Starting phenix.real_space_refine on Sat Mar 23 05:05:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oba_12796/03_2024/7oba_12796.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oba_12796/03_2024/7oba_12796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oba_12796/03_2024/7oba_12796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oba_12796/03_2024/7oba_12796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oba_12796/03_2024/7oba_12796.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oba_12796/03_2024/7oba_12796.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 7 6.06 5 S 248 5.16 5 C 22728 2.51 5 N 6181 2.21 5 O 6515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 565": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "A ARG 667": "NH1" <-> "NH2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "A ARG 740": "NH1" <-> "NH2" Residue "A ARG 793": "NH1" <-> "NH2" Residue "A ARG 814": "NH1" <-> "NH2" Residue "A ARG 828": "NH1" <-> "NH2" Residue "A ARG 843": "NH1" <-> "NH2" Residue "A ARG 856": "NH1" <-> "NH2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A ARG 990": "NH1" <-> "NH2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A ARG 1110": "NH1" <-> "NH2" Residue "A ARG 1113": "NH1" <-> "NH2" Residue "A ARG 1132": "NH1" <-> "NH2" Residue "A ARG 1133": "NH1" <-> "NH2" Residue "A ARG 1151": "NH1" <-> "NH2" Residue "A ARG 1191": "NH1" <-> "NH2" Residue "A ARG 1249": "NH1" <-> "NH2" Residue "A ARG 1277": "NH1" <-> "NH2" Residue "A ARG 1287": "NH1" <-> "NH2" Residue "A ARG 1334": "NH1" <-> "NH2" Residue "A ARG 1340": "NH1" <-> "NH2" Residue "A ARG 1345": "NH1" <-> "NH2" Residue "A ARG 1506": "NH1" <-> "NH2" Residue "A ARG 1599": "NH1" <-> "NH2" Residue "A ARG 1663": "NH1" <-> "NH2" Residue "A ARG 1694": "NH1" <-> "NH2" Residue "A ARG 1707": "NH1" <-> "NH2" Residue "A PHE 1713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "B ARG 548": "NH1" <-> "NH2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 723": "NH1" <-> "NH2" Residue "B TYR 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 978": "NH1" <-> "NH2" Residue "B ARG 1057": "NH1" <-> "NH2" Residue "B ARG 1064": "NH1" <-> "NH2" Residue "B ARG 1103": "NH1" <-> "NH2" Residue "B ARG 1117": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 303": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "I ARG 40": "NH1" <-> "NH2" Residue "I ARG 48": "NH1" <-> "NH2" Residue "K ARG 87": "NH1" <-> "NH2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 116": "NH1" <-> "NH2" Residue "N ARG 146": "NH1" <-> "NH2" Residue "N ARG 148": "NH1" <-> "NH2" Residue "O ARG 260": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35679 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 12123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1522, 12123 Classifications: {'peptide': 1522} Link IDs: {'PCIS': 3, 'PTRANS': 76, 'TRANS': 1442} Chain breaks: 7 Chain: "B" Number of atoms: 8949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1127, 8949 Classifications: {'peptide': 1127} Link IDs: {'PTRANS': 66, 'TRANS': 1060} Chain breaks: 1 Chain: "C" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2474 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 16, 'TRANS': 292} Chain: "E" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1728 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 11, 'TRANS': 198} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1241 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 8, 'TRANS': 150} Chain breaks: 1 Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1197 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "I" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 813 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 837 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Chain: "N" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1083 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 25, 'TRANS': 123} Chain: "O" Number of atoms: 2849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2849 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 19, 'TRANS': 327} Chain breaks: 6 Chain: "A" 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: "B" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 64 53.856 86.770 73.937 1.00 98.07 S ATOM 483 SG CYS A 67 54.423 82.319 72.384 1.00 98.16 S ATOM 538 SG CYS A 74 57.631 83.834 73.790 1.00 89.06 S ATOM 776 SG CYS A 104 73.331 106.277 31.858 1.00107.97 S ATOM 798 SG CYS A 107 72.137 104.305 28.743 1.00112.05 S ATOM 1582 SG CYS A 205 75.313 106.092 28.835 1.00114.46 S ATOM 20568 SG CYS B1070 58.990 75.004 57.835 1.00 84.60 S ATOM 20590 SG CYS B1073 60.461 78.045 54.670 1.00 86.20 S ATOM 20788 SG CYS B1098 57.292 78.213 58.486 1.00 90.79 S ATOM 28418 SG CYS I 20 124.589 156.647 59.947 1.00 66.38 S ATOM 28438 SG CYS I 23 121.526 156.467 62.045 1.00 71.12 S ATOM 28538 SG CYS I 38 120.025 155.503 58.637 1.00 77.58 S ATOM 28563 SG CYS I 41 121.836 158.830 59.350 1.00 78.76 S ATOM 28838 SG CYS I 87 129.830 76.373 73.902 1.00 73.85 S ATOM 28862 SG CYS I 90 133.288 75.322 71.993 1.00 82.42 S ATOM 29061 SG CYS I 115 133.139 78.911 73.945 1.00 62.16 S ATOM 29082 SG CYS I 118 130.724 77.494 70.628 1.00 72.48 S ATOM 29207 SG CYS J 7 108.491 83.181 124.141 1.00 22.47 S ATOM 29231 SG CYS J 10 109.609 79.116 125.568 1.00 23.04 S ATOM 29495 SG CYS J 44 111.792 81.102 123.480 1.00 26.57 S ATOM 29501 SG CYS J 45 110.964 81.976 127.312 1.00 27.15 S ATOM 30573 SG CYS L 19 80.824 117.318 122.396 1.00 42.23 S ATOM 30592 SG CYS L 22 80.715 119.056 125.991 1.00 46.03 S ATOM 30709 SG CYS L 36 77.495 118.558 124.388 1.00 45.34 S ATOM 30735 SG CYS L 39 80.758 121.217 123.133 1.00 45.98 S Time building chain proxies: 17.89, per 1000 atoms: 0.50 Number of scatterers: 35679 At special positions: 0 Unit cell: (166.044, 187.416, 165.222, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 7 29.99 S 248 16.00 O 6515 8.00 N 6181 7.00 C 22728 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: 12.57 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" NE2 HIS A 77 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 74 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 64 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 104 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 205 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1070 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1073 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 38 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 41 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 23 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 87 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 118 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 90 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 115 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " Number of angles added : 27 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8414 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 44 sheets defined 31.8% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.01 Creating SS restraints... Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.674A pdb=" N ILE A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 removed outlier: 3.730A pdb=" N ASN A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 171 removed outlier: 3.949A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL A 169 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.649A pdb=" N SER A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 273 removed outlier: 4.267A pdb=" N ALA A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 346 removed outlier: 3.748A pdb=" N LEU A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 403 removed outlier: 3.879A pdb=" N TRP A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 512 through 521 removed outlier: 4.885A pdb=" N VAL A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 580 through 584 removed outlier: 3.969A pdb=" N LYS A 583 " --> pdb=" O ALA A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 633 through 642 removed outlier: 3.622A pdb=" N ALA A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 removed outlier: 3.550A pdb=" N MET A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 658 " --> pdb=" O MET A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 694 removed outlier: 3.665A pdb=" N VAL A 688 " --> pdb=" O GLY