Starting phenix.real_space_refine on Mon Mar 18 20:17:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/03_2024/7kro_23008_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/03_2024/7kro_23008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/03_2024/7kro_23008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/03_2024/7kro_23008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/03_2024/7kro_23008_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kro_23008/03_2024/7kro_23008_updated.pdb" } resolution = 3.6 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= 0.004 sd= 0.091 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 86 5.49 5 Mg 3 5.21 5 S 151 5.16 5 C 13642 2.51 5 N 3707 2.21 5 O 4383 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 337": "NH1" <-> "NH2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E ARG 443": "NH1" <-> "NH2" Residue "E TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 337": "NH1" <-> "NH2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F ARG 443": "NH1" <-> "NH2" Residue "F TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21988 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PTRANS': 30, 'TRANS': 896} Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1424 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1427 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 4602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4602 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 29, 'TRANS': 560} Chain: "F" Number of atoms: 4602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4602 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 29, 'TRANS': 560} Chain: "P" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 776 Classifications: {'RNA': 37} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 21} Link IDs: {'rna3p': 36} Chain: "T" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 914 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 21, 'rna3p_pyr': 18} Link IDs: {'rna2p': 4, 'rna3p': 38} Chain breaks: 1 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 73.888 58.971 122.812 1.00 38.24 S ATOM 2495 SG CYS A 306 74.634 60.042 126.547 1.00 31.54 S ATOM 2527 SG CYS A 310 75.110 56.427 125.385 1.00 44.33 S ATOM 3935 SG CYS A 487 76.891 72.859 108.537 1.00 38.63 S ATOM 5188 SG CYS A 645 77.165 75.182 111.520 1.00 45.39 S ATOM 5194 SG CYS A 646 75.483 71.788 112.024 1.00 43.78 S ATOM 10924 SG CYS E 5 116.902 64.767 51.873 1.00 53.22 S ATOM 10945 SG CYS E 8 120.444 64.603 52.931 1.00 57.87 S ATOM 11083 SG CYS E 26 119.149 68.046 52.383 1.00 57.27 S ATOM 11104 SG CYS E 29 119.574 66.254 49.466 1.00 62.73 S ATOM 11269 SG CYS E 50 101.114 86.502 49.723 1.00 97.32 S ATOM 11299 SG CYS E 55 99.863 86.541 46.164 1.00111.12 S ATOM 11432 SG CYS E 72 102.870 88.588 47.064 1.00106.78 S ATOM 11006 SG CYS E 16 109.047 68.612 45.257 1.00 52.87 S ATOM 11021 SG CYS E 19 108.372 64.927 44.093 1.00 62.83 S ATOM 15526 SG CYS F 5 66.643 74.883 62.030 1.00 81.43 S ATOM 15547 SG CYS F 8 68.614 74.900 58.897 1.00 81.50 S ATOM 15685 SG CYS F 26 68.910 78.000 60.930 1.00 83.74 S ATOM 15706 SG CYS F 29 65.837 77.641 59.405 1.00 92.86 S ATOM 15871 SG CYS F 50 67.340 92.652 82.281 1.00125.84 S ATOM 15901 SG CYS F 55 63.809 93.919 82.685 1.00143.39 S ATOM 16034 SG CYS F 72 66.234 95.897 80.623 1.00127.64 S ATOM 15608 SG CYS F 16 59.677 79.704 68.992 1.00 68.26 S ATOM 15623 SG CYS F 19 57.173 76.750 68.365 1.00 86.69 S Time building chain proxies: 12.11, per 1000 atoms: 0.55 Number of scatterers: 21988 At special positions: 0 Unit cell: (143.775, 160.815, 184.245, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 151 16.00 P 86 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4383 8.00 N 3707 7.00 C 13642 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: 9.02 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 26 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 95 helices and 22 sheets defined 37.9% alpha, 10.4% beta 33 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 9.88 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 removed outlier: 4.052A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 169 through 197 removed outlier: 3.888A pdb=" N ALA A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS A 193 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 240 through 247 Proline residue: A 243 - end of helix removed outlier: 3.904A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 247 " --> pdb=" O ILE A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 247' Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.529A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.679A pdb=" N TYR A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 removed outlier: 5.061A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 504 through 507 No H-bonds generated for 'chain 'A' and resid 504 through 507' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.895A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 581 removed outlier: 4.310A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 628 through 639 removed outlier: 3.616A pdb=" N ALA A 639 " --> pdb=" O SER A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 688 through 708 Processing helix chain 'A' and resid 718 through 732 removed outlier: 3.863A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 789 Processing helix chain 'A' and resid 796 through 798 No H-bonds generated for 'chain 'A' and resid 796 through 798' Processing helix chain 'A' and resid 836 through 842 Processing helix chain 'A' and resid 847 through 851 removed outlier: 3.532A pdb=" N ASP A 851 " --> pdb=" O VAL A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 