Starting phenix.real_space_refine on Mon Feb 19 01:13:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsz_33437/02_2024/7xsz_33437.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsz_33437/02_2024/7xsz_33437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsz_33437/02_2024/7xsz_33437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsz_33437/02_2024/7xsz_33437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsz_33437/02_2024/7xsz_33437.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xsz_33437/02_2024/7xsz_33437.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 340 5.49 5 Mg 1 5.21 5 S 294 5.16 5 C 47240 2.51 5 N 13461 2.21 5 O 15202 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" Residue "h TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 76548 Number of models: 1 Model: "" Number of chains: 41 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: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3186 Classifications: {'DNA': 155} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 154} Chain breaks: 1 Chain: "P" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 417 Classifications: {'RNA': 20} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 3, 'rna3p_pyr': 10} Link IDs: {'rna2p': 6, 'rna3p': 13} Chain: "T" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 3397 Classifications: {'DNA': 166} Link IDs: {'rna3p': 165} Chain: "V" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "W" Number of atoms: 4232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4232 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Chain breaks: 2 Chain: "m" Number of atoms: 9730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9730 Classifications: {'peptide': 1187} Link IDs: {'PTRANS': 45, 'TRANS': 1141} Chain breaks: 3 Chain: "n" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 8, 'TRANS': 130} Chain: "q" Number of atoms: 7552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7552 Classifications: {'peptide': 930} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 910} Chain: "r" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2139 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 259} Chain breaks: 2 Chain: "u" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1707 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "v" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2878 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 22, 'TRANS': 326} Chain breaks: 3 Chain: "x" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "a" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 746 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "b" Number of atoms: 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: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 795 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 757 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "h" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} 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 67 156.566 90.961 82.678 1.00 65.15 S ATOM 549 SG CYS A 70 160.160 89.856 83.282 1.00 51.72 S ATOM 594 SG CYS A 77 159.115 93.440 84.080 1.00 41.11 S ATOM 829 SG CYS A 107 159.567 116.860 41.840 1.00119.82 S ATOM 851 SG CYS A 110 161.541 113.848 40.607 1.00129.86 S ATOM 1157 SG CYS A 148 161.846 117.168 38.861 1.00156.05 S ATOM 1229 SG CYS A 168 158.439 115.299 38.745 1.00164.95 S ATOM 19880 SG CYS B1163 170.162 91.382 69.950 1.00 33.29 S ATOM 19898 SG CYS B1166 168.207 94.581 69.668 1.00 33.06 S ATOM 20021 SG CYS B1182 166.358 91.295 70.251 1.00 52.25 S ATOM 20044 SG CYS B1185 168.022 92.112 66.877 1.00 55.31 S ATOM 20989 SG CYS C 85 171.102 101.025 150.408 1.00 69.37 S ATOM 21002 SG CYS C 87 167.727 99.858 149.116 1.00 84.38 S ATOM 21037 SG CYS C 91 167.890 101.647 152.285 1.00 63.35 S ATOM 21060 SG CYS C 94 168.648 103.709 149.238 1.00 53.25 S ATOM 29206 SG CYS I 78 162.759 196.121 96.483 1.00196.72 S ATOM 29422 SG CYS I 103 163.507 191.767 95.786 1.00170.01 S ATOM 28659 SG CYS I 10 140.217 176.620 56.094 1.00168.46 S ATOM 28822 SG CYS I 29 144.195 177.165 53.938 1.00169.39 S ATOM 28847 SG CYS I 32 142.361 178.844 53.383 1.00171.39 S ATOM 29563 SG CYS J 7 171.825 134.685 140.136 1.00 14.85 S ATOM 29586 SG CYS J 10 174.528 133.773 142.746 1.00 16.52 S ATOM 29862 SG CYS J 44 174.912 136.852 140.424 1.00 19.23 S ATOM 29868 SG CYS J 45 172.580 136.703 143.376 1.00 18.60 S ATOM 31039 SG CYS L 33 131.629 120.566 128.146 1.00 60.68 S ATOM 31054 SG CYS L 36 129.729 120.976 131.436 1.00 73.57 S ATOM 31164 SG CYS L 50 128.732 118.235 128.966 1.00 84.33 S ATOM 31188 SG CYS L 53 128.252 121.900 128.032 1.00 93.61 S ATOM 31445 SG CYS M 25 132.238 139.046 44.393 1.00217.12 S ATOM 31470 SG CYS M 28 132.407 135.309 44.452 1.00226.66 S ATOM 31628 SG CYS M 49 135.328 137.264 42.997 1.00214.54 S ATOM 31652 SG CYS M 52 131.868 136.980 41.192 1.00219.85 S ATOM 38900 SG CYS V 12 103.770 106.375 57.003 1.00212.99 S ATOM 38922 SG CYS V 15 104.845 109.513 55.332 1.00203.73 S ATOM 39024 SG CYS V 29 101.304 109.356 56.157 1.00205.83 S ATOM 39045 SG CYS V 32 102.621 107.183 53.374 1.00217.97 S Time building chain proxies: 28.82, per 1000 atoms: 0.38 Number of scatterers: 76548 At special positions: 0 Unit cell: (293.832, 219.632, 204.792, 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 294 16.00 P 340 15.00 Mg 1 11.99 O 15202 8.00 N 13461 7.00 C 47240 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: 24.61 Conformation dependent library (CDL) restraints added in 9.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 168 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " 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 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 78 " 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 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16434 Finding SS restraints... Secondary structure from input PDB file: 359 helices and 80 sheets defined 50.4% alpha, 13.3% beta 162 base pairs and 270 stacking pairs defined. Time for finding SS restraints: 19.90 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: 4.089A 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: 3.702A pdb=" N MET A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 3.710A pdb=" N LEU A 330 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.524A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 473 through 477 removed outlier: 3.890A pdb=" N SER A 477 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 506 Processing helix chain 'A' and resid 507 through 512 removed outlier: 3.679A 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: 3.504A pdb=" N ASN A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 583 removed outlier: 3.768A 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: 3.583A pdb=" N PHE A 647 " --> pdb=" O CYS A 643 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.725A pdb=" N ILE A 671 " --> pdb=" O GLY A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 700 removed outlier: 3.617A pdb=" N GLU A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 738 Processing helix chain 'A' and resid 742 through 750 Processing helix chain 'A' and resid 755 through 764 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 810 through 847 removed outlier: 4.729A pdb=" N ALA A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) removed outlier: 3.758A 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: 3.685A 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: 3.570A 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: 3.635A pdb=" N GLY A1343 " --> pdb=" O LEU A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1344 through 1361 Processing helix chain 'A' and resid 1367 through 1379 removed outlier: 3.986A pdb=" N MET A1371 " --> pdb=" O ASN A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1393 Processing helix chain 'A' and resid 1398 through 1404 removed outlier: 3.514A pdb=" N SER A1404 " --> pdb=" O LEU A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1418 Processing helix chain 'A' and resid 1426 through 1433 removed outlier: 3.811A pdb=" N ASN A1430 " --> pdb=" O GLY A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1439 through 1442 Processing helix chain 'A' and resid 1451 through 1455 Processing helix chain 'B' and resid 13 through 28 Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.662A pdb=" N TYR B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.532A 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: 3.647A 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: 4.198A 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 removed outlier: 3.645A pdb=" N ALA B 465 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'B' and resid 501 through 506 removed outlier: 4.207A pdb=" N ARG B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 522 through 526 removed outlier: 4.347A pdb=" N ALA B 525 " --> pdb=" O GLU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 560 through 562 No H-bonds generated for 'chain 'B' and resid 560 through 562' Processing helix chain 'B' and resid 585 through 599 removed outlier: 3.575A 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: 3.746A 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: 3.535A 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: 3.508A 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: 3.521A pdb=" N GLY B 926 " --> pdb=" O GLU B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 removed outlier: 3.655A pdb=" N MET B 999 " --> pdb=" O HIS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.633A 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: 3.960A 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: 3.610A pdb=" N GLU C 210 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 266 removed outlier: 3.978A 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: 3.995A 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: 4.193A pdb=" N ALA D 165 " --> pdb=" O PRO D 161 " (cutoff:3.500A) removed outlier: 3.792A 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: 3.589A pdb=" N MET E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 removed outlier: 3.584A 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: 3.640A 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: 3.706A 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: 3.527A 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: 3.891A 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: 3.816A 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: 4.208A pdb=" N ASP W 308 " --> pdb=" O VAL W 304 " (cutoff:3.500A) removed outlier: 3.858A 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: 3.798A 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: 4.416A pdb=" N TRP m 249 " --> pdb=" O THR m 245 " (cutoff:3.500A) removed outlier: 5.697A 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: 3.936A pdb=" N ALA m 392 " --> pdb=" O ARG m 388 " (cutoff:3.500A) Processing helix chain 'm' and resid 410 through 442 removed outlier: 3.942A pdb=" N ASP m 429 " --> pdb=" O HIS m 425 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS m 430 " --> pdb=" O SER m 426 " (cutoff:3.500A) Processing helix chain 'm' and resid 447 through 456 removed outlier: 3.604A 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: 