A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'A' and resid 760 through 765 Processing helix chain 'A' and resid 773 through 787 removed outlier: 3.944A pdb=" N THR A 779 " --> pdb=" O GLY A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 removed outlier: 4.002A pdb=" N THR A 820 " --> pdb=" O GLU A 817 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS A 821 " --> pdb=" O GLU A 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 817 through 821' Processing helix chain 'A' and resid 824 through 829 removed outlier: 3.786A pdb=" N ALA A 829 " --> pdb=" O GLN A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 850 Processing helix chain 'A' and resid 861 through 869 removed outlier: 4.297A pdb=" N GLU A 867 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 881 removed outlier: 3.642A pdb=" N ILE A 876 " --> pdb=" O TYR A 872 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 944 through 949 removed outlier: 3.698A pdb=" N GLY A 949 " --> pdb=" O ARG A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 980 removed outlier: 3.659A pdb=" N HIS A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A 974 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 996 Processing helix chain 'A' and resid 1018 through 1022 removed outlier: 3.793A pdb=" N ASP A1022 " --> pdb=" O TYR A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1030 removed outlier: 3.910A pdb=" N THR A1029 " --> pdb=" O ILE A1026 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1026 through 1030' Processing helix chain 'A' and resid 1033 through 1036 Processing helix chain 'A' and resid 1037 through 1042 Processing helix chain 'A' and resid 1043 through 1048 removed outlier: 3.975A pdb=" N ILE A1047 " --> pdb=" O ASN A1043 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET A1048 " --> pdb=" O TYR A1044 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1043 through 1048' Processing helix chain 'A' and resid 1061 through 1065 removed outlier: 4.454A pdb=" N LYS A1064 " --> pdb=" O ASP A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1076 removed outlier: 3.969A pdb=" N LYS A1073 " --> pdb=" O PHE A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 removed outlier: 3.612A pdb=" N TYR A1092 " --> pdb=" O ALA A1088 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A1094 " --> pdb=" O LEU A1090 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A1095 " --> pdb=" O SER A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1126 removed outlier: 3.795A pdb=" N GLU A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1138 Processing helix chain 'A' and resid 1160 through 1178 removed outlier: 3.782A pdb=" N THR A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A1175 " --> pdb=" O SER A1171 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1203 removed outlier: 3.773A pdb=" N THR A1194 " --> pdb=" O ASP A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1215 removed outlier: 3.569A pdb=" N LEU A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1253 removed outlier: 3.865A pdb=" N GLU A1250 " --> pdb=" O PRO A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1284 removed outlier: 4.182A pdb=" N LYS A1276 " --> pdb=" O LYS A1272 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG A1277 " --> pdb=" O LYS A1273 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A1278 " --> pdb=" O ALA A1274 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A1283 " --> pdb=" O LYS A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1289 through 1293 removed outlier: 3.790A pdb=" N VAL A1293 " --> pdb=" O CYS A1289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1289 through 1293' Processing helix chain 'A' and resid 1323 through 1327 removed outlier: 3.569A pdb=" N TYR A1327 " --> pdb=" O HIS A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1345 removed outlier: 3.992A pdb=" N MET A1342 " --> pdb=" O ILE A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1346 through 1358 removed outlier: 3.604A pdb=" N LYS A1355 " --> pdb=" O MET A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1507 Processing helix chain 'A' and resid 1542 through 1548 Processing helix chain 'A' and resid 1584 through 1589 removed outlier: 3.913A pdb=" N LEU A1588 " --> pdb=" O ASN A1584 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1600 removed outlier: 3.888A pdb=" N LEU A1600 " --> pdb=" O LEU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1630 removed outlier: 4.181A pdb=" N VAL A1628 " --> pdb=" O GLU A1624 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1649 removed outlier: 3.773A pdb=" N LEU A1641 " --> pdb=" O ASP A1637 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A1643 " --> pdb=" O ARG A1639 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A1644 " --> pdb=" O HIS A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1675 removed outlier: 3.862A pdb=" N THR A1673 " --> pdb=" O LEU A1669 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A1675 " --> pdb=" O GLN A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1678 through 1687 removed outlier: 3.917A pdb=" N ALA A1684 " --> pdb=" O PHE A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1697 through 1701 removed outlier: 3.879A pdb=" N LEU A1700 " --> pdb=" O SER A1697 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 49 removed outlier: 3.867A pdb=" N SER B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 46 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.848A pdb=" N GLY B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 removed outlier: 3.674A pdb=" N CYS B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 removed outlier: 3.600A pdb=" N ILE B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.697A pdb=" N THR B 200 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.660A pdb=" N ALA B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 3.639A pdb=" N LEU B 268 " --> pdb=" O ILE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 292 removed outlier: 3.557A pdb=" N ASN B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 338 through 358 removed outlier: 3.804A pdb=" N PHE B 343 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 348 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 378 through 405 removed outlier: 3.645A pdb=" N PHE B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 437 removed outlier: 4.403A pdb=" N LEU B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 467 removed outlier: 3.605A pdb=" N TYR B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.697A pdb=" N ARG B 488 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 528 through 537 removed outlier: 4.649A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 637 through 641 removed outlier: 3.755A pdb=" N ILE B 640 " --> pdb=" O MET B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.538A pdb=" N PHE B 673 " --> pdb=" O VAL B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 689 Processing helix chain 'B' and resid 725 through 730 Processing helix chain 'B' and resid 761 through 767 Processing helix chain 'B' and resid 800 through 804 removed outlier: 3.503A pdb=" N VAL B 803 " --> pdb=" O ASP B 800 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU B 804 " --> pdb=" O PRO B 801 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 800 through 804' Processing helix chain 'B' and resid 898 through 902 Processing helix chain 'B' and resid 926 through 940 Processing helix chain 'B' and resid 961 through 969 Processing helix chain 'B' and resid 1038 through 1049 removed outlier: 3.511A pdb=" N ARG B1042 " --> pdb=" O GLY B1038 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP B1043 " --> pdb=" O GLU B1039 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B1044 " --> pdb=" O MET B1040 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1060 Processing helix chain 'B' and resid 1115 through 1124 Processing helix chain 'C' and resid 41 through 46 Processing helix chain 'C' and resid 69 through 83 removed outlier: 3.759A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 82 " --> pdb=" O ARG C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 removed outlier: 3.515A pdb=" N LEU C 112 " --> pdb=" O HIS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.578A pdb=" N LEU C 121 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.946A pdb=" N LEU C 184 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 185' Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.760A pdb=" N SER C 226 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.734A pdb=" N ARG C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS C 256 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 removed outlier: 3.533A pdb=" N ASP C 281 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 317 through 344 removed outlier: 3.518A pdb=" N VAL C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C 330 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 337 " --> pdb=" O CYS C 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.920A pdb=" N ILE E 17 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS E 22 " --> pdb=" O MET E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 25 No H-bonds generated for 'chain 'E' and resid 23 through 25' Processing helix chain 'E' and resid 29 through 33 Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'E' and resid 89 through 96 removed outlier: 3.622A pdb=" N ARG E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 120 removed outlier: 3.980A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 136 removed outlier: 4.152A pdb=" N LEU E 136 " --> pdb=" O GLN E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 133 through 136' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 removed outlier: 3.741A pdb=" N THR E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 72 removed outlier: 3.647A pdb=" N ALA F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 removed outlier: 3.538A pdb=" N ILE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU F 97 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS F 98 " --> pdb=" O MET F 94 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 41 removed outlier: 3.792A pdb=" N VAL G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 77 removed outlier: 3.759A pdb=" N ALA G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 53 removed outlier: 3.528A pdb=" N GLU I 51 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY I 52 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 27 removed outlier: 4.318A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 39 removed outlier: 3.518A pdb=" N LEU J 38 " --> pdb=" O LEU J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.654A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 60 removed outlier: 3.556A pdb=" N MET K 60 " --> pdb=" O ARG K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 116 removed outlier: 3.650A pdb=" N PHE K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS K 109 " --> pdb=" O ASN K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 126 removed outlier: 3.994A pdb=" N GLN K 124 " --> pdb=" O ASP K 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 57 Processing helix chain 'N' and resid 52 through 57 removed outlier: 4.007A pdb=" N PHE N 56 " --> pdb=" O PRO N 53 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN N 57 " --> pdb=" O GLU N 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 114 Processing helix chain 'O' and resid 127 through 139 removed outlier: 4.051A pdb=" N ALA O 139 " --> pdb=" O ASN O 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 143 Processing helix chain 'O' and resid 144 through 154 removed outlier: 3.597A pdb=" N LEU O 148 " --> pdb=" O LEU O 144 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER O 149 " --> pdb=" O ARG O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 197 removed outlier: 3.784A pdb=" N VAL O 197 " --> pdb=" O ILE O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 204 removed outlier: 4.343A pdb=" N TRP O 202 " --> pdb=" O PRO O 198 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 211 Processing helix chain 'O' and resid 218 through 236 removed outlier: 3.578A pdb=" N LEU O 222 " --> pdb=" O SER O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 239 through 257 removed outlier: 3.517A pdb=" N ILE O 243 " --> pdb=" O LEU O 239 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN O 257 " --> pdb=" O LYS O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 309 through 329 Processing helix chain 'O' and resid 342 through 355 Processing helix chain 'O' and resid 364 through 372 removed outlier: 4.283A pdb=" N MET O 368 " --> pdb=" O VAL O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 375 through 392 Processing helix chain 'O' and resid 396 through 413 Processing helix chain 'O' and resid 418 through 440 removed outlier: 3.727A pdb=" N VAL O 422 " --> pdb=" O PRO O 418 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN O 439 " --> pdb=" O ILE O 435 " (cutoff:3.500A) Processing helix chain 'O' and resid 454 through 470 Processing helix chain 'O' and resid 483 through 485 No H-bonds generated for 'chain 'O' and resid 483 through 485' Processing helix chain 'O' and resid 486 through 496 removed outlier: 3.606A pdb=" N MET O 496 " --> pdb=" O GLU O 492 " (cutoff:3.500A) Processing helix chain 'O' and resid 506 through 520 Processing helix chain 'O' and resid 554 through 559 removed outlier: 4.189A pdb=" N PHE O 559 " --> pdb=" O PRO O 555 " (cutoff:3.500A) Processing helix chain 'O' and resid 570 through 575 removed outlier: 3.614A pdb=" N ILE O 574 " --> pdb=" O SER O 570 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 19 removed outlier: 4.052A pdb=" N GLY A 14 " --> pdb=" O ASP B1133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 removed outlier: 6.641A pdb=" N LYS A 31 " --> pdb=" O HIS A 80 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLU A 82 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASP A 300 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N LEU A 85 " --> pdb=" O PHE A 298 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N PHE A 298 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 218 removed outlier: 3.599A pdb=" N LYS A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 436 through 437 removed outlier: 3.527A pdb=" N ILE B1035 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 440 through 447 removed outlier: 7.511A pdb=" N LEU A 575 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL A 444 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU A 577 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N CYS A 446 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 467 through 471 Processing sheet with id=AA7, first strand: chain 'A' and resid 647 through 648 Processing sheet with id=AA8, first strand: chain 'A' and resid 675 through 677 removed outlier: 6.506A pdb=" N VAL H 91 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE H 15 " --> pdb=" O ARG H 27 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG H 27 " --> pdb=" O ILE H 15 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 705 through 706 removed outlier: 6.274A pdb=" N ILE A 738 " --> pdb=" O LEU A 745 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1007 through 1008 removed outlier: 6.758A pdb=" N VAL A1007 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1577 through 1580 removed outlier: 3.725A pdb=" N MET A1264 " --> pdb=" O THR A1580 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1526 through 1527 removed outlier: 3.935A pdb=" N VAL A1527 " --> pdb=" O LEU A1317 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG A1318 " --> pdb=" O ILE A1297 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE A1297 " --> pdb=" O ARG A1318 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN A1320 " --> pdb=" O GLN A1295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1304 through 1305 Processing sheet with id=AB5, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.645A pdb=" N GLU A1714 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU A1715 " --> pdb=" O ILE G 105 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A1717 " --> pdb=" O GLY G 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 67 removed outlier: 3.721A pdb=" N VAL B 122 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 82 removed outlier: 6.728A pdb=" N ASP B 117 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALA B 80 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 115 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 82 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS B 113 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA B 116 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N PHE B 133 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE B 118 