871 Proline residue: A 868 - end of helix removed outlier: 4.885A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.306A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.595A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 32 through 96 removed outlier: 3.610A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.768A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.746A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.574A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 60 removed outlier: 3.854A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 74 removed outlier: 3.657A pdb=" N GLU C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU C 74 " --> pdb=" O LYS C 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 32 through 81 removed outlier: 4.373A pdb=" N LYS D 37 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 98 removed outlier: 4.344A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 128 through 148 Processing helix chain 'E' and resid 263 through 274 removed outlier: 4.675A pdb=" N ALA E 267 " --> pdb=" O SER E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 Processing helix chain 'E' and resid 312 through 324 Processing helix chain 'E' and resid 327 through 329 No H-bonds generated for 'chain 'E' and resid 327 through 329' Processing helix chain 'E' and resid 376 through 378 No H-bonds generated for 'chain 'E' and resid 376 through 378' Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 424 through 432 Processing helix chain 'E' and resid 446 through 454 Processing helix chain 'E' and resid 490 through 499 Processing helix chain 'E' and resid 504 through 508 removed outlier: 4.048A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 525 removed outlier: 3.658A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 567 removed outlier: 4.326A pdb=" N ARG E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 584 Processing helix chain 'F' and resid 27 through 34 Processing helix chain 'F' and resid 60 through 62 No H-bonds generated for 'chain 'F' and resid 60 through 62' Processing helix chain 'F' and resid 94 through 96 No H-bonds generated for 'chain 'F' and resid 94 through 96' Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 117 through 122 Processing helix chain 'F' and resid 128 through 148 Processing helix chain 'F' and resid 263 through 274 removed outlier: 4.676A pdb=" N ALA F 267 " --> pdb=" O SER F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 298 Processing helix chain 'F' and resid 312 through 324 Processing helix chain 'F' and resid 327 through 329 No H-bonds generated for 'chain 'F' and resid 327 through 329' Processing helix chain 'F' and resid 376 through 378 No H-bonds generated for 'chain 'F' and resid 376 through 378' Processing helix chain 'F' and resid 381 through 390 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 432 Processing helix chain 'F' and resid 446 through 454 Processing helix chain 'F' and resid 490 through 499 Processing helix chain 'F' and resid 504 through 508 removed outlier: 4.049A pdb=" N LYS F 508 " --> pdb=" O ALA F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 525 removed outlier: 3.658A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 567 removed outlier: 4.326A pdb=" N ARG F 567 " --> pdb=" O VAL F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 584 Processing sheet with id= A, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.036A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 33 Processing sheet with id= C, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= D, first strand: chain 'A' and resid 99 through 105 Processing sheet with id= E, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.644A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= G, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= H, first strand: chain 'A' and resid 556 through 560 removed outlier: 6.469A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= J, first strand: chain 'A' and resid 815 through 822 Processing sheet with id= K, first strand: chain 'B' and resid 127 through 132 removed outlier: 3.510A pdb=" N ILE B 132 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.452A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= N, first strand: chain 'E' and resid 224 through 227 removed outlier: 4.338A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 277 through 280 removed outlier: 6.562A pdb=" N TYR E 396 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU E 280 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR E 398 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASP E 374 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR E 307 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N THR E 359 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 471 through 474 removed outlier: 6.598A pdb=" N ILE E 572 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N MET E 474 " --> pdb=" O ILE E 572 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N CYS E 574 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 152 through 157 removed outlier: 7.341A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 64 through 66 Processing sheet with id= S, first strand: chain 'F' and resid 224 through 227 removed outlier: 4.337A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.561A pdb=" N TYR F 396 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU F 280 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR F 398 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP F 374 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR F 307 " --> pdb=" O ASP F 374 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR F 359 " --> pdb=" O