4.043A 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: 3.530A 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: 3.910A 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: 4.059A pdb=" N LYS m 834 " --> pdb=" O ILE m 830 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU m 835 " --> pdb=" O HIS m 831 " (cutoff:3.500A) Processing helix chain 'm' and resid 878 through 887 removed outlier: 3.749A pdb=" N HIS m 886 " --> pdb=" O ARG m 882 " (cutoff:3.500A) Processing helix chain 'm' and resid 887 through 894 removed outlier: 3.689A pdb=" N SER m 891 " --> pdb=" O SER m 887 " (cutoff:3.500A) Processing helix chain 'm' and resid 898 through 913 Processing helix chain 'm' and resid 913 through 921 Processing helix chain 'm' and resid 922 through 928 removed outlier: 4.124A pdb=" N MET m 925 " --> pdb=" O ASP m 922 " (cutoff:3.500A) Processing helix chain 'm' and resid 938 through 958 Processing helix chain 'm' and resid 961 through 967 Processing helix chain 'm' and resid 967 through 972 Processing helix chain 'm' and resid 973 through 977 Processing helix chain 'm' and resid 981 through 996 Processing helix chain 'm' and resid 1003 through 1008 Processing helix chain 'm' and resid 1012 through 1020 Processing helix chain 'm' and resid 1030 through 1034 removed outlier: 3.950A 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: 3.558A 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: 3.707A pdb=" N ALA m1300 " --> pdb=" O ASP m1296 " (cutoff:3.500A) Processing helix chain 'm' and resid 1358 through 1380 removed outlier: 3.930A 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: 4.554A pdb=" N VAL n 259 " --> pdb=" O GLY n 255 " (cutoff:3.500A) Processing helix chain 'n' and resid 270 through 289 Proline residue: n 287 - end of helix Processing helix chain 'q' and resid 5 through 13 removed outlier: 3.879A pdb=" N TYR q 9 " --> pdb=" O ASP q 5 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 20 removed outlier: 3.750A pdb=" N GLU q 20 " --> pdb=" O ASP q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 21 through 23 No H-bonds generated for 'chain 'q' and resid 21 through 23' Processing helix chain 'q' and resid 46 through 58 Processing helix chain 'q' and resid 60 through 74 removed outlier: 3.663A pdb=" N TRP q 64 " --> pdb=" O ARG q 60 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 89 Processing helix chain 'q' and resid 90 through 96 Processing helix chain 'q' and resid 97 through 120 removed outlier: 3.873A pdb=" N THR q 101 " --> pdb=" O SER q 97 " (cutoff:3.500A) removed outlier: 3.512A 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: 3.691A 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: 4.128A 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: 3.716A pdb=" N TYR q 304 " --> pdb=" O VAL q 300 " (cutoff:3.500A) Processing helix chain 'q' and resid 310 through 325 Processing helix chain 'q' and resid 328 through 347 removed outlier: 3.553A pdb=" N VAL q 332 " --> pdb=" O ASN q 328 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS q 345 " --> pdb=" O ARG q 341 " (cutoff:3.500A) removed outlier: 3.626A 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: 3.544A 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: 3.532A pdb=" N ALA q 539 " --> pdb=" O ASN q 535 " (cutoff:3.500A) Processing helix chain 'q' and resid 553 through 569 removed outlier: 4.099A pdb=" N LYS q 557 " --> pdb=" O TYR q 553 " (cutoff:3.500A) Processing helix chain 'q' and resid 572 through 583 Processing helix chain 'q' and resid 586 through 605 removed outlier: 6.251A pdb=" N ARG q 602 " --> pdb=" O LYS q 598 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS q 603 " --> pdb=" O ARG q 599 " (cutoff:3.500A) Processing helix chain 'q' and resid 609 through 622 Processing helix chain 'q' and resid 626 through 644 Processing helix chain 'q' and resid 648 through 673 Processing helix chain 'q' and resid 676 through 690 removed outlier: 3.546A pdb=" N ALA q 680 " --> pdb=" O ASN q 676 " (cutoff:3.500A) Processing helix chain 'q' and resid 692 through 707 Processing helix chain 'q' and resid 709 through 723 Processing helix chain 'q' and resid 725 through 740 Processing helix chain 'q' and resid 745 through 764 removed outlier: 3.789A pdb=" N LEU q 749 " --> pdb=" O ASP q 745 " (cutoff:3.500A) Processing helix chain 'q' and resid 765 through 784 removed outlier: 3.673A 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: 3.779A 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: 3.913A 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: 3.802A pdb=" N ILE r 204 " --> pdb=" O ASP r 200 " (cutoff:3.500A) Processing helix chain 'r' and resid 207 through 215 Processing helix chain 'r' and resid 219 through 225 Processing helix chain 'r' and resid 287 through 289 No H-bonds generated for 'chain 'r' and resid 287 through 289' Processing helix chain 'r' and resid 295 through 310 Processing helix chain 'r' and resid 315 through 332 Processing helix chain 'r' and resid 335 through 350 Processing helix chain 'r' and resid 353 through 374 Processing helix chain 'r' and resid 378 through 391 removed outlier: 3.613A pdb=" N ARG r 382 " --> pdb=" O GLU r 378 " (cutoff:3.500A) Processing helix chain 'r' and resid 398 through 433 removed outlier: 3.829A pdb=" N ARG r 420 " --> pdb=" O ASN r 416 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU r 428 " --> pdb=" O MET r 424 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS r 429 " --> pdb=" O ALA r 425 " (cutoff:3.500A) Processing helix chain 'r' and resid 486 through 490 Processing helix chain 'r' and resid 492 through 497 Processing helix chain 'r' and resid 498 through 505 Processing helix chain 'u' and resid 122 through 129 Processing helix chain 'u' and resid 135 through 149 Processing helix chain 'u' and resid 228 through 242 removed outlier: 3.625A pdb=" N GLN u 242 " --> pdb=" O LEU u 238 " (cutoff:3.500A) Processing helix chain 'u' and resid 258 through 282 Processing helix chain 'v' and resid 32 through 35 Processing helix chain 'v' and resid 36 through 45 Processing helix chain 'v' and resid 47 through 58 Processing helix chain 'v' and resid 64 through 71 removed outlier: 3.575A pdb=" N ASP v 68 " --> pdb=" O GLU v 65 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY v 69 " --> pdb=" O THR v 66 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP v 71 " --> pdb=" O ASP v 68 " (cutoff:3.500A) Processing helix chain 'v' and resid 73 through 77 removed outlier: 3.609A pdb=" N ILE v 77 " --> pdb=" O TYR v 74 " (cutoff:3.500A) Processing helix chain 'v' and resid 85 through 94 Processing helix chain 'v' and resid 103 through 109 Processing helix chain 'v' and resid 158 through 172 Processing helix chain 'v' and resid 178 through 185 Processing helix chain 'v' and resid 218 through 221 Processing helix chain 'v' and resid 225 through 233 Processing helix chain 'v' and resid 244 through 249 Processing helix chain 'v' and resid 271 through 284 Processing helix chain 'v' and resid 345 through 347 No H-bonds generated for 'chain 'v' and resid 345 through 347' Processing helix chain 'v' and resid 348 through 353 Processing helix chain 'v' and resid 368 through 380 Processing helix chain 'x' and resid 136 through 145 Processing helix chain 'x' and resid 153 through 157 removed outlier: 4.065A pdb=" N LEU x 156 " --> pdb=" O ASN x 153 " (cutoff:3.500A) Processing helix chain 'x' and resid 164 through 175 Processing helix chain 'x' and resid 224 through 230 Processing helix chain 'x' and resid 275 through 280 removed outlier: 3.547A pdb=" N TYR x 278 " --> pdb=" O LYS x 275 " (cutoff:3.500A) Processing helix chain 'x' and resid 290 through 295 removed outlier: 3.648A pdb=" N GLN x 293 " --> pdb=" O LYS x 290 " (cutoff:3.500A) removed outlier: 3.700A 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 45 through 57 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 removed outlier: 3.511A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) 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: 3.733A pdb=" N ASP b 68 " --> pdb=" O ASN b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 17 through 21 Processing helix chain 'c' and resid 26 through 36 removed outlier: 3.707A pdb=" N VAL c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.442A 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: 3.561A pdb=" N ALA d 121 " --> pdb=" O LYS d 117 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 76 Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 131 Processing helix chain 'f' and resid 25 through 29 removed outlier: 3.510A pdb=" N ILE f 29 " --> pdb=" O ILE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 41 Processing helix chain 'f' and resid 49 through 76 Processing helix chain 'f' and resid 82 through 94 removed outlier: 3.660A pdb=" N VAL f 86 " --> pdb=" O THR f 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 46 through 73 removed outlier: 3.548A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 34 through 46 Processing helix chain 'h' and resid 52 through 81 Processing helix chain 'h' and resid 87 through 99 Processing helix chain 'h' and resid 100 through 121 Processing 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: 10.190A 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: 3.571A 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: 3.693A 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: 6.812A pdb=" N MET A 464 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL A 367 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.967A pdb=" N TYR A 405 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N HIS A 436 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 7.070A 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: 6.330A 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: 4.156A 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: 3.635A 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: 6.739A pdb=" N THR A 857 " --> pdb=" O ILE A 865 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 883 Processing sheet with id=AB5, first strand: chain 'A' and resid 1284 through 1295 removed outlier: 3.969A pdb=" N LYS A1284 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 3.903A 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: 4.333A pdb=" N LEU A1238 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A1244 " --> pdb=" O TRP A1193 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TRP A1193 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR A1156 " --> pdb=" O LYS I 42 " (cutoff:3.500A) removed outlier: 6.503A 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: 4.939A 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: 6.519A pdb=" N TYR B 116 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N LEU B 84 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N SER B 113 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS B 160 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.862A 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: 3.951A pdb=" N HIS B 227 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 243 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN B 246 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 537 through 538 removed outlier: 