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LYS B 131 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AB9, first strand: chain 'B' and resid 372 through 375 removed outlier: 3.639A pdb=" N LEU B 182 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N MET B 181 " --> pdb=" O HIS B 473 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 191 through 194 removed outlier: 5.198A pdb=" N TYR B 208 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN B 223 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE B 239 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 519 through 520 removed outlier: 3.560A pdb=" N LYS B 630 " --> pdb=" O ASN B 625 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AC4, first strand: chain 'B' and resid 539 through 541 removed outlier: 6.887A pdb=" N VAL B 556 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TRP B 565 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR B 554 " --> pdb=" O TRP B 565 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU B 610 " --> pdb=" O CYS B 553 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU B 612 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU B 557 " --> pdb=" O LEU B 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 710 through 714 removed outlier: 3.629A pdb=" N LEU B 711 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS B 866 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL B 854 " --> pdb=" O CYS B 866 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS B 868 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE B 852 " --> pdb=" O CYS B 868 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR B 870 " --> pdb=" O ASP B 850 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 710 through 714 removed outlier: 3.629A pdb=" N LEU B 711 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS B 866 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL B 854 " --> pdb=" O CYS B 866 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS B 868 " --> pdb=" O ILE B 852 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ILE B 852 " --> pdb=" O CYS B 868 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR B 870 " --> pdb=" O ASP B 850 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE B 852 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 722 through 723 Processing sheet with id=AC8, first strand: chain 'B' and resid 976 through 977 removed outlier: 3.942A pdb=" N ALA B 884 " --> pdb=" O GLN B1000 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL B 759 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 896 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ILE B 913 " --> pdb=" O ASN B 740 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE B 742 " --> pdb=" O ILE B 913 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE B 915 " --> pdb=" O ILE B 742 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA B 744 " --> pdb=" O PHE B 915 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE B 993 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 792 through 794 Processing sheet with id=AD1, first strand: chain 'B' and resid 824 through 826 removed outlier: 6.933A pdb=" N MET B 839 " --> pdb=" O TYR B 825 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1064 through 1070 removed outlier: 3.664A pdb=" N SER B1065 " --> pdb=" O VAL B1112 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 53 through 57 removed outlier: 6.805A pdb=" N GLU C 62 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N MET C 56 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 63 " --> pdb=" O PHE C 308 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 306 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ARG C 301 " --> pdb=" O ILE C 239 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE C 239 " --> pdb=" O ARG C 301 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ARG C 303 " --> pdb=" O PRO C 237 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N HIS C 305 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU C 235 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 307 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR C 233 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER C 309 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA C 231 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU C 311 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 173 through 175 removed outlier: 3.724A pdb=" N PHE C 140 " --> pdb=" O MET C 212 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 209 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL C 215 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL C 89 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY C 217 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N MET C 87 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL L 53 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 147 through 148 removed outlier: 3.568A pdb=" N THR C 147 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 262 through 267 removed outlier: 3.780A pdb=" N LYS C 270 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 60 through 63 removed outlier: 3.558A pdb=" N VAL E 60 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA E 102 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N PHE E 130 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.836A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE E 194 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 52 through 54 Processing sheet with id=AE1, first strand: chain 'G' and resid 57 through 59 Processing sheet with id=AE2, first strand: chain 'G' and resid 135 through 138 removed outlier: 7.310A pdb=" N GLY G 144 " --> pdb=" O ASN G 136 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS G 193 " --> pdb=" O ASP G 185 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP G 185 " --> pdb=" O CYS G 193 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG G 195 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG G 183 " --> pdb=" O ARG G 195 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 35 through 37 Processing sheet with id=AE4, first strand: chain 'I' and resid 82 through 83 Processing sheet with id=AE5, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AE6, first strand: chain 'M' and resid 11 through 13 removed outlier: 5.984A pdb=" N GLN M 12 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ASP M 103 " --> pdb=" O GLN M 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL M 89 " --> pdb=" O TYR M 102 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N HIS M 87 " --> pdb=" O ALA M 104 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 24 through 25 removed outlier: 6.236A pdb=" N ALA M 23 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE M 107 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU M 25 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET M 109 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLN M 27 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL M 26 " --> pdb=" O THR N 93 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR N 93 " --> pdb=" O VAL M 26 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 66 through 67 removed outlier: 3.831A pdb=" N GLN N 67 " --> pdb=" O VAL N 82 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL N 82 " --> pdb=" O GLN N 67 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 2907 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.82 Time building geometry restraints manager: 13.82 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: 9822 1.33 - 1.45: 7273 1.45 - 1.58: 18971 1.58 - 1.70: 1 1.70 - 1.82: 380 Bond restraints: 36447 Sorted by residual: bond pdb=" C PRO N 22 " pdb=" N PRO N 23 " ideal model delta sigma weight residual 1.333 1.391 -0.058 7.80e-03 1.64e+04 5.59e+01 bond pdb=" CA PRO N 138 " pdb=" C PRO N 138 " ideal model delta sigma weight residual 1.517 1.541 -0.024 6.70e-03 2.23e+04 1.30e+01 bond pdb=" CB VAL B 566 " pdb=" CG2 VAL B 566 " ideal model delta sigma weight residual 1.521 1.409 0.112 3.30e-02 9.18e+02 1.15e+01 bond pdb=" C ILE A1026 " pdb=" N PRO A1027 " ideal model delta sigma weight residual 1.335 1.379 -0.044 1.30e-02 5.92e+03 1.14e+01 bond pdb=" C ASP O 575 " pdb=" N PRO O 576 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.30e-02 5.92e+03 1.05e+01 ... (remaining 36442 not shown) Histogram of bond angle deviations from ideal: 95.35 - 