ILE F 333 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 471 through 474 removed outlier: 6.598A pdb=" N ILE F 572 " --> pdb=" O PHE F 472 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N MET F 474 " --> pdb=" O ILE F 572 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS F 574 " --> pdb=" O MET F 474 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL F 510 " --> pdb=" O ILE F 545 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR F 547 " --> pdb=" O VAL F 510 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 152 through 157 removed outlier: 7.342A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 7.80 Time building geometry restraints manager: 9.71 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: 5398 1.33 - 1.45: 4823 1.45 - 1.57: 11962 1.57 - 1.69: 219 1.69 - 1.81: 220 Bond restraints: 22622 Sorted by residual: bond pdb=" F3 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F3 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.62e+01 bond pdb=" F1 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" F1 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" F2 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.48e+01 ... (remaining 22617 not shown) Histogram of bond angle deviations from ideal: 97.63 - 105.26: 761 105.26 - 112.89: 12455 112.89 - 120.52: 9886 120.52 - 128.14: 7777 128.14 - 135.77: 243 Bond angle restraints: 31122 Sorted by residual: angle pdb=" N ILE A 856 " pdb=" CA ILE A 856 " pdb=" C ILE A 856 " ideal model delta sigma weight residual 112.96 105.97 6.99 1.00e+00 1.00e+00 4.89e+01 angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 129.64 -8.10 1.91e+00 2.74e-01 1.80e+01 angle pdb=" O3' C P 25 " pdb=" C3' C P 25 " pdb=" C2' C P 25 " ideal model delta sigma weight residual 113.70 119.77 -6.07 1.50e+00 4.44e-01 1.64e+01 angle pdb=" N TRP D 182 " pdb=" CA TRP D 182 " pdb=" C TRP D 182 " ideal model delta sigma weight residual 109.81 118.59 -8.78 2.21e+00 2.05e-01 1.58e+01 angle pdb=" C PHE F 499 " pdb=" N LEU F 500 " pdb=" CA LEU F 500 " ideal model delta sigma weight residual 121.54 129.13 -7.59 1.91e+00 2.74e-01 1.58e+01 ... (remaining 31117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 13237 33.68 - 67.37: 498 67.37 - 101.05: 64 101.05 - 134.74: 18 134.74 - 168.42: 2 Dihedral angle restraints: 13819 sinusoidal: 6260 harmonic: 7559 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual -180.00 -107.57 -72.43 0 5.00e+00 4.00e-02 2.10e+02 dihedral pdb=" CA PRO E 514 " pdb=" C PRO E 514 " pdb=" N TYR E 515 " pdb=" CA TYR E 515 " ideal model delta harmonic sigma weight residual 180.00 134.35 45.65 0 5.00e+00 4.00e-02 8.34e+01 dihedral pdb=" CA PRO F 514 " pdb=" C PRO F 514 " pdb=" N TYR F 515 " pdb=" CA TYR F 515 " ideal model delta harmonic sigma weight residual 180.00 134.37 45.63 0 5.00e+00 4.00e-02 8.33e+01 ... (remaining 13816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.029: 3614 1.029 - 2.059: 0 2.059 - 3.088: 0 3.088 - 4.118: 0 4.118 - 5.147: 2 Chirality restraints: 3616 Sorted by residual: chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.72 -5.15 2.00e-01 2.50e+01 6.62e+02 chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.54 5.07 2.00e-01 2.50e+01 6.43e+02 chirality pdb=" C15 1N7 A1005 " pdb=" C14 1N7 A1005 " pdb=" C16 1N7 A1005 " pdb=" C2 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.47 -2.88 0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 3613 not shown) Planarity restraints: 3649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO B 183 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " -0.040 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO A 927 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 93 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO A 94 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.028 5.00e-02 4.00e+02 ... (remaining 3646 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 39 2.27 - 2.93: 9654 2.93 - 3.59: 32445 3.59 - 4.24: 51821 4.24 - 4.90: 84732 Nonbonded interactions: 178691 Sorted by model distance: nonbonded pdb="MG MG A1003 " pdb=" O2A ADP A1004 " model vdw 1.614 2.170 nonbonded pdb=" O1B ADP A1004 " pdb=" O2A ADP A1004 " model vdw 1.807 3.040 nonbonded pdb=" O3B ADP F1003 " pdb="MG MG F1004 " model vdw 1.841 2.170 nonbonded pdb=" O3B ADP E 704 " pdb="MG MG E 705 " model vdw 1.841 2.170 nonbonded pdb=" OD2 ASP A 218 " pdb=" O2A ADP A1004 " model vdw 1.845 3.040 ... (remaining 178686 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 7 through 191) selection = (chain 'D' and (resid 7 through 19 or (resid 20 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 23 or (resid 24 through \ 25 and (name N or name CA or name C or name O or name CB )) or resid 26 through \ 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 590 or resid 701 through 706)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.020 Extract box with map and model: 8.090 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 68.870 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.009 0.164 22622 Z= 0.538 Angle : 0.782 11.165 31122 Z= 0.408 Chirality : 0.131 5.147 3616 Planarity : 0.005 0.104 3649 Dihedral : 17.609 168.423 8945 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.93 % Favored : 92.76 % Rotamer: Outliers : 9.40 % Allowed : 10.39 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.20 % 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: -1.73 (0.16), residues: 2541 helix: -0.55 (0.16), residues: 1012 sheet: -1.05 (0.29), residues: 331 loop : -1.64 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 182 HIS 0.008 0.001 HIS F 290 PHE 0.021 0.002 PHE A 920 TYR 0.023 0.002 TYR A 748 ARG 0.005 