3.967A pdb=" N GLU B 644 " --> pdb=" O GLU B 634 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 644 through 645 current: chain 'B' and resid 740 through 741 Processing sheet with id=AC6, first strand: chain 'B' and resid 557 through 558 removed outlier: 5.659A pdb=" N TRP B 579 " --> pdb=" O VAL B 575 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL B 575 " --> pdb=" O TRP B 579 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 581 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 6.756A 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: 8.661A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 6.052A 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: 7.004A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 6.223A 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: 4.241A 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: 7.425A 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: 3.538A 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: 6.589A pdb=" N GLU C 18 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.701A 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: 3.810A pdb=" N GLU C 233 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 119 through 122 removed outlier: 6.730A pdb=" N VAL C 97 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG C 156 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE C 50 " --> pdb=" O ARG C 156 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE C 158 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 5.698A 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: 6.067A pdb=" N ASP C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY C 162 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.734A 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: 6.475A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL C 113 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 5 through 6 current: chain 'G' and resid 2 through 13 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 2 through 13 current: chain 'G' and resid 43 through 48 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 43 through 48 current: chain 'G' and resid 68 through 79 No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 37 through 39 Processing sheet with id=AE2, first strand: chain 'E' and resid 59 through 61 removed outlier: 6.468A pdb=" N TRP E 78 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE E 110 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU E 80 " --> pdb=" O ILE E 110 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 86 through 87 removed outlier: 3.522A pdb=" N VAL E 87 " --> pdb=" O ASN E 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.118A pdb=" N LYS E 151 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.593A 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: 5.587A pdb=" N VAL G 147 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER G 162 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASN G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA G 159 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.510A 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: 7.050A pdb=" N GLY G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.529A 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: 6.966A 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: 6.639A pdb=" N PHE V 54 " --> pdb=" O VAL V 86 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 337 through 339 Processing sheet with id=AF5, first strand: chain 'W' and resid 349 through 354 removed outlier: 4.661A 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: 7.777A pdb=" N ILE W 506 " --> pdb=" O VAL W 501 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL W 501 " --> pdb=" O ILE W 506 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER W 508 " --> pdb=" O SER W 499 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 572 through 576 removed outlier: 6.042A pdb=" N ILE W 565 " --> pdb=" O ILE W 554 " (cutoff:3.500A) removed outlier: 5.914A 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: 6.905A 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: 6.676A pdb=" N PHE W 685 " --> pdb=" O LEU W 677 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 787 through 791 removed outlier: 4.574A pdb=" N LYS W 787 " --> pdb=" O LEU W 782 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG W 779 " --> pdb=" O LYS W 771 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THR W 755 " --> pdb=" O GLU W 799 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'm' and resid 396 through 397 Processing sheet with id=AG4, first strand: chain 'm' and resid 644 through 645 Processing sheet with id=AG5, first strand: chain 'm' and resid 790 through 796 removed outlier: 3.832A 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: 6.876A 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: 6.711A 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: 7.190A 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: 5.300A 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: 5.751A pdb=" N ILE m1220 " --> pdb=" O SER m1233 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'm' and resid 1306 through 1310 removed outlier: 6.746A pdb=" N LEU m1328 " --> pdb=" O VAL m1324 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'm' and resid 1407 through 1412 Processing sheet with id=AH1, first strand: chain 'q' and resid 25 through 29 Processing sheet with id=AH2, first strand: chain 'r' and resid 228 through 232 removed outlier: 4.020A pdb=" N LEU r 229 " --> pdb=" O VAL r 246 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL r 246 " --> pdb=" O LEU r 229 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N VAL r 248 " --> pdb=" O ALA r 275 " (cutoff:3.500A) removed outlier: 6.880A 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: 4.923A 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: 6.451A pdb=" N ILE v 264 " --> pdb=" O ASP v 302 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP v 302 " --> pdb=" O ILE v 264 " (cutoff:3.500A) removed outlier: 7.102A 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: 4.464A 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: 8.194A 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: 5.933A 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: 6.348A pdb=" N ILE x 285 " --> pdb=" O ILE x 209 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL x 211 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N PHE x 312 " --> pdb=" O VAL x 283 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE x 285 " --> pdb=" O PHE x 312 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE x 314 " --> pdb=" O ILE x 285 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY x 311 " --> pdb=" O LYS x 331 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU x 333 " --> pdb=" O GLY x 311 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR x 313 " --> pdb=" O LEU x 333 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ILE x 335 " --> pdb=" O TYR x 313 " (cutoff:3.500A) removed outlier: 6.553A 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: 7.119A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AI1, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AI2, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.696A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AI4, first strand: chain 'c' and resid 101 through 102 removed outlier: 6.909A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.862A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AI7, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.360A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'g' and resid 77 through 78 3456 hydrogen bonds defined for protein. 9852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 413 hydrogen bonds 826 hydrogen bond angles 0 basepair planarities 162 basepair parallelities 270 stacking parallelities Total time for adding SS restraints: 42.69 Time building geometry restraints manager: 26.90 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: 17634 1.33 - 1.45: 17216 1.45 - 1.57: 42629 1.57 - 1.69: 682 1.69 - 1.81: 480 Bond restraints: 78641 Sorted by residual: bond pdb=" C1' DG T -11 " pdb=" N9 DG T -11 " ideal model delta sigma weight residual 1.460 1.351 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C1' DG T -3 " pdb=" N9 DG T -3 " ideal model delta sigma weight residual 1.460 1.355 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C1' DG N -7 " pdb=" N9 DG N -7 " ideal model delta sigma weight residual 1.460 1.358 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" C1' DA T 13 " pdb=" N9 DA T 13 " ideal model delta sigma weight residual 1.460 1.358 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C1' DA T 87 " pdb=" N9 DA T 87 " ideal model delta sigma weight residual 1.460 1.360 0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 78636 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.52: 2791 105.52 - 112.66: 41988 112.66 - 119.79: 26323 119.79 - 126.93: 35069 126.93 - 134.06: 1466 Bond angle restraints: 107637 Sorted by residual: angle pdb=" O3' U P -2 " pdb=" C3' U P -2 " pdb=" C2' U P -2 " ideal model delta sigma weight residual 109.50 120.06 -10.56 1.50e+00 4.44e-01 4.96e+01 angle pdb=" N VAL A1001 " pdb=" CA VAL A1001 " pdb=" C VAL A1001 " ideal model delta sigma weight residual 112.96 107.27 5.69 1.00e+00 1.00e+00 3.24e+01 angle pdb=" O3' DG T -19 " pdb=" C3' DG T -19 " pdb=" C2' DG T -19 " ideal model delta sigma weight residual 111.50 104.46 7.04 1.50e+00 4.44e-01 2.20e+01 angle pdb=" OE1 GLN B 462 " pdb=" CD GLN B 462 " pdb=" NE2 GLN B 462 " ideal model delta sigma weight residual 122.60 118.17 4.43 1.00e+00 1.00e+00 1.96e+01 angle pdb=" O3' DG N -33 " pdb=" C3' DG N -33 " pdb=" C2' DG N -33 " ideal model delta sigma weight residual 111.50 105.57 5.93 1.50e+00 4.44e-01 1.56e+01 ... (remaining 107632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 44218 28.35 - 56.70: 2739 56.70 - 85.05: 324 85.05 - 113.40: 13 113.40 - 141.75: 4 Dihedral angle restraints: 47298 sinusoidal: 21939 harmonic: 25359 Sorted by residual: dihedral pdb=" O4' C P -6 " pdb=" C1' C P -6 " pdb=" N1 C P -6 " pdb=" C2 C P -6 " ideal model delta sinusoidal sigma weight residual -160.00 -59.97 -100.03 1 1.50e+01 4.44e-03 5.01e+01 dihedral pdb=" O4' U P -4 " pdb=" C1' U P -4 " pdb=" N1 U P -4 " pdb=" C2 U P -4 " ideal model delta sinusoidal sigma weight residual 232.00 115.61 116.39 1 1.70e+01 3.46e-03 4.80e+01 dihedral pdb=" C4' U P -2 " pdb=" O4' U P -2 " pdb=" C1' U P -2 " pdb=" C2' U P -2 " ideal model delta sinusoidal sigma weight residual -21.00 14.56 -35.56 1 8.00e+00 1.56e-02 2.80e+01 ... (remaining 47295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 10670 0.072 - 0.145: 1277 0.145 - 0.217: 74 0.217 - 0.289: 1 0.289 - 0.361: 2 Chirality restraints: 12024 Sorted by residual: chirality pdb=" C1' DA T 87 " pdb=" O4' DA T 87 " pdb=" C2' DA T 87 " pdb=" N9 DA T 87 " both_signs ideal model delta sigma weight residual False 2.42 2.06 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" P C P 11 " pdb=" OP1 C P 11 " pdb=" OP2 C P 11 " pdb=" O5' C P 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.76 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C1' DG N -75 " pdb=" O4' DG N -75 " pdb=" C2' DG N -75 " pdb=" N9 DG N -75 " both_signs ideal model delta sigma weight residual False 2.42 2.20 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 12021 not shown) Planarity restraints: 12728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT N 15 " -0.129 2.00e-02 2.50e+03 5.61e-02 7.87e+01 pdb=" N1 DT N 15 " 0.052 2.00e-02 2.50e+03 pdb=" C2 DT N 15 " 0.032 2.00e-02 2.50e+03 pdb=" O2 DT N 15 " 0.044 2.00e-02 2.50e+03 pdb=" N3 DT N 15 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DT N 15 " -0.020 2.00e-02 2.50e+03 pdb=" O4 DT N 15 " -0.066 2.00e-02 2.50e+03 pdb=" C5 DT N 15 " 0.021 2.00e-02 2.50e+03 pdb=" C7 DT N 15 " 0.011 2.00e-02 2.50e+03 pdb=" C6 DT N 15 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T -28 " 0.134 2.00e-02 2.50e+03 5.33e-02 7.82e+01 pdb=" N9 DA T -28 " -0.053 2.00e-02 2.50e+03 pdb=" C8 DA T -28 " -0.044 2.00e-02 2.50e+03 pdb=" N7 DA T -28 " -0.018 2.00e-02 2.50e+03 pdb=" C5 DA T -28 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DA T -28 " 0.017 2.00e-02 2.50e+03 pdb=" N6 DA T -28 " 0.064 2.00e-02 2.50e+03 pdb=" N1 DA T -28 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DA T -28 " -0.018 2.00e-02 2.50e+03 pdb=" N3 DA T -28 " -0.041 2.00e-02 2.50e+03 pdb=" C4 DA T -28 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T -17 " 0.116 2.00e-02 2.50e+03 4.66e-02 5.97e+01 pdb=" N9 DA T -17 " -0.046 2.00e-02 2.50e+03 pdb=" C8 DA T -17 " -0.038 2.00e-02 2.50e+03 pdb=" N7 DA T -17 " -0.016 2.00e-02 2.50e+03 pdb=" C5 DA T -17 " -0.014 2.00e-02 2.50e+03 pdb=" C6 DA T -17 " 0.015 2.00e-02 2.50e+03 pdb=" N6 DA T -17 " 0.058 2.00e-02 2.50e+03 pdb=" N1 DA T -17 " 0.010 2.00e-02 2.50e+03 pdb=" C2 DA T -17 " -0.016 2.00e-02 2.50e+03 pdb=" N3 DA T -17 " -0.036 2.00e-02 2.50e+03 pdb=" C4 DA T -17 " -0.034 2.00e-02 2.50e+03 ... (remaining 12725 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 379 2.50 - 3.10: 53770 3.10 - 3.70: 120273 3.70 - 4.30: 174423 4.30 - 4.90: 283605 Nonbonded interactions: 632450 Sorted by model distance: nonbonded pdb=" OD2 ASP V 42 " pdb=" O ASN g 73 " model vdw 1.896 3.040 nonbonded pdb=" OD1 ASP A 484 " pdb="MG MG A1803 " model vdw 2.020 2.170 nonbonded pdb=" NH2 ARG b 92 " pdb=" O LEU d 97 " model vdw 2.082 2.520 nonbonded pdb=" O2 DC N -54 " pdb=" N2 DG T 54 " model vdw 2.119 2.520 nonbonded pdb=" NH2 ARG g 88 " pdb=" O LEU g 97 " model vdw 2.143 2.520 ... (remaining 632445 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'a' selection = (chain 'e' and resid 43 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 16 through 111) selection = (chain 'g' and resid 16 through 111) } ncs_group { reference = (chain 'd' and resid 32 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 6.170 Check model and map are aligned: 0.820 Set scattering table: 0.520 Process input model: 188.700 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 78641 Z= 0.316 Angle : 0.589 10.987 107637 Z= 0.345 Chirality : 0.045 0.361 12024 Planarity : 0.004 0.074 12728 Dihedral : 16.994 141.753 30864 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.31 % Favored : 97.68 % Rotamer: Outliers : 0.01 % Allowed : 0.10 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.09), residues: 8561 helix: 1.94 (0.08), residues: 3932 sheet: 0.30 (0.15), residues: 1163 loop : 0.06 (0.11), residues: 3466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 170 HIS 0.009 0.001 HIS A 817 PHE 0.018 0.001 PHE B 363 TYR 0.029 0.001 TYR g 50 ARG 0.015 0.001 ARG e 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 870 time to evaluate : 6.241 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: A 108 MET cc_start: 0.8501 (mmm) cc_final: 0.8139 (mmm) REVERT: A 146 MET cc_start: 0.8441 (tpp) cc_final: 0.8060 (tpt) REVERT: A 211 VAL cc_start: 0.8921 (t) cc_final: 0.8671 (t) REVERT: B 123 MET cc_start: 0.5738 (mmm) cc_final: 0.5472 (ttm) REVERT: B 302 MET cc_start: 0.8212 (ptm) cc_final: 0.7910 (ptp) REVERT: B 469 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7411 (ttp-170) REVERT: B 635 ASP cc_start: 0.6542 (p0) cc_final: 0.6205 (t0) REVERT: B 1208 MET cc_start: 0.8148 (mtp) cc_final: 0.7760 (mtm) REVERT: E 92 MET cc_start: 0.8696 (tpp) cc_final: 0.8321 (tpp) REVERT: G 153 ASP cc_start: 0.8010 (t0) cc_final: 0.7632 (t70) REVERT: I 13 MET cc_start: 0.8730 (ttm) cc_final: 0.8465 (tpp) REVERT: I 89 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7498 (tp40) REVERT: I 104 LEU cc_start: 0.7270 (mm) cc_final: 0.6947 (pt) REVERT: I 108 LYS cc_start: 0.8607 (tttp) cc_final: 0.8190 (ptmm) REVERT: M 40 LYS cc_start: 0.7505 (pptt) cc_final: 0.6638 (ttpt) REVERT: M 64 SER cc_start: 0.7630 (p) cc_final: 0.7421 (t) REVERT: V 78 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7652 (mm110) REVERT: W 692 VAL cc_start: 0.7927 (t) cc_final: 0.7603 (p) REVERT: m 290 LYS cc_start: 0.5668 (tmmt) cc_final: 0.5461 (pttm) REVERT: m 318 LYS cc_start: 0.7933 (mttt) cc_final: 0.7650 (tmtt) REVERT: m 511 MET cc_start: 0.1169 (tmm) cc_final: -0.0792 (tpt) REVERT: m 676 MET cc_start: 0.1265 (mmp) cc_final: -0.0358 (ptt) REVERT: m 696 ILE cc_start: 0.5348 (mt) cc_final: 0.4850 (pt) REVERT: m 700 TRP cc_start: -0.0561 (m100) cc_final: -0.1163 (m100) REVERT: m 797 ASP cc_start: 0.7033 (p0) cc_final: 0.6800 (m-30) REVERT: m 940 GLU cc_start: 0.8617 (pm20) cc_final: 0.8406 (pm20) REVERT: m 1384 MET cc_start: 0.3404 (ttm) cc_final: 0.1344 (mmt) REVERT: m 1444 TYR cc_start: -0.0235 (m-80) cc_final: -0.0446 (m-80) REVERT: n 161 GLN cc_start: 0.7501 (mt0) cc_final: 0.7206 (mm-40) REVERT: n 167 MET cc_start: 0.7820 (mtp) cc_final: 0.7330 (mtp) REVERT: n 202 ASN cc_start: 0.6067 (p0) cc_final: 0.4538 (p0) REVERT: n 263 TYR cc_start: 0.8007 (m-80) cc_final: 0.7567 (m-80) REVERT: q 114 MET cc_start: 0.1653 (mmm) cc_final: 0.1399 (tpt) REVERT: q 862 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7330 (mm-30) REVERT: q 895 GLU cc_start: 0.7468 (tt0) cc_final: 0.6954 (pt0) REVERT: q 902 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7079 (pt0) REVERT: r 314 MET cc_start: -0.0809 (ttm) cc_final: -0.1189 (ptt) REVERT: r 430 ARG cc_start: 0.6464 (mmp-170) cc_final: 0.5955 (tpm170) REVERT: u 88 ILE cc_start: 0.6325 (pt) cc_final: 0.6032 (tt) REVERT: u 124 ARG cc_start: 0.7248 (mpp80) cc_final: 0.6976 (mmp-170) REVERT: x 316 TYR cc_start: 0.8361 (m-80) cc_final: 0.8160 (m-80) REVERT: b 52 GLU cc_start: 0.2705 (mm-30) cc_final: 0.1925 (pt0) REVERT: e 122 LYS cc_start: 0.1697 (ptmt) cc_final: 0.1400 (mppt) outliers start: 1 outliers final: 0 residues processed: 870 average time/residue: 0.7740 time to fit residues: 1113.7306 Evaluate side-chains 398 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 6.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 748 optimal weight: 40.0000 chunk 671 optimal weight: 50.0000 chunk 372 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 452 optimal weight: 30.0000 chunk 358 optimal weight: 30.0000 chunk 694 optimal weight: 40.0000 chunk 268 optimal weight: 4.9990 chunk 422 optimal weight: 30.0000 chunk 516 optimal weight: 7.9990 chunk 804 optimal weight: 40.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN A 588 HIS A1112 ASN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS B1074 ASN ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN D 170 ASN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 HIS I 105 ASN M 30 HIS V 43 GLN ** W 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 642 ASN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 351 GLN m 425 HIS m 480 ASN m 705 ASN ** m 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 722 ASN m 998 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 132 ASN q 187 GLN q 239 ASN q 319 ASN ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 810 GLN r 340 ASN ** u 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 133 HIS u 172 GLN ** u 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 162 GLN v 292 ASN x 153 ASN a 68 GLN ** a 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 94 ASN e 68 GLN g 68 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.174 78641 Z= 0.632 Angle : 0.756 10.136 107637 Z= 0.401 Chirality : 0.048 0.261 12024 Planarity : 0.006 0.075 12728 Dihedral : 18.802 134.391 13311 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.93 % Favored : 97.06 % Rotamer: Outliers : 1.11 % Allowed : 6.55 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 1.00 (0.09), residues: 8561 helix: 1.62 (0.08), residues: 3963 sheet: 0.02 (0.15), residues: 1144 loop : -0.15 (0.11), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP m 415 HIS 0.016 0.002 HIS A 817 PHE 0.025 0.003 PHE B 980 TYR 0.039 0.003 TYR B 479 ARG 0.015 0.001 ARG h 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 409 time to evaluate : 6.312 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: A 84 MET cc_start: 0.7783 (ttm) cc_final: 0.7551 (ttm) REVERT: A 122 MET cc_start: 0.8637 (tpp) cc_final: 0.8380 (ttp) REVERT: A 146 MET cc_start: 0.8437 (tpp) cc_final: 0.8003 (tpt) REVERT: A 321 ARG cc_start: 0.7841 (tpt170) cc_final: 0.7181 (tpp-160) REVERT: A 1199 LEU cc_start: 0.8051 (mt) cc_final: 0.7604 (tt) REVERT: B 305 MET cc_start: 0.8110 (mtp) cc_final: 0.7816 (mtp) REVERT: B 635 ASP cc_start: 0.6734 (p0) cc_final: 0.6380 (t0) REVERT: B 1208 MET cc_start: 0.8249 (mtp) cc_final: 0.7937 (mtm) REVERT: E 92 MET cc_start: 0.8823 (tpp) cc_final: 0.8419 (tpp) REVERT: E 122 MET cc_start: 0.7411 (tmm) cc_final: 0.7127 (tmm) REVERT: I 104 LEU cc_start: 0.7804 (mm) cc_final: 0.7486 (pt) REVERT: I 108 LYS cc_start: 0.8825 (tttp) cc_final: 0.8279 (ptmm) REVERT: M 64 SER cc_start: 0.7752 (p) cc_final: 0.7439 (t) REVERT: m 318 LYS cc_start: 0.7615 (mttt) cc_final: 0.7329 (tmtt) REVERT: m 511 MET cc_start: 0.1402 (tmm) cc_final: -0.0071 (tpt) REVERT: m 565 MET cc_start: 0.0847 (ttm) cc_final: 0.0202 (ttp) REVERT: m 676 MET cc_start: 0.1679 (mmp) cc_final: -0.0053 (ptp) REVERT: m 696 ILE cc_start: 0.5591 (mt) cc_final: 0.5092 (pt) REVERT: m 700 TRP cc_start: -0.0649 (m100) cc_final: -0.1117 (m100) REVERT: m 1039 MET cc_start: 0.3963 (tpt) cc_final: 0.2726 (ptt) REVERT: m 1384 MET cc_start: 0.4156 (ttm) cc_final: 0.1624 (mmt) REVERT: n 161 GLN cc_start: 0.7610 (mt0) cc_final: 0.7309 (mm-40) REVERT: n 263 TYR cc_start: 0.7698 (m-80) cc_final: 0.7190 (m-80) REVERT: n 289 MET cc_start: 0.5460 (mpp) cc_final: 0.4328 (tpt) REVERT: q 114 MET cc_start: 0.1525 (mmm) cc_final: 0.1305 (tpt) REVERT: q 895 GLU cc_start: 0.7317 (tt0) cc_final: 0.7034 (pt0) REVERT: q 902 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7274 (mm-30) REVERT: r 314 MET cc_start: -0.0671 (ttm) cc_final: -0.1086 (tpp) REVERT: r 329 MET cc_start: 0.2691 (ttt) cc_final: 0.2487 (ttt) REVERT: r 430 ARG cc_start: 0.6572 (mmp-170) cc_final: 0.6020 (tpm170) REVERT: u 210 MET cc_start: 0.1658 (tpt) cc_final: 0.1440 (tpt) REVERT: x 209 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8578 (tp) REVERT: a 120 MET cc_start: 0.4052 (mtt) cc_final: 0.3815 (mpp) REVERT: b 52 GLU cc_start: 0.2797 (mm-30) cc_final: 0.1738 (pt0) REVERT: h 105 LYS cc_start: 0.6152 (ttmt) cc_final: 0.5815 (mttp) outliers start: 85 outliers final: 54 residues processed: 471 average time/residue: 0.7509 time to fit residues: 607.3573 Evaluate side-chains 388 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 333 time to evaluate : 6.