103.45: 579 103.45 - 111.56: 14996 111.56 - 119.67: 16095 119.67 - 127.77: 17264 127.77 - 135.88: 345 Bond angle restraints: 49279 Sorted by residual: angle pdb=" N THR A 464 " pdb=" CA THR A 464 " pdb=" C THR A 464 " ideal model delta sigma weight residual 114.31 101.99 12.32 1.29e+00 6.01e-01 9.13e+01 angle pdb=" N LEU A 935 " pdb=" CA LEU A 935 " pdb=" C LEU A 935 " ideal model delta sigma weight residual 108.22 101.63 6.59 9.00e-01 1.23e+00 5.36e+01 angle pdb=" N VAL A1254 " pdb=" CA VAL A1254 " pdb=" C VAL A1254 " ideal model delta sigma weight residual 112.96 107.45 5.51 1.00e+00 1.00e+00 3.04e+01 angle pdb=" C LYS B 69 " pdb=" N ASP B 70 " pdb=" CA ASP B 70 " ideal model delta sigma weight residual 121.54 131.62 -10.08 1.91e+00 2.74e-01 2.78e+01 angle pdb=" C LEU B 558 " pdb=" N ASP B 559 " pdb=" CA ASP B 559 " ideal model delta sigma weight residual 121.54 131.61 -10.07 1.91e+00 2.74e-01 2.78e+01 ... (remaining 49274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.63: 20567 15.63 - 31.26: 1284 31.26 - 46.88: 286 46.88 - 62.51: 23 62.51 - 78.14: 27 Dihedral angle restraints: 22187 sinusoidal: 9166 harmonic: 13021 Sorted by residual: dihedral pdb=" CA SER O 138 " pdb=" C SER O 138 " pdb=" N ALA O 139 " pdb=" CA ALA O 139 " ideal model delta harmonic sigma weight residual 180.00 135.19 44.81 0 5.00e+00 4.00e-02 8.03e+01 dihedral pdb=" CA HIS A 491 " pdb=" C HIS A 491 " pdb=" N PRO A 492 " pdb=" CA PRO A 492 " ideal model delta harmonic sigma weight residual 180.00 136.55 43.45 0 5.00e+00 4.00e-02 7.55e+01 dihedral pdb=" CA GLU I 77 " pdb=" C GLU I 77 " pdb=" N CYS I 78 " pdb=" CA CYS I 78 " ideal model delta harmonic sigma weight residual 180.00 -143.78 -36.22 0 5.00e+00 4.00e-02 5.25e+01 ... (remaining 22184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3663 0.060 - 0.120: 1416 0.120 - 0.181: 298 0.181 - 0.241: 54 0.241 - 0.301: 16 Chirality restraints: 5447 Sorted by residual: chirality pdb=" CB ILE A1338 " pdb=" CA ILE A1338 " pdb=" CG1 ILE A1338 " pdb=" CG2 ILE A1338 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CG LEU A1040 " pdb=" CB LEU A1040 " pdb=" CD1 LEU A1040 " pdb=" CD2 LEU A1040 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CB ILE G 112 " pdb=" CA ILE G 112 " pdb=" CG1 ILE G 112 " pdb=" CG2 ILE G 112 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 5444 not shown) Planarity restraints: 6375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 387 " 0.035 2.00e-02 2.50e+03 7.13e-02 5.08e+01 pdb=" C LEU A 387 " -0.123 2.00e-02 2.50e+03 pdb=" O LEU A 387 " 0.048 2.00e-02 2.50e+03 pdb=" N TYR A 388 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY N 154 " -0.030 2.00e-02 2.50e+03 5.81e-02 3.38e+01 pdb=" C GLY N 154 " 0.101 2.00e-02 2.50e+03 pdb=" O GLY N 154 " -0.037 2.00e-02 2.50e+03 pdb=" N ASN N 155 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 501 " 0.030 2.00e-02 2.50e+03 5.81e-02 3.38e+01 pdb=" C ASP A 501 " -0.101 2.00e-02 2.50e+03 pdb=" O ASP A 501 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY A 502 " 0.033 2.00e-02 2.50e+03 ... (remaining 6372 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7408 2.78 - 3.31: 31292 3.31 - 3.84: 57728 3.84 - 4.37: 68468 4.37 - 4.90: 118830 Nonbonded interactions: 283726 Sorted by model distance: nonbonded pdb=" OE1 GLU A 997 " pdb=" OG SER A1697 " model vdw 2.250 2.440 nonbonded pdb=" O ALA A 483 " pdb=" OG SER A 495 " model vdw 2.261 2.440 nonbonded pdb=" OE1 GLU A1021 " pdb=" OG SER E 197 " model vdw 2.271 2.440 nonbonded pdb=" OG SER I 15 " pdb=" O ASN M 30 " model vdw 2.273 2.440 nonbonded pdb=" OD1 ASP H 8 " pdb=" OG SER H 34 " model vdw 2.275 2.440 ... (remaining 283721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 1.420 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: 0.030 Extract box with map and model: 7.370 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 96.440 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 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 : 0.011 0.113 36447 Z= 0.706 Angle : 1.138 14.399 49279 Z= 0.604 Chirality : 0.066 0.301 5447 Planarity : 0.009 0.102 6375 Dihedral : 11.314 78.140 13773 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.00 % Favored : 91.96 % Rotamer: Outliers : 0.48 % Allowed : 3.86 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.14 % 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: -4.57 (0.10), residues: 4415 helix: -3.52 (0.09), residues: 1387 sheet: -2.62 (0.18), residues: 654 loop : -2.86 (0.10), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP A 846 HIS 0.026 0.004 HIS A 541 PHE 0.052 0.004 PHE B 883 TYR 0.067 0.004 TYR B 999 ARG 0.019 0.001 ARG A 972 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 738 time to evaluate : 3.791 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: A 954 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7173 (ptt90) REVERT: B 1091 MET cc_start: 0.5335 (mtp) cc_final: 0.4614 (ttm) REVERT: C 345 MET cc_start: 0.7180 (mpt) cc_final: 0.6833 (mmt) REVERT: F 52 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7335 (pp) REVERT: G 75 LEU cc_start: 0.9162 (mt) cc_final: 0.8925 (mp) REVERT: O 223 GLU cc_start: 0.0109 (tt0) cc_final: -0.0747 (tm-30) REVERT: O 251 LEU cc_start: 0.7691 (mt) cc_final: 0.7366 (tt) outliers start: 19 outliers final: 2 residues processed: 756 average time/residue: 0.5244 time to fit residues: 620.0970 Evaluate side-chains 391 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 387 time to evaluate : 4.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 370 optimal weight: 3.9990 chunk 332 optimal weight: 50.0000 chunk 184 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 344 optimal weight: 2.9990 chunk 133 optimal weight: 0.0030 chunk 209 optimal weight: 0.9990 chunk 256 optimal weight: 7.9990 chunk 398 optimal weight: 8.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 HIS A 108 HIS ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN A 180 HIS A 199 HIS A 264 HIS A 381 GLN A 476 ASN A 521 GLN A 581 ASN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS A 704 ASN ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 995 HIS A1036 GLN ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 HIS ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1118 GLN A1526 GLN ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 ASN A1584 ASN A1606 HIS A1610 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 263 GLN B 313 ASN ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN B 643 ASN B 679 HIS ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 740 ASN B 787 GLN B 846 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1060 ASN C 172 HIS ** C 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 142 HIS G 53 HIS ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN G 148 HIS G 152 ASN G 165 GLN H 44 ASN I 92 HIS I 117 ASN K 45 HIS K 108 GLN K 109 HIS L 26 ASN O 395 ASN ** O 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 440 GLN O 478 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36447 Z= 0.217 Angle : 0.696 15.692 49279 Z= 0.356 Chirality : 0.045 0.174 5447 Planarity : 0.006 0.072 6375 Dihedral : 6.137 47.408 4885 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.80 % Allowed : 9.99 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.11), residues: 4415 helix: -2.17 (0.12), residues: 1441 sheet: -2.15 (0.19), residues: 643 loop : -2.33 (0.11), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 846 HIS 0.011 0.001 HIS G 53 PHE 0.026 0.001 PHE A1319 TYR 0.027 0.002 TYR A1044 ARG 0.009 0.001 ARG N 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 426 time to evaluate : 4.310 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: A 308 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7365 (mtp-110) REVERT: A 954 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6827 (ptt90) REVERT: A 1540 MET cc_start: 0.6763 (mmm) cc_final: 0.6308 (mmm) REVERT: B 639 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7330 (pt0) REVERT: B 1091 MET cc_start: 0.5252 (mtp) cc_final: 0.4379 (ttm) REVERT: C 345 MET cc_start: 0.7106 (mpt) cc_final: 0.6767 (mmt) REVERT: F 52 ILE cc_start: 0.7577 (OUTLIER) cc_final: 0.7355 (pp) REVERT: F 56 TYR cc_start: 0.7651 (m-10) cc_final: 0.7352 (m-80) REVERT: O 251 LEU cc_start: 0.7625 (mt) cc_final: 0.7402 (tt) REVERT: O 496 MET cc_start: 0.5453 (tmm) cc_final: 0.5228 (tmm) REVERT: O 507 PRO cc_start: 0.7613 (Cg_exo) cc_final: 0.7353 (Cg_endo) REVERT: O 509 VAL cc_start: 0.8195 (t) cc_final: 0.7802 (p) outliers start: 71 outliers final: 31 residues processed: 476 average time/residue: 0.4808 time to fit residues: 372.1212 Evaluate side-chains 392 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 357 time to evaluate : 4.