET cc_start: 0.0358 (mmm) cc_final: 0.0089 (mmm) REVERT: a 129 ARG cc_start: 0.5626 (ttt180) cc_final: 0.4928 (mmt-90) REVERT: a 134 ARG cc_start: 0.4113 (mpt-90) cc_final: 0.3477 (tmm160) REVERT: d 59 MET cc_start: 0.4437 (ttm) cc_final: 0.3686 (mmm) REVERT: j 774 ASP cc_start: 0.2508 (OUTLIER) cc_final: 0.1469 (t70) REVERT: j 900 TRP cc_start: 0.1434 (OUTLIER) cc_final: 0.0661 (t60) outliers start: 135 outliers final: 111 residues processed: 447 average time/residue: 0.6980 time to fit residues: 560.8181 Evaluate side-chains 448 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 325 time to evaluate : 7.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 69 GLU Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 436 ILE Chi-restraints excluded: chain W residue 506 ILE Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 689 ARG Chi-restraints excluded: chain W residue 781 GLU Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 611 PHE Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 725 GLU Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 922 ASP Chi-restraints excluded: chain m residue 935 ASN Chi-restraints excluded: chain m residue 1004 HIS Chi-restraints excluded: chain m residue 1197 ILE Chi-restraints excluded: chain m residue 1384 MET Chi-restraints excluded: chain n residue 178 ILE Chi-restraints excluded: chain n residue 194 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 460 VAL Chi-restraints excluded: chain q residue 614 HIS Chi-restraints excluded: chain r residue 369 GLU Chi-restraints excluded: chain r residue 395 VAL Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 261 GLN Chi-restraints excluded: chain v residue 103 HIS Chi-restraints excluded: chain v residue 174 ILE Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 343 ASP Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain f residue 61 PHE Chi-restraints excluded: chain j residue 602 THR Chi-restraints excluded: chain j residue 628 MET Chi-restraints excluded: chain j residue 717 HIS Chi-restraints excluded: chain j residue 774 ASP Chi-restraints excluded: chain j residue 900 TRP Chi-restraints excluded: chain k residue 10 PHE Chi-restraints excluded: chain k residue 60 TYR Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 239 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 565 optimal weight: 4.9990 chunk 909 optimal weight: 20.0000 chunk 555 optimal weight: 30.0000 chunk 431 optimal weight: 30.0000 chunk 632 optimal weight: 7.9990 chunk 954 optimal weight: 50.0000 chunk 878 optimal weight: 10.0000 chunk 760 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 587 optimal weight: 8.9990 chunk 466 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 864 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 83085 Z= 0.292 Angle : 0.542 15.216 113104 Z= 0.284 Chirality : 0.041 0.222 12586 Planarity : 0.004 0.051 13869 Dihedral : 15.042 162.424 12963 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.19 % Favored : 96.79 % Rotamer: Outliers : 1.56 % Allowed : 13.02 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 1.33 (0.09), residues: 9406 helix: 2.01 (0.08), residues: 4143 sheet: -0.02 (0.14), residues: 1376 loop : 0.07 (0.11), residues: 3887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP x 292 HIS 0.005 0.001 HIS A 852 PHE 0.038 0.001 PHE n 238 TYR 0.017 0.001 TYR e 99 ARG 0.010 0.000 ARG E 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18812 Ramachandran restraints generated. 