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 827 ASP Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 544 HIS Chi-restraints excluded: chain m residue 321 LYS Chi-restraints excluded: chain m residue 399 ASP Chi-restraints excluded: chain m residue 660 ILE Chi-restraints excluded: chain m residue 693 THR Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 735 LEU Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 607 LYS Chi-restraints excluded: chain q residue 746 SER Chi-restraints excluded: chain q residue 793 VAL Chi-restraints excluded: chain q residue 897 GLU Chi-restraints excluded: chain u residue 159 THR Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 209 ILE Chi-restraints excluded: chain x residue 259 THR Chi-restraints excluded: chain x residue 287 THR Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 335 ILE Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 51 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 447 optimal weight: 30.0000 chunk 249 optimal weight: 0.9980 chunk 669 optimal weight: 7.9990 chunk 547 optimal weight: 30.0000 chunk 221 optimal weight: 0.5980 chunk 806 optimal weight: 7.9990 chunk 870 optimal weight: 30.0000 chunk 717 optimal weight: 3.9990 chunk 799 optimal weight: 20.0000 chunk 274 optimal weight: 0.9990 chunk 646 optimal weight: 40.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 ASN A 436 HIS A1112 ASN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 GLN C 126 ASN D 130 ASN ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN W 642 ASN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 299 ASN m 710 GLN m 896 ASN ** m1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 170 ASN q 239 ASN ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 293 GLN ** x 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 104 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 78641 Z= 0.221 Angle : 0.511 9.832 107637 Z= 0.279 Chirality : 0.040 0.169 12024 Planarity : 0.004 0.055 12728 Dihedral : 18.545 129.858 13311 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.03 % Favored : 97.96 % Rotamer: Outliers : 0.91 % Allowed : 8.02 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.09), residues: 8561 helix: 2.01 (0.08), residues: 3979 sheet: 0.17 (0.15), residues: 1110 loop : -0.01 (0.11), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP n 284 HIS 0.007 0.001 HIS A 852 PHE 0.019 0.001 PHE B 363 TYR 0.021 0.001 TYR B 479 ARG 0.013 0.000 ARG B 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 370 time to evaluate : 6.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8332 (tpp) cc_final: 0.7940 (tpt) REVERT: A 1240 ILE cc_start: 0.8769 (OUTLIER) cc_final: 0.8545 (mp) REVERT: B 635 ASP cc_start: 0.6596 (p0) cc_final: 0.6319 (t0) REVERT: B 1211 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8305 (t0) REVERT: E 92 MET cc_start: 0.8744 (tpp) cc_final: 0.8225 (tpp) REVERT: I 104 LEU cc_start: 0.7761 (mm) cc_final: 0.7393 (pt) REVERT: I 108 LYS cc_start: 0.8773 (tttp) cc_final: 0.8368 (ptmm) REVERT: M 64 SER cc_start: 0.7360 (p) cc_final: 0.7094 (t) REVERT: m 318 LYS cc_start: 0.7642 (mttt) cc_final: 0.7330 (tmtt) REVERT: m 511 MET cc_start: 0.1541 (tmm) cc_final: 0.0165 (tpt) REVERT: m 676 MET cc_start: 0.0565 (mmp) cc_final: 0.0096 (ptp) REVERT: m 696 ILE cc_start: 0.5557 (mt) cc_final: 0.5063 (pt) REVERT: m 700 TRP cc_start: -0.0751 (m100) cc_final: -0.1177 (m100) REVERT: m 1039 MET cc_start: 0.4146 (tpt) cc_final: 0.2889 (ptt) REVERT: m 1384 MET cc_start: 0.3551 (ttm) cc_final: 0.1345 (mmt) REVERT: n 161 GLN cc_start: 0.7572 (mt0) cc_final: 0.7303 (mm-40) REVERT: n 169 GLU cc_start: 0.8414 (pt0) cc_final: 0.8112 (pt0) REVERT: n 263 TYR cc_start: 0.7755 (m-80) cc_final: 0.7254 (m-80) REVERT: n 278 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7900 (mt-10) REVERT: n 289 MET cc_start: 0.5581 (mpp) cc_final: 0.4252 (tpt) REVERT: q 114 MET cc_start: 0.1514 (mmm) cc_final: 0.1302 (tpt) REVERT: q 789 ARG cc_start: 0.5725 (ttt180) cc_final: 0.5513 (mtt-85) REVERT: q 884 ARG cc_start: 0.8173 (mmt180) cc_final: 0.7907 (mmp80) REVERT: q 895 GLU cc_start: 0.7240 (tt0) cc_final: 0.6895 (pt0) REVERT: q 902 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7296 (pt0) REVERT: r 314 MET cc_start: -0.0570 (ttm) cc_final: -0.1392 (mmt) REVERT: r 329 MET cc_start: 0.2446 (ttt) cc_final: 0.1764 (ttt) REVERT: r 430 ARG cc_start: 0.6631 (mmp-170) cc_final: 0.5934 (tpm170) REVERT: x 209 ILE cc_start: 0.9090 (mt) cc_final: 0.8675 (tp) REVERT: b 52 GLU cc_start: 0.2699 (mm-30) cc_final: 0.1721 (pt0) REVERT: h 105 LYS cc_start: 0.5861 (ttmt) cc_final: 0.5537 (mttp) outliers start: 70 outliers final: 40 residues processed: 420 average time/residue: 0.7026 time to fit residues: 513.1554 Evaluate side-chains 377 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 335 time to evaluate : 6.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 699 MET Chi-restraints excluded: chain B residue 1211 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 470 GLU Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 735 LEU Chi-restraints excluded: chain m residue 1320 ILE Chi-restraints excluded: chain n residue 167 MET Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 607 LYS Chi-restraints excluded: chain q residue 746 SER Chi-restraints excluded: chain q residue 793 VAL Chi-restraints excluded: chain q residue 897 GLU Chi-restraints excluded: chain u residue 159 THR Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 259 THR Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 335 ILE Chi-restraints excluded: chain e residue 59 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 796 optimal weight: 0.8980 chunk 606 optimal weight: 50.0000 chunk 418 optimal weight: 50.0000 chunk 89 optimal weight: 8.9990 chunk 384 optimal weight: 0.9980 chunk 541 optimal weight: 40.0000 chunk 808 optimal weight: 20.0000 chunk 856 optimal weight: 50.0000 chunk 422 optimal weight: 50.0000 chunk 766 optimal weight: 8.9990 chunk 230 optimal weight: 2.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN B 63 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN E 145 HIS H 51 GLN ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 291 ASN W 642 ASN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 648 GLN m 464 GLN m 816 ASN m1338 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 483 ASN ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 293 GLN ** x 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 78641 Z= 0.312 Angle : 0.536 11.081 107637 Z= 0.289 Chirality : 0.040 0.168 12024 Planarity : 0.004 0.057 12728 Dihedral : 18.521 128.570 13311 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.72 % Favored : 97.27 % Rotamer: Outliers : 1.37 % Allowed : 9.35 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 1.39 (0.09), residues: 8561 helix: 2.04 (0.08), residues: 3974 sheet: 0.09 (0.15), residues: 1122 loop : -0.03 (0.11), residues: 3465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP x 292 HIS 0.008 0.001 HIS A 852 PHE 0.018 0.001 PHE r 508 TYR 0.026 0.001 TYR M 70 ARG 0.008 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 352 time to evaluate : 6.451 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 146 MET cc_start: 0.8332 (tpp) cc_final: 0.8028 (tpt) REVERT: A 578 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8429 (mm) REVERT: B 635 ASP cc_start: 0.6714 (p0) cc_final: 0.6438 (t0) REVERT: B 889 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8529 (p) REVERT: B 929 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8285 (p) REVERT: E 92 MET cc_start: 0.8764 (tpp) cc_final: 0.8038 (tpp) REVERT: E 122 MET cc_start: 0.7330 (tmm) cc_final: 0.6848 (tmm) REVERT: I 13 MET cc_start: 0.7786 (tpp) cc_final: 0.7551 (tpt) REVERT: I 108 LYS cc_start: 0.8794 (tttp) cc_final: 0.8262 (mtpp) REVERT: m 318 LYS cc_start: 0.7705 (mttt) cc_final: 0.7334 (tmtt) REVERT: m 511 MET cc_start: 0.1245 (tmm) cc_final: -0.0642 (tpt) REVERT: m 676 MET cc_start: 0.0124 (mmp) cc_final: -0.0103 (ptp) REVERT: m 696 ILE cc_start: 0.5569 (mt) cc_final: 0.5052 (pt) REVERT: m 700 TRP cc_start: -0.0709 (m100) cc_final: -0.1254 (m100) REVERT: m 1039 MET cc_start: 0.4156 (tpt) cc_final: 0.3934 (mmm) REVERT: m 1384 MET cc_start: 0.3637 (ttm) cc_final: 0.1424 (mmt) REVERT: n 161 GLN cc_start: 0.7482 (mt0) cc_final: 0.7198 (mm-40) REVERT: n 263 TYR cc_start: 0.7833 (m-80) cc_final: 0.7330 (m-80) REVERT: n 278 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: n 289 MET cc_start: 0.5501 (mpp) cc_final: 0.4201 (tpt) REVERT: q 44 ASP cc_start: 0.3479 (OUTLIER) cc_final: 0.2698 (t70) REVERT: q 466 MET cc_start: 0.5156 (ptt) cc_final: 0.3908 (tpt) REVERT: q 895 GLU cc_start: 0.7280 (tt0) cc_final: 0.6894 (pt0) REVERT: q 902 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7246 (pt0) REVERT: r 314 MET cc_start: -0.0080 (ttm) cc_final: -0.1210 (mmt) REVERT: r 430 ARG cc_start: 0.6631 (mmp-170) cc_final: 0.5917 (tpm170) REVERT: r 505 LYS cc_start: 0.3796 (mttt) cc_final: 0.3495 (tttm) REVERT: u 124 ARG cc_start: 0.5787 (mmp-170) cc_final: 0.5333 (mmp-170) REVERT: x 209 ILE cc_start: 0.9093 (mt) cc_final: 0.8656 (tp) REVERT: x 304 ILE cc_start: 0.8433 (pt) cc_final: 0.7617 (pt) REVERT: x 307 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7625 (mp10) REVERT: b 52 GLU cc_start: 0.2706 (mm-30) cc_final: 0.1668 (pt0) REVERT: h 105 LYS cc_start: 0.6136 (ttmt) cc_final: 0.5527 (mttm) outliers start: 105 outliers final: 72 residues processed: 432 average time/residue: 0.7158 time to fit residues: 537.7001 Evaluate side-chains 398 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 320 time to evaluate : 6.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1447 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 699 MET Chi-restraints excluded: chain B residue 889 THR Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 470 GLU Chi-restraints excluded: chain W residue 544 HIS Chi-restraints excluded: chain m residue 399 ASP Chi-restraints excluded: chain m residue 693 THR Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 735 LEU Chi-restraints excluded: chain m residue 949 SER Chi-restraints excluded: chain m residue 1320 ILE Chi-restraints excluded: chain m residue 1367 VAL Chi-restraints excluded: chain n residue 167 MET Chi-restraints excluded: chain n residue 278 GLU Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 44 ASP Chi-restraints excluded: chain q residue 474 ASP Chi-restraints excluded: chain q residue 607 LYS Chi-restraints excluded: chain q residue 619 LEU Chi-restraints excluded: chain q residue 746 SER Chi-restraints excluded: chain q residue 897 GLU Chi-restraints excluded: chain r residue 227 MET Chi-restraints excluded: chain u residue 159 THR Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 259 THR Chi-restraints excluded: chain x residue 287 THR Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 335 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 713 optimal weight: 30.0000 chunk 486 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 637 optimal weight: 50.0000 chunk 353 optimal weight: 0.7980 chunk 730 optimal weight: 20.0000 chunk 591 optimal weight: 40.0000 chunk 1 optimal weight: 0.9990 chunk 437 optimal weight: 30.0000 chunk 768 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 overall best weight: 3.