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1261 THR Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 639 GLN Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 103 ASP Chi-restraints excluded: chain O residue 154 HIS Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 407 ILE Chi-restraints excluded: chain O residue 475 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 221 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 331 optimal weight: 0.6980 chunk 271 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 399 optimal weight: 40.0000 chunk 431 optimal weight: 20.0000 chunk 355 optimal weight: 5.9990 chunk 396 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 320 optimal weight: 7.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN A 476 ASN A 595 ASN A 821 HIS ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 HIS ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1109 ASN A1368 ASN ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1690 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN B 322 GLN ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 GLN B 832 ASN ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN C 305 HIS E 129 GLN E 168 ASN G 53 HIS G 113 HIS G 115 ASN J 52 HIS L 26 ASN N 131 GLN ** O 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 490 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 36447 Z= 0.299 Angle : 0.670 12.636 49279 Z= 0.341 Chirality : 0.045 0.207 5447 Planarity : 0.005 0.068 6375 Dihedral : 5.668 45.272 4885 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.47 % Allowed : 11.56 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.12), residues: 4415 helix: -1.44 (0.13), residues: 1442 sheet: -1.80 (0.19), residues: 646 loop : -1.94 (0.12), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 40 HIS 0.011 0.001 HIS A 541 PHE 0.024 0.001 PHE G 120 TYR 0.027 0.002 TYR G 45 ARG 0.007 0.000 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 372 time to evaluate : 4.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 512 MET cc_start: 0.8252 (tpt) cc_final: 0.7093 (tpt) REVERT: A 954 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.6970 (ptt90) REVERT: A 1540 MET cc_start: 0.6729 (mmm) cc_final: 0.6460 (mmm) REVERT: B 1091 MET cc_start: 0.5357 (mtp) cc_final: 0.4379 (ttm) REVERT: C 345 MET cc_start: 0.7141 (mpt) cc_final: 0.6658 (mmt) REVERT: F 52 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7377 (pp) REVERT: I 29 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8514 (mt) REVERT: O 388 LYS cc_start: 0.8029 (pttt) cc_final: 0.7804 (pptt) REVERT: O 466 THR cc_start: 0.8589 (m) cc_final: 0.8325 (t) REVERT: O 507 PRO cc_start: 0.7619 (Cg_exo) cc_final: 0.7367 (Cg_endo) REVERT: O 509 VAL cc_start: 0.8243 (t) cc_final: 0.7843 (p) outliers start: 97 outliers final: 55 residues processed: 437 average time/residue: 0.4603 time to fit residues: 332.9383 Evaluate side-chains 400 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 342 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 99 MET Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain O residue 184 ASP Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 407 ILE Chi-restraints excluded: chain O residue 475 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 394 optimal weight: 7.9990 chunk 300 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 268 optimal weight: 0.4980 chunk 400 optimal weight: 50.0000 chunk 424 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 chunk 379 optimal weight: 8.9990 chunk 114 optimal weight: 9.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 ASN G 53 HIS ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 HIS ** O 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 36447 Z= 0.281 Angle : 0.643 12.571 49279 Z= 0.326 Chirality : 0.045 0.218 5447 Planarity : 0.004 0.063 6375 Dihedral : 5.392 45.238 4885 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.72 % Allowed : 12.33 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.12), residues: 4415 helix: -0.99 (0.14), residues: 1447 sheet: -1.63 (0.20), residues: 629 loop : -1.71 (0.12), residues: 2339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 40 HIS 0.012 0.001 HIS A 541 PHE 0.013 0.001 PHE C 140 TYR 0.029 0.002 TYR G 45 ARG 0.010 0.000 ARG G 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 360 time to evaluate : 4.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 954 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7021 (ptt90) REVERT: A 1540 MET cc_start: 0.6757 (mmm) cc_final: 0.6493 (mmm) REVERT: B 1091 MET cc_start: 0.5198 (mtp) cc_final: 0.4283 (ttm) REVERT: C 345 MET cc_start: 0.7159 (mpt) cc_final: 0.6626 (mmt) REVERT: E 27 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7911 (mm) REVERT: I 29 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8413 (mt) REVERT: M 99 MET cc_start: 0.7062 (tpp) cc_final: 0.6735 (tpp) REVERT: O 466 THR cc_start: 0.8532 (m) cc_final: 0.8235 (t) REVERT: O 507 PRO cc_start: 0.7644 (Cg_exo) cc_final: 0.7387 (Cg_endo) REVERT: O 509 VAL cc_start: 0.8256 (t) cc_final: 0.7864 (p) outliers start: 107 outliers final: 67 residues processed: 432 average time/residue: 0.4579 time to fit residues: 325.6190 Evaluate side-chains 399 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 329 time to evaluate : 3.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 TYR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1205 CYS Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 122 GLU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 56 ASP Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 184 ASP Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 238 THR Chi-restraints excluded: chain O residue 376 LEU Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 407 ILE Chi-restraints excluded: chain O residue 469 PHE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 553 THR Chi-restraints excluded: chain O residue 558 THR Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 353 optimal weight: 3.9990 chunk 240 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 315 optimal weight: 0.0870 chunk 175 optimal weight: 9.9990 chunk 362 optimal weight: 6.9990 chunk 293 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 216 optimal weight: 8.9990 chunk 380 optimal weight: 9.9990 chunk 107 optimal weight: 0.0970 overall best weight: 2.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 HIS ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN B 365 ASN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 ASN E 43 GLN G 53 HIS ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN ** N 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36447 Z= 0.193 Angle : 0.600 12.520 49279 Z= 0.302 Chirality : 0.043 0.177 5447 Planarity : 0.004 0.064 6375 Dihedral : 5.070 45.731 4883 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.31 % Allowed : 13.65 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.12), residues: 4415 helix: -0.64 (0.14), residues: 1435 sheet: -1.45 (0.19), residues: 657 loop : -1.55 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 40 HIS 0.011 0.001 HIS A 541 PHE 0.020 0.001 PHE G 120 TYR 0.022 0.001 TYR O 235 ARG 0.006 0.000 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 350 time to evaluate : 4.048 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 449 MET cc_start: 0.7268 (tmm) cc_final: 0.6976 (ttp) REVERT: A 915 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8052 (pp) REVERT: A 954 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6942 (ptt90) REVERT: A 1540 MET cc_start: 0.6734 (mmm) cc_final: 0.6504 (mmm) REVERT: B 1091 MET cc_start: 0.5047 (mtp) cc_final: 0.4187 (ttm) REVERT: C 345 MET cc_start: 0.7189 (mpt) cc_final: 0.6665 (mmt) REVERT: E 110 MET cc_start: 0.7448 (tpp) cc_final: 0.7183 (tpp) REVERT: G 132 MET cc_start: 0.2823 (mtt) cc_final: 0.2453 (mtp) REVERT: I 29 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8532 (mt) REVERT: O 466 THR cc_start: 0.8534 (m) cc_final: 0.8291 (t) REVERT: O 507 PRO cc_start: 0.7716 (Cg_exo) cc_final: 0.7486 (Cg_endo) outliers start: 91 outliers final: 58 residues processed: 407 average time/residue: 0.4701 time to fit residues: 320.2344 Evaluate side-chains 393 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 332 time to evaluate : 4.