9406 Oldfield, 0 Emsley, 9406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 337 time to evaluate : 7.157 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 337 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9022 (mm) REVERT: A 438 MET cc_start: 0.8416 (mmm) cc_final: 0.7225 (mtt) REVERT: A 548 MET cc_start: 0.8486 (mtm) cc_final: 0.8067 (mtp) REVERT: A 709 MET cc_start: 0.7989 (mpp) cc_final: 0.7768 (mpp) REVERT: A 903 MET cc_start: 0.8392 (mmt) cc_final: 0.7814 (mmm) REVERT: A 914 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9226 (mt) REVERT: A 1112 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.7653 (p0) REVERT: A 1229 MET cc_start: 0.7735 (mmm) cc_final: 0.7304 (mmm) REVERT: A 1262 MET cc_start: 0.8125 (tpp) cc_final: 0.7816 (tpp) REVERT: B 190 MET cc_start: 0.7974 (pmm) cc_final: 0.7770 (pmm) REVERT: B 363 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7475 (t80) REVERT: B 556 MET cc_start: 0.8752 (ttt) cc_final: 0.8158 (ttt) REVERT: B 864 LYS cc_start: 0.9124 (ptmt) cc_final: 0.8907 (ptmm) REVERT: B 1152 MET cc_start: 0.8552 (mmm) cc_final: 0.8238 (mmm) REVERT: C 36 MET cc_start: 0.8025 (mtp) cc_final: 0.7769 (mtp) REVERT: E 49 MET cc_start: 0.8996 (pmm) cc_final: 0.8327 (pmm) REVERT: E 83 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: G 156 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8241 (mp0) REVERT: H 125 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: I 52 ILE cc_start: 0.7974 (mt) cc_final: 0.7730 (pt) REVERT: J 57 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6997 (mm-30) REVERT: K 55 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7211 (p0) REVERT: V 25 MET cc_start: 0.7715 (tpp) cc_final: 0.7259 (tpt) REVERT: W 771 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8847 (mmmm) REVERT: m 511 MET cc_start: 0.3102 (tpt) cc_final: 0.2565 (mmm) REVERT: m 563 MET cc_start: 0.3776 (tpp) cc_final: 0.2888 (ppp) REVERT: m 661 GLN cc_start: 0.8254 (mm110) cc_final: 0.7965 (pt0) REVERT: m 925 MET cc_start: 0.8218 (mmm) cc_final: 0.7611 (mpp) REVERT: m 1289 MET cc_start: 0.5792 (mmp) cc_final: 0.5106 (mtp) REVERT: n 153 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7242 (tm-30) REVERT: n 275 ARG cc_start: 0.8662 (mtt180) cc_final: 0.8156 (ttp80) REVERT: n 289 MET cc_start: 0.7201 (mtp) cc_final: 0.6762 (mtt) REVERT: q 644 MET cc_start: 0.0741 (tmm) cc_final: -0.1467 (tpp) REVERT: q 744 MET cc_start: 0.3503 (ptt) cc_final: 0.3235 (ptt) REVERT: q 766 MET cc_start: 0.9379 (pmm) cc_final: 0.8941 (tpt) REVERT: q 873 MET cc_start: 0.9454 (mmp) cc_final: 0.9248 (mmp) REVERT: r 211 MET cc_start: 0.4880 (mtt) cc_final: 0.4431 (ptp) REVERT: r 314 MET cc_start: -0.0781 (ttm) cc_final: -0.2629 (mmm) REVERT: r 329 MET cc_start: 0.3360 (tmm) cc_final: 0.2333 (tpt) REVERT: u 261 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6893 (tp40) REVERT: v 351 MET cc_start: 0.5478 (tmm) cc_final: 0.5138 (ttp) REVERT: v 366 ASN cc_start: 0.3205 (m-40) cc_final: 0.2771 (p0) REVERT: x 307 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.6966 (mt0) REVERT: a 120 MET cc_start: 0.0090 (mmm) cc_final: -0.0212 (mmm) REVERT: a 129 ARG cc_start: 0.5650 (ttt180) cc_final: 0.4996 (mmt-90) REVERT: a 134 ARG cc_start: 0.4175 (mpt-90) cc_final: 0.3468 (tmm160) REVERT: d 59 MET cc_start: 0.4449 (ttm) cc_final: 0.3690 (mmm) REVERT: j 774 ASP cc_start: 0.2696 (OUTLIER) cc_final: 0.1742 (t70) REVERT: j 900 TRP cc_start: 0.1521 (OUTLIER) cc_final: 0.0469 (t60) REVERT: k 84 ASP cc_start: 0.4887 (m-30) cc_final: 0.4070 (t70) REVERT: k 166 THR cc_start: 0.0860 (OUTLIER) cc_final: 0.0632 (t) outliers start: 132 outliers final: 114 residues processed: 448 average time/residue: 0.7162 time to fit residues: 577.6957 Evaluate side-chains 452 residues out of total 8477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 326 time to evaluate : 7.