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN B 63 GLN ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN B 770 GLN ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 283 ASN W 642 ASN ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 753 ASN ** m1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 260 HIS x 296 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 104 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 78641 Z= 0.265 Angle : 0.507 8.503 107637 Z= 0.275 Chirality : 0.040 0.165 12024 Planarity : 0.004 0.078 12728 Dihedral : 18.453 125.231 13311 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 1.55 % Allowed : 10.35 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 1.47 (0.09), residues: 8561 helix: 2.14 (0.08), residues: 3968 sheet: 0.11 (0.15), residues: 1111 loop : -0.02 (0.11), residues: 3482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP n 284 HIS 0.006 0.001 HIS A 852 PHE 0.024 0.001 PHE q 104 TYR 0.023 0.001 TYR V 105 ARG 0.008 0.000 ARG B 865 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 343 time to evaluate : 6.419 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: 0.8339 (ttm) cc_final: 0.8020 (ttp) REVERT: A 146 MET cc_start: 0.8265 (tpp) cc_final: 0.7977 (tpt) REVERT: A 578 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8431 (mm) REVERT: A 912 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7981 (p0) REVERT: B 635 ASP cc_start: 0.6843 (p0) cc_final: 0.6573 (t0) REVERT: B 929 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8310 (p) REVERT: B 1082 MET cc_start: 0.8731 (tpt) cc_final: 0.8334 (tpt) REVERT: E 92 MET cc_start: 0.8786 (tpp) cc_final: 0.8189 (tpp) REVERT: E 122 MET cc_start: 0.7507 (tmm) cc_final: 0.7010 (tmm) REVERT: G 166 ASP cc_start: 0.8212 (t70) cc_final: 0.7925 (p0) REVERT: I 13 MET cc_start: 0.7921 (tpp) cc_final: 0.7657 (tpt) REVERT: I 108 LYS cc_start: 0.8777 (tttp) cc_final: 0.8282 (mtpp) REVERT: V 13 MET cc_start: 0.7640 (mtp) cc_final: 0.7382 (mtp) REVERT: m 318 LYS cc_start: 0.7561 (mttt) cc_final: 0.7120 (ttpt) REVERT: m 511 MET cc_start: 0.1232 (tmm) cc_final: -0.0548 (tpt) REVERT: m 676 MET cc_start: 0.0096 (mmp) cc_final: -0.0248 (ptp) REVERT: m 696 ILE cc_start: 0.5536 (mt) cc_final: 0.5332 (pt) REVERT: m 1384 MET cc_start: 0.4288 (ttm) cc_final: 0.1715 (mmt) REVERT: n 161 GLN cc_start: 0.7550 (mt0) cc_final: 0.7308 (mm-40) REVERT: n 263 TYR cc_start: 0.7704 (m-80) cc_final: 0.7239 (m-80) REVERT: n 278 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: n 289 MET cc_start: 0.5374 (mpp) cc_final: 0.4018 (tpt) REVERT: q 44 ASP cc_start: 0.3523 (OUTLIER) cc_final: 0.2710 (t70) REVERT: q 895 GLU cc_start: 0.7270 (tt0) cc_final: 0.6844 (pt0) REVERT: q 902 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7228 (pt0) REVERT: r 314 MET cc_start: -0.0036 (ttm) cc_final: -0.1301 (mmt) REVERT: r 328 GLU cc_start: 0.6538 (tm-30) cc_final: 0.5954 (pp20) REVERT: r 329 MET cc_start: 0.2514 (ttt) cc_final: 0.1611 (ttt) REVERT: r 430 ARG cc_start: 0.6611 (mmp-170) cc_final: 0.5917 (tpm170) REVERT: r 505 LYS cc_start: 0.3698 (mttt) cc_final: 0.3373 (tttm) REVERT: u 128 MET cc_start: 0.2803 (mmm) cc_final: 0.2585 (mmp) REVERT: x 209 ILE cc_start: 0.9092 (mt) cc_final: 0.8670 (tp) REVERT: x 304 ILE cc_start: 0.8525 (pt) cc_final: 0.7761 (pt) REVERT: x 307 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: b 52 GLU cc_start: 0.2555 (mm-30) cc_final: 0.1284 (pt0) REVERT: d 122 LYS cc_start: 0.2332 (tptp) cc_final: 0.1914 (tptt) REVERT: h 105 LYS cc_start: 0.6010 (ttmt) cc_final: 0.5354 (mttm) outliers start: 119 outliers final: 82 residues processed: 433 average time/residue: 0.7015 time to fit residues: 533.4410 Evaluate side-chains 406 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 318 time to evaluate : 6.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1447 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 699 MET Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1045 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 470 GLU Chi-restraints excluded: chain W residue 544 HIS Chi-restraints excluded: chain m residue 321 LYS Chi-restraints excluded: chain m residue 693 THR Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 735 LEU Chi-restraints excluded: chain m residue 949 SER Chi-restraints excluded: chain m residue 1320 ILE Chi-restraints excluded: chain m residue 1367 VAL Chi-restraints excluded: chain n residue 167 MET Chi-restraints excluded: chain n residue 272 ASN Chi-restraints excluded: chain n residue 278 GLU Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 44 ASP Chi-restraints excluded: chain q residue 474 ASP Chi-restraints excluded: chain q residue 607 LYS Chi-restraints excluded: chain q residue 619 LEU Chi-restraints excluded: chain q residue 746 SER Chi-restraints excluded: chain u residue 159 THR Chi-restraints excluded: chain u residue 226 PHE Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 287 THR Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 335 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 288 optimal weight: 2.9990 chunk 771 optimal weight: 30.0000 chunk 169 optimal weight: 20.0000 chunk 502 optimal weight: 50.0000 chunk 211 optimal weight: 6.9990 chunk 857 optimal weight: 50.0000 chunk 711 optimal weight: 5.9990 chunk 396 optimal weight: 40.0000 chunk 71 optimal weight: 0.7980 chunk 283 optimal weight: 30.0000 chunk 450 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 HIS A1112 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 ASN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 774 ASN ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 132 GLN v 212 HIS ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 64 ASN h 92 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 78641 Z= 0.269 Angle : 0.512 21.057 107637 Z= 0.275 Chirality : 0.040 0.252 12024 Planarity : 0.004 0.055 12728 Dihedral : 18.400 125.992 13311 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.90 % Favored : 97.09 % Rotamer: Outliers : 1.63 % Allowed : 10.85 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 1.48 (0.09), residues: 8561 helix: 2.16 (0.08), residues: 3987 sheet: 0.12 (0.15), residues: 1080 loop : -0.05 (0.11), residues: 3494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 64 HIS 0.006 0.001 HIS C 64 PHE 0.039 0.001 PHE q 104 TYR 0.028 0.001 TYR M 70 ARG 0.006 0.000 ARG B 865 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 342 time to evaluate : 6.374 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: 0.8209 (tpp) cc_final: 0.7931 (tpt) REVERT: A 578 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8445 (mm) REVERT: A 912 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7990 (p0) REVERT: A 1204 MET cc_start: 0.7504 (tpt) cc_final: 0.7288 (tpt) REVERT: B 635 ASP cc_start: 0.6832 (p0) cc_final: 0.6610 (t0) REVERT: B 929 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8196 (p) REVERT: B 1082 MET cc_start: 0.8717 (tpt) cc_final: 0.8361 (tpt) REVERT: E 92 MET cc_start: 0.8661 (tpp) cc_final: 0.8425 (tpp) REVERT: I 108 LYS cc_start: 0.8771 (tttp) cc_final: 0.8383 (mtpp) REVERT: V 13 MET cc_start: 0.7590 (mtp) cc_final: 0.7279 (mtp) REVERT: W 322 ARG cc_start: 0.6231 (mtt180) cc_final: 0.5222 (mtp-110) REVERT: m 318 LYS cc_start: 0.7640 (mttt) cc_final: 0.7281 (ttpp) REVERT: m 511 MET cc_start: 0.1282 (tmm) cc_final: -0.0568 (tpt) REVERT: m 565 MET cc_start: -0.1833 (ptp) cc_final: -0.2646 (ttp) REVERT: m 696 ILE cc_start: 0.5543 (mt) cc_final: 0.5018 (pt) REVERT: m 700 TRP cc_start: -0.0860 (m100) cc_final: -0.1269 (m100) REVERT: m 1384 MET cc_start: 0.4295 (ttm) cc_final: 0.1728 (mmt) REVERT: n 161 GLN cc_start: 0.7440 (mt0) cc_final: 0.7207 (mm-40) REVERT: n 263 TYR cc_start: 0.7663 (m-80) cc_final: 0.7170 (m-80) REVERT: n 278 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: n 289 MET cc_start: 0.5439 (mpp) cc_final: 0.4221 (tpt) REVERT: q 44 ASP cc_start: 0.3668 (OUTLIER) cc_final: 0.2822 (t70) REVERT: q 104 PHE cc_start: -0.0393 (OUTLIER) cc_final: -0.0620 (t80) REVERT: q 228 ASN cc_start: 0.4952 (t0) cc_final: 0.4609 (t0) REVERT: q 902 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7215 (pt0) REVERT: r 314 MET cc_start: -0.0389 (ttm) cc_final: -0.1769 (mmt) REVERT: r 328 GLU cc_start: 0.6768 (tm-30) cc_final: 0.6454 (pp20) REVERT: r 430 ARG cc_start: 0.6456 (mmp-170) cc_final: 0.5743 (tpm170) REVERT: v 299 HIS cc_start: 0.0534 (OUTLIER) cc_final: -0.0094 (t-170) REVERT: x 209 ILE cc_start: 0.9089 (mt) cc_final: 0.8670 (tp) REVERT: x 304 ILE cc_start: 0.8503 (pt) cc_final: 0.7733 (pt) REVERT: x 307 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7575 (mp10) REVERT: b 52 GLU cc_start: 0.2373 (mm-30) cc_final: 0.1442 (pt0) REVERT: f 66 ILE cc_start: 0.4475 (OUTLIER) cc_final: 0.4087 (tp) REVERT: h 105 LYS cc_start: 0.6141 (ttmt) cc_final: 0.5435 (mttp) outliers start: 125 outliers final: 88 residues processed: 441 average time/residue: 0.7009 time to fit residues: 542.9304 Evaluate side-chains 422 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 325 time to evaluate : 6.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1447 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 699 MET Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1045 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 155 ASN Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain m residue 321 LYS Chi-restraints excluded: chain m residue 693 THR Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 735 LEU Chi-restraints excluded: chain m residue 949 SER Chi-restraints excluded: chain m residue 1320 ILE Chi-restraints excluded: chain m residue 1367 VAL Chi-restraints excluded: chain n residue 167 MET Chi-restraints excluded: chain n residue 278 GLU Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 44 ASP Chi-restraints excluded: chain q residue 104 PHE Chi-restraints excluded: chain q residue 474 ASP Chi-restraints excluded: chain q residue 607 LYS Chi-restraints excluded: chain q residue 619 LEU Chi-restraints excluded: chain q residue 746 SER Chi-restraints excluded: chain r residue 227 MET Chi-restraints excluded: chain u residue 159 THR Chi-restraints excluded: chain u residue 226 PHE Chi-restraints excluded: chain v residue 125 VAL Chi-restraints excluded: chain v residue 299 HIS Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 259 THR Chi-restraints excluded: chain x residue 287 THR Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 335 ILE Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 826 optimal weight: 50.0000 chunk 96 optimal weight: 2.9990 chunk 488 optimal weight: 10.0000 chunk 626 optimal weight: 0.8980 chunk 485 optimal weight: 6.9990 chunk 721 optimal weight: 50.0000 chunk 478 optimal weight: 0.1980 chunk 853 optimal weight: 40.0000 chunk 534 optimal weight: 40.0000 chunk 520 optimal weight: 8.9990 chunk 394 optimal weight: 6.