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 311 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8432 (tp-100) cc_final: 0.7982 (tp40) REVERT: A 105 ARG cc_start: 0.7475 (tpp80) cc_final: 0.7176 (tpp-160) REVERT: A 131 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8193 (tt) REVERT: A 231 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8693 (p) REVERT: A 280 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8218 (mt) REVERT: A 349 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7746 (ttm-80) REVERT: A 542 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7719 (mtt) REVERT: A 610 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.7039 (mm-30) REVERT: A 633 MET cc_start: 0.8363 (tmm) cc_final: 0.7874 (tmm) REVERT: A 658 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6517 (mt-10) REVERT: A 682 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8238 (t) REVERT: A 807 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7566 (tptp) REVERT: A 855 MET cc_start: 0.7330 (mmt) cc_final: 0.7098 (mmt) REVERT: A 911 ASN cc_start: 0.8238 (t0) cc_final: 0.7862 (t0) REVERT: B 39 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8201 (tppt) REVERT: B 50 ASP cc_start: 0.8418 (t0) cc_final: 0.8092 (t70) REVERT: B 60 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6784 (tm-30) REVERT: B 69 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8500 (tm-30) REVERT: B 78 ASP cc_start: 0.7697 (t0) cc_final: 0.7467 (t0) REVERT: B 127 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8160 (mtpt) REVERT: D 97 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8222 (ttpt) REVERT: E 62 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7391 (pp30) REVERT: E 122 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8014 (tt) REVERT: E 168 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: E 187 VAL cc_start: 0.7168 (OUTLIER) cc_final: 0.6935 (p) REVERT: E 194 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: E 261 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: E 319 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7617 (tt0) REVERT: E 327 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7782 (mp) REVERT: E 347 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7796 (ptmm) REVERT: E 350 SER cc_start: 0.7166 (t) cc_final: 0.6821 (t) REVERT: E 465 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.5300 (mptt) REVERT: E 471 CYS cc_start: 0.6925 (m) cc_final: 0.5995 (m) REVERT: E 493 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7786 (tt) REVERT: E 526 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8679 (pp) REVERT: E 543 TYR cc_start: 0.7075 (m-80) cc_final: 0.6593 (m-80) REVERT: F 62 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6584 (pp30) REVERT: F 161 ARG cc_start: 0.5478 (ttp-110) cc_final: 0.4626 (mmm160) REVERT: F 211 TYR cc_start: 0.1296 (p90) cc_final: 0.0823 (p90) REVERT: F 227 LEU cc_start: 0.0908 (OUTLIER) cc_final: 0.0554 (tt) REVERT: F 261 GLU cc_start: 0.3738 (OUTLIER) cc_final: 0.3518 (pm20) REVERT: F 378 MET cc_start: 0.7691 (mmm) cc_final: 0.7262 (mmm) REVERT: F 426 CYS cc_start: 0.7415 (m) cc_final: 0.6795 (t) REVERT: F 447 GLU cc_start: 0.5173 (OUTLIER) cc_final: 0.4757 (tp30) REVERT: F 467 LYS cc_start: 0.5400 (mttt) cc_final: 0.4542 (tptt) REVERT: F 562 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.6629 (t0) outliers start: 209 outliers final: 74 residues processed: 507 average time/residue: 0.3317 time to fit residues: 259.2120 Evaluate side-chains 304 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 202 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 672 SER Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 722 ASN A 724 GLN D 65 GLN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN D 179 ASN E 548 GLN F 194 GLN F 265 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22622 Z= 0.209 Angle : 0.592 9.296 31122 Z= 0.295 Chirality : 0.041 0.311 3616 Planarity : 0.004 0.089 3649 Dihedral : 16.111 169.442 4468 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.63 % Favored : 94.06 % Rotamer: Outliers : 6.52 % Allowed : 15.43 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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 (0.16), residues: 2541 helix: 0.03 (0.17), residues: 1006 sheet: -0.97 (0.29), residues: 326 loop : -1.55 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 182 HIS 0.004 0.001 HIS E 290 PHE 0.028 0.001 PHE E 475 TYR 0.021 0.001 TYR F 324 ARG 0.009 0.000 ARG F 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 230 time to evaluate : 2.407 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 5 GLN cc_start: 0.8513 (tp-100) cc_final: 0.8066 (tp40) REVERT: A 105 ARG cc_start: 0.7852 (tpp80) cc_final: 0.7054 (tpp-160) REVERT: A 131 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8054 (tt) REVERT: A 154 ASP cc_start: 0.8247 (t0) cc_final: 0.7930 (t0) REVERT: A 231 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8785 (p) REVERT: A 247 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8604 (tp) REVERT: A 261 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7876 (tt) REVERT: A 610 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7186 (mm-30) REVERT: A 613 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7824 (m-70) REVERT: A 633 MET cc_start: 0.8321 (tmm) cc_final: 0.7827 (tmm) REVERT: A 666 MET cc_start: 0.8270 (mmm) cc_final: 0.8001 (mmm) REVERT: A 724 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: A 750 ARG cc_start: 0.8110 (mmm-85) cc_final: 0.7442 (mtp85) REVERT: A 807 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7414 (tptp) REVERT: A 855 MET cc_start: 0.7283 (mmt) cc_final: 0.7073 (mmt) REVERT: A 911 ASN