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1140 ILE Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1347 THR Chi-restraints excluded: chain A residue 1359 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 878 THR Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 959 GLU Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1103 ILE Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 134 CYS Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 102 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 29 CYS Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 94 ASP Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 55 ASP Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain V residue 40 ASP Chi-restraints excluded: chain V residue 100 GLN Chi-restraints excluded: chain W residue 221 VAL Chi-restraints excluded: chain W residue 300 LEU Chi-restraints excluded: chain W residue 436 ILE Chi-restraints excluded: chain W residue 506 ILE Chi-restraints excluded: chain W residue 578 ASN Chi-restraints excluded: chain W residue 689 ARG Chi-restraints excluded: chain W residue 781 GLU Chi-restraints excluded: chain W residue 784 ASN Chi-restraints excluded: chain m residue 611 PHE Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 725 GLU Chi-restraints excluded: chain m residue 797 ASP Chi-restraints excluded: chain m residue 921 LEU Chi-restraints excluded: chain m residue 922 ASP Chi-restraints excluded: chain m residue 1004 HIS Chi-restraints excluded: chain m residue 1384 MET Chi-restraints excluded: chain n residue 194 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 460 VAL Chi-restraints excluded: chain q residue 614 HIS Chi-restraints excluded: chain q residue 859 ASN Chi-restraints excluded: chain r residue 369 GLU Chi-restraints excluded: chain r residue 395 VAL Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 261 GLN Chi-restraints excluded: chain v residue 103 HIS Chi-restraints excluded: chain v residue 174 ILE Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 343 ASP Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain c residue 25 PHE Chi-restraints excluded: chain f residue 61 PHE Chi-restraints excluded: chain j residue 602 THR Chi-restraints excluded: chain j residue 717 HIS Chi-restraints excluded: chain j residue 774 ASP Chi-restraints excluded: chain j residue 900 TRP Chi-restraints excluded: chain k residue 10 PHE Chi-restraints excluded: chain k residue 60 TYR Chi-restraints excluded: chain k residue 166 THR Chi-restraints excluded: chain k residue 239 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 958 random chunks: chunk 603 optimal weight: 20.0000 chunk 809 optimal weight: 6.9990 chunk 232 optimal weight: 2.9990 chunk 700 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 761 optimal weight: 20.0000 chunk 318 optimal weight: 2.9990 chunk 781 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 GLN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** V 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 947 GLN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 426 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.137384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092784 restraints weight = 300277.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.090603 restraints weight = 207159.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.091288 restraints weight = 166784.477| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 83085 Z= 0.168 Angle : 0.504 20.693 113104 Z= 0.264 Chirality : 0.040 0.222 12586 Planarity : 0.003 0.071 13869 Dihedral : 14.968 162.377 12963 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.27 % Rotamer: Outliers : 1.35 % Allowed : 13.33 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.89 % 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: 9406 helix: 2.15 (0.08), residues: 4148 sheet: 0.09 (0.14), residues: 1364 loop : 0.14 (0.11), residues: 3894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP x 292 HIS 0.005 0.001 HIS k 148 PHE 0.040 0.001 PHE n 238 TYR 0.026 0.001 TYR m 976 ARG 0.006 0.000 ARG B 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12998.18 seconds wall clock time: 237 minutes 7.90 seconds (14227.90 seconds total)