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 132 GLN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 92 GLN ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 78641 Z= 0.248 Angle : 0.496 8.394 107637 Z= 0.268 Chirality : 0.039 0.159 12024 Planarity : 0.003 0.053 12728 Dihedral : 18.364 126.872 13311 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.55 % Favored : 97.43 % Rotamer: Outliers : 1.61 % Allowed : 11.14 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 1.53 (0.09), residues: 8561 helix: 2.22 (0.08), residues: 3988 sheet: 0.13 (0.15), residues: 1074 loop : -0.05 (0.11), residues: 3499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 64 HIS 0.007 0.001 HIS B 761 PHE 0.031 0.001 PHE q 104 TYR 0.028 0.001 TYR M 70 ARG 0.005 0.000 ARG B 865 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 343 time to evaluate : 6.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8248 (tpp) cc_final: 0.7915 (tpt) REVERT: A 578 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8450 (mm) REVERT: A 912 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7980 (p0) REVERT: B 305 MET cc_start: 0.8085 (mtp) cc_final: 0.7684 (mtp) REVERT: B 1082 MET cc_start: 0.8719 (tpt) cc_final: 0.8348 (tpt) REVERT: G 166 ASP cc_start: 0.8222 (t70) cc_final: 0.7821 (p0) REVERT: I 108 LYS cc_start: 0.8760 (tttp) cc_final: 0.8378 (mtpp) REVERT: V 13 MET cc_start: 0.7584 (mtp) cc_final: 0.7275 (mtp) REVERT: W 322 ARG cc_start: 0.6256 (mtt180) cc_final: 0.5229 (mtp-110) REVERT: m 511 MET cc_start: 0.1555 (tmm) cc_final: -0.0192 (tpt) REVERT: m 565 MET cc_start: -0.1963 (ptp) cc_final: -0.2724 (ttp) REVERT: m 696 ILE cc_start: 0.5540 (mt) cc_final: 0.5015 (pt) REVERT: m 700 TRP cc_start: -0.0943 (m100) cc_final: -0.1375 (m100) REVERT: m 1384 MET cc_start: 0.3638 (ttm) cc_final: 0.1434 (mmt) REVERT: n 161 GLN cc_start: 0.7437 (mt0) cc_final: 0.7218 (mm-40) REVERT: n 263 TYR cc_start: 0.7665 (m-80) cc_final: 0.7171 (m-80) REVERT: n 278 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: n 289 MET cc_start: 0.5434 (mpp) cc_final: 0.4191 (tpt) REVERT: q 44 ASP cc_start: 0.3904 (OUTLIER) cc_final: 0.2981 (t70) REVERT: q 228 ASN cc_start: 0.5029 (t0) cc_final: 0.4626 (t0) REVERT: q 902 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7065 (pt0) REVERT: r 314 MET cc_start: -0.0620 (ttm) cc_final: -0.1433 (tpp) REVERT: r 329 MET cc_start: 0.2101 (ttt) cc_final: 0.1900 (ttt) REVERT: r 430 ARG cc_start: 0.6415 (mmp-170) cc_final: 0.5789 (tpm170) REVERT: u 124 ARG cc_start: 0.5740 (mmp-170) cc_final: 0.5500 (mmp-170) REVERT: v 299 HIS cc_start: 0.0521 (OUTLIER) cc_final: -0.0105 (t-170) REVERT: v 305 GLN cc_start: 0.4220 (tp-100) cc_final: 0.4000 (tp40) REVERT: x 209 ILE cc_start: 0.9094 (mt) cc_final: 0.8671 (tp) REVERT: x 304 ILE cc_start: 0.8503 (pt) cc_final: 0.7740 (pt) REVERT: x 307 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: b 52 GLU cc_start: 0.2361 (mm-30) cc_final: 0.1424 (pt0) REVERT: f 66 ILE cc_start: 0.4482 (OUTLIER) cc_final: 0.4088 (tp) REVERT: h 105 LYS cc_start: 0.6057 (ttmt) cc_final: 0.5317 (mttp) outliers start: 124 outliers final: 98 residues processed: 441 average time/residue: 0.6980 time to fit residues: 542.9168 Evaluate side-chains 426 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 321 time to evaluate : 6.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1081 MET Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 699 MET Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1045 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 544 HIS Chi-restraints excluded: chain W residue 581 ILE Chi-restraints excluded: chain m residue 321 LYS Chi-restraints excluded: chain m residue 582 SER Chi-restraints excluded: chain m residue 693 THR Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 735 LEU Chi-restraints excluded: chain m residue 949 SER Chi-restraints excluded: chain m residue 1320 ILE Chi-restraints excluded: chain m residue 1367 VAL Chi-restraints excluded: chain n residue 167 MET Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 272 ASN Chi-restraints excluded: chain n residue 278 GLU Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 44 ASP Chi-restraints excluded: chain q residue 474 ASP Chi-restraints excluded: chain q residue 607 LYS Chi-restraints excluded: chain q residue 619 LEU Chi-restraints excluded: chain q residue 746 SER Chi-restraints excluded: chain u residue 159 THR Chi-restraints excluded: chain u residue 226 PHE Chi-restraints excluded: chain v residue 299 HIS Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 259 THR Chi-restraints excluded: chain x residue 287 THR Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 335 ILE Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 528 optimal weight: 20.0000 chunk 341 optimal weight: 6.9990 chunk 510 optimal weight: 50.0000 chunk 257 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 165 optimal weight: 10.0000 chunk 542 optimal weight: 30.0000 chunk 581 optimal weight: 9.9990 chunk 422 optimal weight: 40.0000 chunk 79 optimal weight: 2.9990 chunk 671 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN B1013 ASN ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 831 HIS m1288 ASN m1407 HIS ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 363 GLN ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 64 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 78641 Z= 0.324 Angle : 0.536 14.759 107637 Z= 0.287 Chirality : 0.040 0.181 12024 Planarity : 0.004 0.055 12728 Dihedral : 18.391 127.870 13311 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.01 % Favored : 96.96 % Rotamer: Outliers : 1.77 % Allowed : 11.38 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 1.43 (0.09), residues: 8561 helix: 2.14 (0.08), residues: 3993 sheet: 0.12 (0.15), residues: 1068 loop : -0.12 (0.11), residues: 3500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 64 HIS 0.009 0.001 HIS B 761 PHE 0.030 0.001 PHE q 104 TYR 0.049 0.001 TYR r 243 ARG 0.009 0.000 ARG r 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 338 time to evaluate : 6.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8216 (tpp) cc_final: 0.7927 (tpt) REVERT: A 578 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8484 (mm) REVERT: A 912 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.7994 (p0) REVERT: B 305 MET cc_start: 0.8104 (mtp) cc_final: 0.7695 (mtp) REVERT: B 1082 MET cc_start: 0.8719 (tpt) cc_final: 0.8370 (tpt) REVERT: E 92 MET cc_start: 0.8491 (tpp) cc_final: 0.8193 (tpt) REVERT: G 136 LEU cc_start: 0.4487 (OUTLIER) cc_final: 0.3426 (mt) REVERT: G 166 ASP cc_start: 0.8233 (t70) cc_final: 0.7840 (p0) REVERT: I 13 MET cc_start: 0.7999 (tpp) cc_final: 0.7581 (tpt) REVERT: I 108 LYS cc_start: 0.8784 (tttp) cc_final: 0.8400 (mtpp) REVERT: V 13 MET cc_start: 0.7601 (mtp) cc_final: 0.7281 (mtp) REVERT: m 511 MET cc_start: 0.2246 (tmm) cc_final: 0.0577 (tpt) REVERT: m 582 SER cc_start: 0.2882 (OUTLIER) cc_final: 0.2562 (m) REVERT: m 696 ILE cc_start: 0.5564 (mt) cc_final: 0.5343 (pt) REVERT: m 1384 MET cc_start: 0.3657 (ttm) cc_final: 0.1431 (mmt) REVERT: n 161 GLN cc_start: 0.7445 (mt0) cc_final: 0.7217 (mm-40) REVERT: n 263 TYR cc_start: 0.7710 (m-80) cc_final: 0.7200 (m-80) REVERT: n 278 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: n 289 MET cc_start: 0.5489 (mpp) cc_final: 0.4410 (tpt) REVERT: q 44 ASP cc_start: 0.3983 (OUTLIER) cc_final: 0.3030 (t70) REVERT: q 228 ASN cc_start: 0.5068 (t0) cc_final: 0.4678 (t0) REVERT: r 314 MET cc_start: -0.0671 (ttm) cc_final: -0.1479 (tpp) REVERT: r 430 ARG cc_start: 0.6444 (mmp-170) cc_final: 0.5755 (tpm170) REVERT: u 124 ARG cc_start: 0.5628 (mmp-170) cc_final: 0.5265 (mmp-170) REVERT: v 299 HIS cc_start: 0.0542 (OUTLIER) cc_final: -0.0073 (t-170) REVERT: v 305 GLN cc_start: 0.4216 (tp-100) cc_final: 0.3982 (tp40) REVERT: x 209 ILE cc_start: 0.9088 (mt) cc_final: 0.8667 (tp) REVERT: x 304 ILE cc_start: 0.8514 (pt) cc_final: 0.7754 (pt) REVERT: x 307 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7551 (mp10) REVERT: b 52 GLU cc_start: 0.1861 (mm-30) cc_final: 0.0781 (pt0) REVERT: f 66 ILE cc_start: 0.4497 (OUTLIER) cc_final: 0.4102 (tp) outliers start: 136 outliers final: 106 residues processed: 443 average time/residue: 0.6894 time to fit residues: 539.5932 Evaluate side-chains 437 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 322 time to evaluate : 6.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1081 MET Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1447 MET Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 699 MET Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain B residue 1045 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 138 TYR Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 79 HIS Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain V residue 95 VAL Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 581 ILE Chi-restraints excluded: chain m residue 582 SER Chi-restraints excluded: chain m residue 693 THR Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 735 LEU Chi-restraints excluded: chain m residue 949 SER Chi-restraints excluded: chain m residue 1320 ILE Chi-restraints excluded: chain m residue 1367 VAL Chi-restraints excluded: chain n residue 167 MET Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 272 ASN Chi-restraints excluded: chain n residue 278 GLU Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 44 ASP Chi-restraints excluded: chain q residue 474 ASP Chi-restraints excluded: chain q residue 607 LYS Chi-restraints excluded: chain q residue 619 LEU Chi-restraints excluded: chain q residue 746 SER Chi-restraints excluded: chain r residue 405 LEU Chi-restraints excluded: chain u residue 159 THR Chi-restraints excluded: chain u residue 226 PHE Chi-restraints excluded: chain v residue 125 VAL Chi-restraints excluded: chain v residue 299 HIS Chi-restraints excluded: chain v residue 352 VAL Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 259 THR Chi-restraints excluded: chain x residue 287 THR Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 335 ILE Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 776 optimal weight: 8.9990 chunk 818 optimal weight: 40.0000 chunk 746 optimal weight: 4.9990 chunk 795 optimal weight: 30.0000 chunk 817 optimal weight: 30.0000 chunk 478 optimal weight: 9.9990 chunk 346 optimal weight: 2.9990 chunk 624 optimal weight: 0.0470 chunk 244 optimal weight: 0.9990 chunk 719 optimal weight: 8.9990 chunk 752 optimal weight: 50.0000 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1112 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 363 GLN ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 78641 Z= 0.248 Angle : 0.509 9.683 107637 Z= 0.274 Chirality : 0.039 0.167 12024 Planarity : 0.004 0.070 12728 Dihedral : 18.353 127.771 13311 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.80 % Favored : 97.17 % Rotamer: Outliers : 1.48 % Allowed : 11.79 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 8561 helix: 2.19 (0.08), residues: 3995 sheet: 0.09 (0.15), residues: 1090 loop : -0.07 (0.11), residues: 3476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 64 HIS 0.008 0.001 HIS B 761 PHE 0.030 0.001 PHE q 104 TYR 0.046 0.001 TYR r 243 ARG 0.021 0.000 ARG q 884 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 330 time to evaluate : 6.