cc_start: 0.8224 (t0) cc_final: 0.7866 (t0) REVERT: A 928 HIS cc_start: 0.7755 (t70) cc_final: 0.7554 (t-90) REVERT: B 39 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8527 (tptt) REVERT: B 60 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6759 (tm-30) REVERT: B 69 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8466 (tm-30) REVERT: B 78 ASP cc_start: 0.7417 (t0) cc_final: 0.7118 (t0) REVERT: B 127 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8080 (mtpt) REVERT: D 43 ASN cc_start: 0.8627 (m-40) cc_final: 0.8354 (t0) REVERT: E 62 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7530 (pp30) REVERT: E 235 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8457 (pp) REVERT: E 319 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7609 (tt0) REVERT: E 327 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7918 (mp) REVERT: E 465 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.5285 (mptt) REVERT: E 493 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7747 (tt) REVERT: E 526 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8725 (pp) REVERT: E 543 TYR cc_start: 0.7246 (m-80) cc_final: 0.6628 (m-80) REVERT: F 62 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.6483 (pp30) REVERT: F 161 ARG cc_start: 0.5407 (ttp-110) cc_final: 0.4551 (mmm160) REVERT: F 211 TYR cc_start: 0.1417 (p90) cc_final: 0.0760 (p90) REVERT: F 329 LYS cc_start: 0.3582 (OUTLIER) cc_final: 0.2586 (mttt) REVERT: F 534 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.5865 (t70) REVERT: F 562 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6373 (t0) outliers start: 145 outliers final: 84 residues processed: 360 average time/residue: 0.3256 time to fit residues: 183.5727 Evaluate side-chains 296 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 191 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 539 SER Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 431 THR Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 160 optimal weight: 0.0170 chunk 65 optimal weight: 0.7980 chunk 236 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 210 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN E 46 ASN ** E 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22622 Z= 0.221 Angle : 0.563 9.121 31122 Z= 0.283 Chirality : 0.040 0.227 3616 Planarity : 0.004 0.087 3649 Dihedral : 15.156 165.271 4405 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.06 % Favored : 93.62 % Rotamer: Outliers : 6.03 % Allowed : 17.54 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -1.15 (0.17), residues: 2541 helix: 0.15 (0.17), residues: 1015 sheet: -0.95 (0.28), residues: 334 loop : -1.48 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 182 HIS 0.006 0.001 HIS E 290 PHE 0.016 0.001 PHE A 652 TYR 0.019 0.001 TYR F 324 ARG 0.007 0.000 ARG F 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 205 time to evaluate : 2.549 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: A 5 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8096 (tp40) REVERT: A 131 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8082 (tt) REVERT: A 154 ASP cc_start: 0.8303 (t0) cc_final: 0.7914 (t0) REVERT: A 231 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8755 (p) REVERT: A 247 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8606 (tp) REVERT: A 261 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7850 (tt) REVERT: A 610 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7211 (mm-30) REVERT: A 613 HIS cc_start: 0.8119 (OUTLIER) cc_final: 0.7827 (m170) REVERT: A 623 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8421 (p0) REVERT: A 633 MET cc_start: 0.8296 (tmm) cc_final: 0.7788 (tmm) REVERT: A 750 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7481 (mtp85) REVERT: A 911 ASN cc_start: 0.8240 (t0) cc_final: 0.7824 (t0) REVERT: B 39 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8577 (tppt) REVERT: B 60 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6734 (tm-30) REVERT: B 78 ASP cc_start: 0.7416 (t0) cc_final: 0.7150 (t0) REVERT: B 127 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8017 (mtpt) REVERT: C 73 GLU cc_start: 0.7726 (tp30) cc_final: 0.7417 (tp30) REVERT: D 43 ASN cc_start: 0.8619 (m-40) cc_final: 0.7873 (t0) REVERT: E 62 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7382 (pp30) REVERT: E 194 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7218 (mm-40) REVERT: E 235 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8531 (pp) REVERT: E 319 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7612 (tt0) REVERT: E 327 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7820 (mp) REVERT: E 493 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7698 (tt) REVERT: E 526 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8784 (pp) REVERT: E 532 THR cc_start: 0.7599 (OUTLIER) cc_final: 0.7363 (t) REVERT: E 543 TYR cc_start: 0.7263 (m-80) cc_final: 0.6614 (m-80) REVERT: F 62 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.6607 (pp30) REVERT: F 161 ARG cc_start: 0.5397 (ttp-110) cc_final: 0.4532 (mmm160) REVERT: F 211 TYR cc_start: 0.1052 (p90) cc_final: 0.0566 (p90) REVERT: F 274 MET cc_start: 0.6849 (mmt) cc_final: 0.6402 (mmp) REVERT: F 311 HIS cc_start: 0.6751 (OUTLIER) cc_final: 0.6090 (t-90) REVERT: F 329 LYS cc_start: 0.3921 (OUTLIER) cc_final: 0.3093 (mttt) REVERT: F 534 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6331 (t70) REVERT: F 562 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.6471 (t0) outliers start: 134 outliers final: 89 residues processed: 325 average time/residue: 0.3200 time to fit residues: 164.7454 Evaluate side-chains 304 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 