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 880 CYS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 94 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 140 GLN Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 184 ASP Chi-restraints excluded: chain O residue 200 THR Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 376 LEU Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 469 PHE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 142 optimal weight: 10.0000 chunk 382 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 424 optimal weight: 7.9990 chunk 352 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 HIS E 168 ASN G 53 HIS K 53 ASN ** M 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 36447 Z= 0.385 Angle : 0.688 10.782 49279 Z= 0.346 Chirality : 0.046 0.310 5447 Planarity : 0.004 0.063 6375 Dihedral : 5.216 44.234 4883 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.77 % Allowed : 14.13 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.13), residues: 4415 helix: -0.55 (0.14), residues: 1446 sheet: -1.29 (0.20), residues: 633 loop : -1.50 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 40 HIS 0.013 0.001 HIS A 541 PHE 0.016 0.002 PHE C 140 TYR 0.028 0.002 TYR G 45 ARG 0.007 0.001 ARG N 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 335 time to evaluate : 3.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6605 (p90) REVERT: A 449 MET cc_start: 0.7372 (tmm) cc_final: 0.7035 (ttp) REVERT: A 915 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8255 (pp) REVERT: A 954 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7576 (ptt90) REVERT: A 1540 MET cc_start: 0.6879 (mmm) cc_final: 0.6666 (mmm) REVERT: B 1091 MET cc_start: 0.4977 (mtp) cc_final: 0.4125 (ttm) REVERT: C 345 MET cc_start: 0.7313 (mpt) cc_final: 0.6999 (mmt) REVERT: E 27 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8005 (mm) REVERT: E 44 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: F 52 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7349 (pp) REVERT: G 40 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5453 (tt) REVERT: G 132 MET cc_start: 0.2916 (mtt) cc_final: 0.2617 (mtp) REVERT: I 29 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8430 (mt) REVERT: O 150 MET cc_start: 0.5703 (ppp) cc_final: 0.5257 (ppp) REVERT: O 375 LYS cc_start: 0.6578 (mmtt) cc_final: 0.6330 (mmtt) outliers start: 109 outliers final: 79 residues processed: 414 average time/residue: 0.4842 time to fit residues: 330.9886 Evaluate side-chains 402 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 315 time to evaluate : 4.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1068 HIS Chi-restraints excluded: chain A residue 1082 THR Chi-restraints excluded: chain A residue 1190 ASP Chi-restraints excluded: chain A residue 1205 CYS Chi-restraints excluded: chain A residue 1261 THR Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 93 ASN Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 140 GLN Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 154 HIS Chi-restraints excluded: chain O residue 184 ASP Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 372 CYS Chi-restraints excluded: chain O residue 376 LEU Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 409 optimal weight: 40.0000 chunk 47 optimal weight: 30.0000 chunk 242 optimal weight: 0.8980 chunk 310 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 423 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 HIS B1023 ASN G 53 HIS M 87 HIS ** O 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 36447 Z= 0.285 Angle : 0.640 11.611 49279 Z= 0.321 Chirality : 0.045 0.289 5447 Planarity : 0.004 0.061 6375 Dihedral : 5.094 46.478 4883 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.57 % Allowed : 15.04 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 4415 helix: -0.37 (0.14), residues: 1430 sheet: -1.23 (0.20), residues: 633 loop : -1.36 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 40 HIS 0.012 0.001 HIS A 541 PHE 0.021 0.001 PHE H 150 TYR 0.021 0.001 TYR O 235 ARG 0.006 0.000 ARG N 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 332 time to evaluate : 4.358 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 449 MET cc_start: 0.7341 (tmm) cc_final: 0.7022 (ttp) REVERT: A 915 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8156 (pp) REVERT: A 954 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7032 (ptt90) REVERT: B 1091 MET cc_start: 0.4948 (mtp) cc_final: 0.4095 (ttm) REVERT: C 345 MET cc_start: 0.7344 (mpt) cc_final: 0.7097 (mmt) REVERT: E 27 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7939 (mm) REVERT: E 44 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7483 (m-80) REVERT: F 52 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7342 (pp) REVERT: G 40 LEU cc_start: 0.5969 (OUTLIER) cc_final: 0.5391 (tp) REVERT: I 29 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8442 (mt) REVERT: O 150 MET cc_start: 0.5846 (ppp) cc_final: 0.5518 (ppp) outliers start: 101 outliers final: 72 residues processed: 403 average time/residue: 0.4682 time to fit residues: 313.0400 Evaluate side-chains 399 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 320 time to evaluate : 4.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1068 HIS Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 889 GLN Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1006 VAL Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 154 HIS Chi-restraints excluded: chain O residue 184 ASP Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 238 THR Chi-restraints excluded: chain O residue 359 HIS Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 372 CYS Chi-restraints excluded: chain O residue 376 LEU Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 469 PHE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 479 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 261 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 252 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 288 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 332 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 HIS N 78 HIS ** O 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 36447 Z= 0.292 Angle : 0.645 12.563 49279 Z= 0.323 Chirality : 0.045 0.260 5447 Planarity : 0.004 0.063 6375 Dihedral : 5.031 45.745 4883 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.64 % Allowed : 15.12 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 4415 helix: -0.27 (0.14), residues: 1427 sheet: -1.31 (0.20), residues: 620 loop : -1.30 (0.13), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 40 HIS 0.012 0.001 HIS A 541 PHE 0.023 0.001 PHE H 150 TYR 0.029 0.002 TYR G 45 ARG 0.006 0.000 ARG M 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 332 time to evaluate : 4.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.6512 (p90) REVERT: A 449 MET cc_start: 0.7321 (tmm) cc_final: 0.6997 (ttp) REVERT: A 954 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7046 (ptt90) REVERT: B 600 MET cc_start: 0.6842 (mtt) cc_final: 0.6512 (mtt) REVERT: B 1091 MET cc_start: 0.4916 (mtp) cc_final: 0.4070 (ttm) REVERT: E 27 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7930 (mm) REVERT: E 44 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: F 52 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7298 (pp) REVERT: G 40 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5354 (tp) REVERT: I 29 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8528 (mt) REVERT: O 150 MET cc_start: 0.5664 (ppp) cc_final: 0.5434 (ppp) outliers start: 104 outliers final: 83 residues processed: 408 average time/residue: 0.4756 time to fit residues: 319.6897 Evaluate side-chains 406 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 316 time to evaluate : 4.