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 MET cc_start: 0.8176 (tpp) cc_final: 0.7903 (tpt) REVERT: A 578 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8455 (mm) REVERT: A 912 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7979 (p0) REVERT: B 305 MET cc_start: 0.8104 (mtp) cc_final: 0.7685 (mtp) REVERT: B 1082 MET cc_start: 0.8707 (tpt) cc_final: 0.8350 (tpt) REVERT: E 92 MET cc_start: 0.8476 (tpp) cc_final: 0.8256 (tpt) REVERT: G 136 LEU cc_start: 0.4452 (OUTLIER) cc_final: 0.3403 (mt) REVERT: G 166 ASP cc_start: 0.8209 (t70) cc_final: 0.7834 (p0) REVERT: I 13 MET cc_start: 0.8004 (tpp) cc_final: 0.7561 (tpt) REVERT: V 13 MET cc_start: 0.7574 (mtp) cc_final: 0.7304 (mtp) REVERT: V 25 MET cc_start: 0.5750 (tpp) cc_final: 0.5294 (tpp) REVERT: m 511 MET cc_start: 0.2201 (tmm) cc_final: 0.0509 (tpt) REVERT: m 696 ILE cc_start: 0.5559 (mt) cc_final: 0.5345 (pt) REVERT: m 732 GLU cc_start: 0.7056 (tm-30) cc_final: 0.5958 (tm-30) REVERT: m 1384 MET cc_start: 0.3636 (ttm) cc_final: 0.1429 (mmt) REVERT: n 161 GLN cc_start: 0.7434 (mt0) cc_final: 0.7208 (mm-40) REVERT: n 263 TYR cc_start: 0.7711 (m-80) cc_final: 0.7199 (m-80) REVERT: n 278 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: n 289 MET cc_start: 0.4969 (mpp) cc_final: 0.4510 (tpt) REVERT: q 44 ASP cc_start: 0.4097 (OUTLIER) cc_final: 0.3163 (t70) REVERT: q 228 ASN cc_start: 0.5122 (t0) cc_final: 0.4718 (t0) REVERT: q 466 MET cc_start: 0.4280 (ptt) cc_final: 0.2728 (tpt) REVERT: r 314 MET cc_start: -0.0699 (ttm) cc_final: -0.1489 (tpp) REVERT: r 329 MET cc_start: 0.1979 (ttt) cc_final: 0.1446 (tpp) REVERT: r 430 ARG cc_start: 0.6124 (mmp-170) cc_final: 0.5558 (tpm170) REVERT: v 299 HIS cc_start: 0.0523 (OUTLIER) cc_final: -0.0074 (t-170) REVERT: v 305 GLN cc_start: 0.4227 (tp-100) cc_final: 0.3999 (tp40) REVERT: x 209 ILE cc_start: 0.9094 (mt) cc_final: 0.8665 (tp) REVERT: b 52 GLU cc_start: 0.1840 (mm-30) cc_final: 0.0774 (pt0) REVERT: f 66 ILE cc_start: 0.4594 (OUTLIER) cc_final: 0.4213 (tp) outliers start: 114 outliers final: 101 residues processed: 423 average time/residue: 0.6940 time to fit residues: 522.0692 Evaluate side-chains 430 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 322 time to evaluate : 6.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 699 MET Chi-restraints excluded: chain B residue 891 GLU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 970 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 544 HIS Chi-restraints excluded: chain W residue 581 ILE Chi-restraints excluded: chain m residue 693 THR Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 735 LEU Chi-restraints excluded: chain m residue 949 SER Chi-restraints excluded: chain m residue 1320 ILE Chi-restraints excluded: chain m residue 1367 VAL Chi-restraints excluded: chain n residue 167 MET Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 272 ASN Chi-restraints excluded: chain n residue 278 GLU Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 44 ASP Chi-restraints excluded: chain q residue 431 VAL Chi-restraints excluded: chain q residue 474 ASP Chi-restraints excluded: chain q residue 607 LYS Chi-restraints excluded: chain q residue 619 LEU Chi-restraints excluded: chain q residue 746 SER Chi-restraints excluded: chain r residue 405 LEU Chi-restraints excluded: chain u residue 159 THR Chi-restraints excluded: chain v residue 125 VAL Chi-restraints excluded: chain v residue 299 HIS Chi-restraints excluded: chain v residue 352 VAL Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 259 THR Chi-restraints excluded: chain x residue 287 THR Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 338 VAL Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 793 optimal weight: 30.0000 chunk 522 optimal weight: 2.9990 chunk 841 optimal weight: 0.0980 chunk 513 optimal weight: 9.9990 chunk 399 optimal weight: 50.0000 chunk 584 optimal weight: 20.0000 chunk 882 optimal weight: 1.9990 chunk 812 optimal weight: 0.0770 chunk 702 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 542 optimal weight: 30.0000 overall best weight: 3.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 363 GLN ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 78641 Z= 0.218 Angle : 0.496 10.614 107637 Z= 0.267 Chirality : 0.039 0.163 12024 Planarity : 0.003 0.054 12728 Dihedral : 18.285 127.665 13311 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.77 % Favored : 97.21 % Rotamer: Outliers : 1.37 % Allowed : 11.92 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 1.55 (0.09), residues: 8561 helix: 2.24 (0.08), residues: 3997 sheet: 0.15 (0.15), residues: 1089 loop : -0.05 (0.11), residues: 3475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 110 HIS 0.007 0.001 HIS B 761 PHE 0.036 0.001 PHE q 104 TYR 0.027 0.001 TYR r 243 ARG 0.009 0.000 ARG q 884 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17122 Ramachandran restraints generated. 8561 Oldfield, 0 Emsley, 8561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 329 time to evaluate : 6.493 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: 0.8163 (tpp) cc_final: 0.7777 (tpt) REVERT: A 282 MET cc_start: 0.8174 (tpp) cc_final: 0.7892 (tpp) REVERT: A 578 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8445 (mm) REVERT: A 912 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7978 (p0) REVERT: B 305 MET cc_start: 0.8093 (mtp) cc_final: 0.7681 (mtp) REVERT: B 1082 MET cc_start: 0.8709 (tpt) cc_final: 0.8327 (tpt) REVERT: E 92 MET cc_start: 0.8480 (tpp) cc_final: 0.8228 (tpt) REVERT: E 122 MET cc_start: 0.7841 (tpp) cc_final: 0.7030 (tpp) REVERT: G 136 LEU cc_start: 0.4381 (OUTLIER) cc_final: 0.3218 (mt) REVERT: G 166 ASP cc_start: 0.8057 (t70) cc_final: 0.7628 (p0) REVERT: I 13 MET cc_start: 0.8009 (tpp) cc_final: 0.7532 (tpt) REVERT: M 47 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6584 (mp) REVERT: V 13 MET cc_start: 0.7679 (mtp) cc_final: 0.7321 (mtp) REVERT: V 25 MET cc_start: 0.5782 (tpp) cc_final: 0.5329 (tpp) REVERT: m 511 MET cc_start: 0.2653 (tmm) cc_final: 0.0517 (tpt) REVERT: m 582 SER cc_start: 0.3244 (OUTLIER) cc_final: 0.2939 (m) REVERT: m 696 ILE cc_start: 0.5545 (mt) cc_final: 0.5330 (pt) REVERT: m 732 GLU cc_start: 0.7033 (tm-30) cc_final: 0.5900 (tm-30) REVERT: m 1384 MET cc_start: 0.3619 (ttm) cc_final: 0.1423 (mmt) REVERT: n 161 GLN cc_start: 0.7433 (mt0) cc_final: 0.7202 (mm-40) REVERT: n 263 TYR cc_start: 0.7711 (m-80) cc_final: 0.7197 (m-80) REVERT: n 278 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: n 289 MET cc_start: 0.4979 (mpp) cc_final: 0.4240 (tpt) REVERT: q 44 ASP cc_start: 0.4118 (OUTLIER) cc_final: 0.3170 (t70) REVERT: q 228 ASN cc_start: 0.5184 (t0) cc_final: 0.4777 (t0) REVERT: q 895 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7565 (pp20) REVERT: r 314 MET cc_start: -0.0707 (ttm) cc_final: -0.1487 (tpp) REVERT: r 329 MET cc_start: 0.1859 (ttt) cc_final: 0.1335 (tpp) REVERT: r 430 ARG cc_start: 0.6090 (mmp-170) cc_final: 0.5550 (tpm170) REVERT: x 209 ILE cc_start: 0.9095 (mt) cc_final: 0.8664 (tp) REVERT: x 304 ILE cc_start: 0.8505 (pt) cc_final: 0.7858 (pp) REVERT: x 307 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: a 59 GLU cc_start: 0.2905 (tp30) cc_final: 0.2207 (mm-30) REVERT: b 52 GLU cc_start: 0.1811 (mm-30) cc_final: 0.0767 (pt0) REVERT: f 66 ILE cc_start: 0.4620 (OUTLIER) cc_final: 0.4242 (tp) outliers start: 105 outliers final: 93 residues processed: 415 average time/residue: 0.6816 time to fit residues: 501.0485 Evaluate side-chains 423 residues out of total 7690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 321 time to evaluate : 6.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 CYS Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 308 ASP Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1240 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1274 ILE Chi-restraints excluded: chain A residue 1311 THR Chi-restraints excluded: chain A residue 1377 VAL Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 436 ASN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 622 ASP Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 699 MET Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain E residue 21 MET Chi-restraints excluded: chain E residue 71 TYR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 3 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 14 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 72 VAL Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 43 SER Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 47 LEU Chi-restraints excluded: chain V residue 113 ILE Chi-restraints excluded: chain W residue 238 ASP Chi-restraints excluded: chain W residue 304 VAL Chi-restraints excluded: chain W residue 544 HIS Chi-restraints excluded: chain W residue 581 ILE Chi-restraints excluded: chain m residue 582 SER Chi-restraints excluded: chain m residue 693 THR Chi-restraints excluded: chain m residue 721 LEU Chi-restraints excluded: chain m residue 1320 ILE Chi-restraints excluded: chain m residue 1367 VAL Chi-restraints excluded: chain n residue 167 MET Chi-restraints excluded: chain n residue 219 TRP Chi-restraints excluded: chain n residue 272 ASN Chi-restraints excluded: chain n residue 278 GLU Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 44 ASP Chi-restraints excluded: chain q residue 431 VAL Chi-restraints excluded: chain q residue 607 LYS Chi-restraints excluded: chain q residue 619 LEU Chi-restraints excluded: chain q residue 746 SER Chi-restraints excluded: chain u residue 159 THR Chi-restraints excluded: chain v residue 125 VAL Chi-restraints excluded: chain v residue 362 MET Chi-restraints excluded: chain x residue 150 ILE Chi-restraints excluded: chain x residue 259 THR Chi-restraints excluded: chain x residue 287 THR Chi-restraints excluded: chain x residue 288 THR Chi-restraints excluded: chain x residue 307 GLN Chi-restraints excluded: chain x residue 338 VAL Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 84 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 886 random chunks: chunk 430 optimal weight: 30.0000 chunk 558 optimal weight: 30.0000 chunk 748 optimal weight: 30.0000 chunk 215 optimal weight: 4.9990 chunk 648 optimal weight: 30.0000 chunk 103 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 704 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 722 optimal weight: 50.0000 chunk 89 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 480 ASN ** m1338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 926 ASN ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.144339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.091899 restraints weight = 242361.279| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 4.16 r_work: 0.3061 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 78641 Z= 0.314 Angle : 0.538 9.952 107637 Z= 0.288 Chirality : 0.040 0.158 12024 Planarity : 0.004 0.057 12728 Dihedral : 18.331 128.316 13311 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.17 % Favored : 96.81 % Rotamer: Outliers : 1.46 % Allowed : 11.98 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 8561 helix: 2.14 (0.08), residues: 4003 sheet: 0.12 (0.15), residues: 1081 loop : -0.12 (0.11), residues: 3477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP x 292 HIS 0.008 0.001 HIS B 761 PHE 0.032 0.001 PHE q 104 TYR 0.026 0.001 TYR B 479 ARG 0.008 0.000 ARG q 884 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14016.46 seconds wall clock time: 249 minutes 51.09 seconds (14991.09 seconds total)