193 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 539 SER Chi-restraints excluded: chain E residue 542 ASP Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 456 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 251 optimal weight: 30.0000 chunk 124 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN B 179 ASN ** D 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN D 179 ASN ** E 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 548 GLN F 265 ASN F 531 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.092 22622 Z= 0.626 Angle : 0.777 9.580 31122 Z= 0.397 Chirality : 0.049 0.240 3616 Planarity : 0.005 0.103 3649 Dihedral : 15.234 146.091 4386 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.01 % Favored : 90.67 % Rotamer: Outliers : 8.23 % Allowed : 17.59 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.20 % 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: -1.68 (0.16), residues: 2541 helix: -0.29 (0.16), residues: 1016 sheet: -1.19 (0.28), residues: 341 loop : -1.80 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 182 HIS 0.011 0.001 HIS E 290 PHE 0.027 0.003 PHE A 348 TYR 0.029 0.002 TYR A 748 ARG 0.005 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 188 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8300 (tp40) REVERT: A 131 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8349 (tt) REVERT: A 154 ASP cc_start: 0.8605 (t0) cc_final: 0.8324 (t0) REVERT: A 261 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7906 (tt) REVERT: A 570 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8605 (mt0) REVERT: A 610 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7138 (mm-30) REVERT: A 633 MET cc_start: 0.8483 (tmm) cc_final: 0.7932 (tmm) REVERT: A 791 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.8049 (m110) REVERT: A 911 ASN cc_start: 0.8248 (t0) cc_final: 0.7870 (t0) REVERT: B 39 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8493 (tppt) REVERT: B 60 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: B 62 MET cc_start: 0.8018 (tmm) cc_final: 0.7802 (ttp) REVERT: B 78 ASP cc_start: 0.7558 (t0) cc_final: 0.7253 (t0) REVERT: C 73 GLU cc_start: 0.7871 (tp30) cc_final: 0.7592 (tp30) REVERT: D 43 ASN cc_start: 0.8766 (m-40) cc_final: 0.7975 (t0) REVERT: E 122 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8054 (tp) REVERT: E 194 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7386 (mm-40) REVERT: E 235 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8790 (pp) REVERT: E 347 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7811 (ptmm) REVERT: E 473 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8457 (pttt) REVERT: E 532 THR cc_start: 0.7503 (OUTLIER) cc_final: 0.7249 (t) REVERT: E 543 TYR cc_start: 0.7381 (m-80) cc_final: 0.6413 (m-80) REVERT: E 576 MET cc_start: 0.7897 (mmp) cc_final: 0.7681 (mmp) REVERT: F 62 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.6890 (pp30) REVERT: F 68 MET cc_start: 0.8096 (pmm) cc_final: 0.7521 (mtp) REVERT: F 161 ARG cc_start: 0.5188 (ttp-110) cc_final: 0.4440 (mmm160) REVERT: F 211 TYR cc_start: 0.1195 (p90) cc_final: 0.0770 (p90) REVERT: F 311 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.6540 (t70) REVERT: F 329 LYS cc_start: 0.3940 (OUTLIER) cc_final: 0.2884 (mttt) REVERT: F 394 LYS cc_start: 0.8485 (mptt) cc_final: 0.7583 (tppt) REVERT: F 395 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7758 (m90) REVERT: F 436 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6413 (mtm) REVERT: F 534 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7217 (t70) outliers start: 183 outliers final: 123 residues processed: 350 average time/residue: 0.3155 time to fit residues: 177.3732 Evaluate side-chains 316 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 175 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 542 ASP Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 431 THR Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 534 ASP Chi-restraints excluded: chain F residue 559 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 3 optimal weight: 0.0570 chunk 187 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 214 optimal weight: 7.9990 chunk 173 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 225 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN D 179 ASN E 46 ASN E 531 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22622 Z= 0.211 Angle : 0.565 9.127 31122 Z= 0.284 Chirality : 0.040 0.230 3616 Planarity : 0.004 0.088 3649 Dihedral : 14.678 127.228 4369 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.63 % Favored : 94.06 % Rotamer: Outliers : 5.80 % Allowed : 19.88 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % 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: -1.25 (0.17), residues: 2541 helix: 0.15 (0.17), residues: 1003 sheet: -0.96 (0.29), residues: 327 loop : -1.62 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 182 HIS 0.006 0.001 HIS E 290 PHE 0.019 0.001 PHE A 652 TYR 0.017 0.001 TYR A 903 ARG 0.004 0.000 ARG F 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 196 time to evaluate : 2.656 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 5 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8355 (tp40) REVERT: A 131 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8289 (tt) REVERT: A 154 ASP cc_start: 0.8492 (t0) cc_final: 0.8287 (t0) REVERT: A 261 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7792 (tt) REVERT: A 280 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7957 (mt) REVERT: A 610 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: A 613 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7848 (m170) REVERT: A 628 