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1068 HIS Chi-restraints excluded: chain A residue 1205 CYS Chi-restraints excluded: chain A residue 1261 THR Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1534 MET Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 889 GLN Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 154 HIS Chi-restraints excluded: chain O residue 184 ASP Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 359 HIS Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 372 CYS Chi-restraints excluded: chain O residue 376 LEU Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 469 PHE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 479 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 384 optimal weight: 30.0000 chunk 405 optimal weight: 40.0000 chunk 369 optimal weight: 5.9990 chunk 394 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 309 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 356 optimal weight: 10.0000 chunk 372 optimal weight: 0.9990 chunk 392 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 HIS N 46 GLN ** O 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 36447 Z= 0.275 Angle : 0.642 13.348 49279 Z= 0.321 Chirality : 0.045 0.240 5447 Planarity : 0.004 0.062 6375 Dihedral : 4.981 45.456 4883 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.64 % Allowed : 15.30 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 4415 helix: -0.16 (0.14), residues: 1420 sheet: -1.20 (0.20), residues: 644 loop : -1.25 (0.13), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 40 HIS 0.012 0.001 HIS A 541 PHE 0.021 0.001 PHE H 150 TYR 0.023 0.001 TYR O 235 ARG 0.006 0.000 ARG N 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 329 time to evaluate : 4.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.7114 (OUTLIER) cc_final: 0.6488 (p90) REVERT: A 449 MET cc_start: 0.7352 (tmm) cc_final: 0.7051 (ttp) REVERT: A 915 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8260 (pp) REVERT: A 954 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7062 (ptt90) REVERT: B 600 MET cc_start: 0.6828 (mtt) cc_final: 0.6557 (mtt) REVERT: B 1091 MET cc_start: 0.4890 (mtp) cc_final: 0.4074 (ttm) REVERT: E 27 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7942 (mm) REVERT: E 44 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: E 94 MET cc_start: 0.6028 (ptt) cc_final: 0.5820 (ptt) REVERT: F 52 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7325 (pp) REVERT: G 40 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5376 (tp) REVERT: I 29 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8533 (mt) outliers start: 104 outliers final: 80 residues processed: 402 average time/residue: 0.4765 time to fit residues: 316.9643 Evaluate side-chains 409 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 321 time to evaluate : 4.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1052 HIS Chi-restraints excluded: chain A residue 1068 HIS Chi-restraints excluded: chain A residue 1205 CYS Chi-restraints excluded: chain A residue 1261 THR Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1534 MET Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 889 GLN Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1042 ARG Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain O residue 154 HIS Chi-restraints excluded: chain O residue 184 ASP Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 359 HIS Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 372 CYS Chi-restraints excluded: chain O residue 376 LEU Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 469 PHE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 479 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 258 optimal weight: 30.0000 chunk 416 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 289 optimal weight: 6.9990 chunk 437 optimal weight: 5.9990 chunk 402 optimal weight: 20.0000 chunk 348 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 213 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 36447 Z= 0.330 Angle : 0.678 13.901 49279 Z= 0.338 Chirality : 0.046 0.235 5447 Planarity : 0.004 0.068 6375 Dihedral : 5.038 42.405 4883 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.49 % Allowed : 15.30 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4415 helix: -0.15 (0.14), residues: 1421 sheet: -1.26 (0.20), residues: 626 loop : -1.26 (0.13), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 40 HIS 0.013 0.001 HIS A 541 PHE 0.021 0.001 PHE H 150 TYR 0.031 0.002 TYR G 45 ARG 0.006 0.000 ARG N 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8830 Ramachandran restraints generated. 4415 Oldfield, 0 Emsley, 4415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 324 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6588 (p90) REVERT: A 200 MET cc_start: 0.7764 (tpp) cc_final: 0.7509 (ttm) REVERT: A 449 MET cc_start: 0.7400 (tmm) cc_final: 0.7085 (ttp) REVERT: A 915 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8017 (pp) REVERT: A 954 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7638 (ptt90) REVERT: B 600 MET cc_start: 0.6902 (mtt) cc_final: 0.6642 (mtt) REVERT: B 1091 MET cc_start: 0.4916 (mtp) cc_final: 0.4127 (ttm) REVERT: E 27 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7978 (mm) REVERT: E 44 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: F 52 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7307 (pp) REVERT: G 40 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5843 (mt) REVERT: I 29 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8557 (mt) REVERT: M 99 MET cc_start: 0.7532 (tpp) cc_final: 0.7332 (tpp) REVERT: O 370 TYR cc_start: 0.3810 (OUTLIER) cc_final: 0.3078 (t80) REVERT: O 371 LEU cc_start: 0.6966 (tp) cc_final: 0.6765 (tt) outliers start: 98 outliers final: 82 residues processed: 395 average time/residue: 0.4656 time to fit residues: 305.5774 Evaluate side-chains 406 residues out of total 3935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 315 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 478 GLN Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 786 THR Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 1068 HIS Chi-restraints excluded: chain A residue 1205 CYS Chi-restraints excluded: chain A residue 1261 THR Chi-restraints excluded: chain A residue 1264 MET Chi-restraints excluded: chain A residue 1338 ILE Chi-restraints excluded: chain A residue 1534 MET Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1700 LEU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 889 GLN Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1010 PHE Chi-restraints excluded: chain B residue 1021 VAL Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1077 LEU Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 99 THR Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain M residue 6 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 18 PHE Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain O residue 154 HIS Chi-restraints excluded: chain O residue 184 ASP Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 359 HIS Chi-restraints excluded: chain O residue 362 CYS Chi-restraints excluded: chain O residue 370 TYR Chi-restraints excluded: chain O residue 372 CYS Chi-restraints excluded: chain O residue 376 LEU Chi-restraints excluded: chain O residue 398 ILE Chi-restraints excluded: chain O residue 469 PHE Chi-restraints excluded: chain O residue 475 LEU Chi-restraints excluded: chain O residue 567 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 276 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 321 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 358 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 0.2980 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 GLN ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.084595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.061293 restraints weight = 130393.850| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.84 r_work: 0.3160 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 36447 Z= 0.319 Angle : 0.669 12.946 49279 Z= 0.334 Chirality : 0.046 0.225 5447 Planarity : 0.004 0.064 6375 Dihedral : 5.024 39.853 4883 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.54 % Allowed : 15.37 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.40 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4415 helix: -0.05 (0.14), residues: 1413 sheet: -1.21 (0.20), residues: 624 loop : -1.21 (0.13), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 40 HIS 0.013 0.001 HIS A 541 PHE 0.020 0.001 PHE H 150 TYR 0.025 0.002 TYR G 45 ARG 0.006 0.000 ARG B1013 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9076.11 seconds wall clock time: 163 minutes 51.38 seconds (9831.38 seconds total)