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8180 (m-40) REVERT: A 633 MET cc_start: 0.8340 (tmm) cc_final: 0.7755 (tmm) REVERT: A 724 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: A 750 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7386 (mtp85) REVERT: A 791 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8110 (m110) REVERT: A 911 ASN cc_start: 0.8271 (t0) cc_final: 0.7886 (t0) REVERT: B 60 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: B 78 ASP cc_start: 0.7321 (t0) cc_final: 0.7005 (t0) REVERT: C 73 GLU cc_start: 0.7768 (tp30) cc_final: 0.7480 (tp30) REVERT: D 43 ASN cc_start: 0.8720 (m-40) cc_final: 0.8463 (t0) REVERT: E 62 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7371 (pp30) REVERT: E 198 TYR cc_start: 0.7827 (m-80) cc_final: 0.7547 (m-80) REVERT: E 235 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8686 (pp) REVERT: E 325 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7504 (mp) REVERT: E 347 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7771 (ptmm) REVERT: E 532 THR cc_start: 0.7375 (OUTLIER) cc_final: 0.7102 (t) REVERT: E 543 TYR cc_start: 0.7291 (m-80) cc_final: 0.6469 (m-80) REVERT: F 62 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7870 (pp30) REVERT: F 68 MET cc_start: 0.8100 (pmm) cc_final: 0.7545 (mtp) REVERT: F 161 ARG cc_start: 0.5137 (ttp-110) cc_final: 0.4460 (mmm160) REVERT: F 329 LYS cc_start: 0.3859 (OUTLIER) cc_final: 0.2999 (mttt) REVERT: F 394 LYS cc_start: 0.8409 (mptt) cc_final: 0.7469 (tppt) REVERT: F 395 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7726 (m90) REVERT: F 436 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6343 (mtm) REVERT: F 534 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7050 (t70) outliers start: 129 outliers final: 83 residues processed: 312 average time/residue: 0.3210 time to fit residues: 157.6575 Evaluate side-chains 284 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 182 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 613 HIS Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 539 SER Chi-restraints excluded: chain E residue 542 ASP Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 346 PHE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 534 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 1.9990 chunk 226 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 132 optimal weight: 2.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN D 179 ASN E 388 ASN E 516 ASN E 548 GLN F 265 ASN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22622 Z= 0.257 Angle : 0.572 12.190 31122 Z= 0.286 Chirality : 0.040 0.228 3616 Planarity : 0.004 0.090 3649 Dihedral : 14.450 125.132 4361 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.57 % Favored : 93.11 % Rotamer: Outliers : 5.62 % Allowed : 20.51 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2541 helix: 0.24 (0.17), residues: 1009 sheet: -0.67 (0.30), residues: 311 loop : -1.58 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 182 HIS 0.006 0.001 HIS E 290 PHE 0.021 0.001 PHE E 475 TYR 0.017 0.001 TYR B 138 ARG 0.006 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 190 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8366 (tp40) REVERT: A 59 LYS cc_start: 0.8215 (mtpp) cc_final: 0.7629 (mtpp) REVERT: A 131 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8230 (tt) REVERT: A 261 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7721 (tt) REVERT: A 280 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7946 (mt) REVERT: A 610 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: A 615 MET cc_start: 0.6948 (tpp) cc_final: 0.6227 (ttt) REVERT: A 628 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8231 (m-40) REVERT: A 633 MET cc_start: 0.8317 (tmm) cc_final: 0.7733 (tmm) REVERT: A 791 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8092 (m110) REVERT: A 911 ASN cc_start: 0.8277 (t0) cc_final: 0.7889 (t0) REVERT: B 60 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6652 (tm-30) REVERT: B 78 ASP cc_start: 0.7344 (t0) cc_final: 0.7084 (t0) REVERT: C 75 MET cc_start: 0.8090 (ptm) cc_final: 0.7874 (ptm) REVERT: D 43 ASN cc_start: 0.8701 (m-40) cc_final: 0.7904 (t0) REVERT: E 21 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7682 (tpp-160) REVERT: E 62 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7322 (pp30) REVERT: E 198 TYR cc_start: 0.7729 (m-80) cc_final: 0.7368 (m-80) REVERT: E 235 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8673 (pp) REVERT: E 325 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7522 (mp) REVERT: E 347 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7787 (ptmm) REVERT: E 438 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7465 (pp) REVERT: E 475 PHE cc_start: 0.7090 (t80) cc_final: 0.6791 (t80) REVERT: E 532 THR cc_start: 0.7299 (OUTLIER) cc_final: 0.7019 (t) REVERT: E 543 TYR cc_start: 0.7316 (m-80) cc_final: 0.6456 (m-80) REVERT: F 62 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.6747 (pp30) REVERT: F 68 MET cc_start: 0.7912 (pmm) cc_final: 0.7289 (mtp) REVERT: F 161 ARG cc_start: 0.5387 (ttp-110) cc_final: 0.4722 (mmm160) REVERT: F 274 MET cc_start: 0.6642 (mmt) cc_final: 0.6306 (mmp) REVERT: F 329 LYS cc_start: 0.3958 (OUTLIER) cc_final: 0.3131 (mttt) REVERT: F 394 LYS cc_start: 0.8404 (mptt) cc_final: 0.7434 (tppt) REVERT: F 436 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6288 (mtm) REVERT: F 534 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7179 (t70) outliers start: 125 outliers final: 92 residues processed: 302 average time/residue: 0.3227 time to fit residues: 153.0312 Evaluate side-chains 291 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 181 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 539 SER Chi-restraints excluded: chain E residue 542 ASP Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 534 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 40.0000 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 142 optimal weight: 0.7980 chunk 211 optimal weight: 0.0270 chunk 140 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 152 optimal weight: 0.0270 chunk 115 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN D 179 ASN E 548 GLN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22622 Z= 0.174 Angle : 0.543 13.569 31122 Z= 0.270 Chirality : 0.039 0.220 3616 Planarity : 0.004 0.085 3649 Dihedral : 14.202 125.046 4359 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.43 % Favored : 94.25 % Rotamer: Outliers : 5.40 % Allowed : 20.51 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2541 helix: 0.38 (0.17), residues: 1004 sheet: -0.65 (0.30), residues: 319 loop : -1.44 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 182 HIS 0.005 0.001 HIS A 309 PHE 0.016 0.001 PHE A 652 TYR 0.015 0.001 TYR F 515 ARG 0.007 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 197 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8377 (tp40) REVERT: A 555 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7484 (ptp90) REVERT: A 610 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7173 (mm-30) REVERT: A 615 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6133 (ttt) REVERT: A 628 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.8119 (m-40) REVERT: A 633 MET cc_start: 0.8265 (tmm) cc_final: 0.7690 (tmm) REVERT: A 750 ARG cc_start: 0.8030 (mmm-85) cc_final: 0.7392 (mtp85) REVERT: A 911 ASN cc_start: 0.8241 (t0) cc_final: 0.7852 (t0) REVERT: B 50 ASP cc_start: 0.8157 (m-30) cc_final: 0.7582 (t70) REVERT: B 60 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6562 (tm-30) REVERT: B 78 ASP cc_start: 0.7324 (t0) cc_final: 0.6978 (t0) REVERT: B 96 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7783 (ttm-80) REVERT: E 62 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7334 (pp30) REVERT: E 109 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7809 (mp) REVERT: E 122 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7990 (tp) REVERT: E 235 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8625 (pp) REVERT: E 325 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7461 (mp) REVERT: E 347 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7730 (ptmm) REVERT: E 532 THR cc_start: 0.7211 (OUTLIER) cc_final: 0.6938 (t) REVERT: E 543 TYR cc_start: 0.7315 (m-80) cc_final: 0.6484 (m-80) REVERT: F 62 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.6718 (pp30) REVERT: F 68 MET cc_start: 0.7996 (pmm) cc_final: 0.7385 (mtp) REVERT: F 161 ARG cc_start: 0.5339 (ttp-110) cc_final: 0.4672 (mmm160) REVERT: F 274 MET cc_start: 0.6632 (mmt) cc_final: 0.6294 (mmp) REVERT: F 329 LYS cc_start: 0.3981 (OUTLIER) cc_final: 0.3357 (mttt) REVERT: F 394 LYS cc_start: 0.8396 (mptt) cc_final: 0.7445 (tppt) REVERT: F 395 HIS cc_start: 0.8037 (OUTLIER) cc_final: 0.7614 (m90) REVERT: F 436 MET cc_start: 0.6485 (mtt) cc_final: 0.6095 (mtm) REVERT: F 534 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.6919 (t70) outliers start: 120 outliers final: 87 residues processed: 300 average time/residue: 0.3318 time to fit residues: 155.6054 Evaluate side-chains 291 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 188 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 542 ASP Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 534 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 170 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN D 179 ASN E 46 ASN E 548 GLN F 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 0.047 22622 Z= 0.297 Angle : 0.597 12.923 31122 Z= 0.298 Chirality : 0.041 0.223 3616 Planarity : 0.004 0.091 3649 Dihedral : 14.064 125.045 4349 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.93 % Favored : 92.76 % Rotamer: Outliers : 5.71 % Allowed : 20.83 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2541 helix: 0.33 (0.17), residues: 1001 sheet: -0.73 (0.29), residues: 329 loop : -1.49 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 182 HIS 0.006 0.001 HIS E 290 PHE 0.016 0.002 PHE E 343 TYR 0.018 0.001 TYR A 748 ARG 0.009 0.000 ARG F 443 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 190 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8374 (tp40) REVERT: A 261 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7709 (tt) REVERT: A 280 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7976 (mt) REVERT: A 543 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8747 (p0) REVERT: A 610 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7056 (mm-30) REVERT: A 615 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6339 (ttt) REVERT: A 633 MET cc_start: 0.8310 (tmm) cc_final: 0.7745 (tmm) REVERT: A 750 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7438 (mtp85) REVERT: A 911 ASN cc_start: 0.8258 (t0) cc_final: 0.7850 (t0) REVERT: B 60 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6401 (tm-30) REVERT: B 78 ASP cc_start: 0.7371 (t0) cc_final: 0.7072 (t0) REVERT: E 21 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7617 (tpp-160) REVERT: E 62 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7358 (pp30) REVERT: E 122 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7959 (tp) REVERT: E 235 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8677 (pp) REVERT: E 325 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7560 (mp) REVERT: E 347 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7832 (ptmm) REVERT: E 543 TYR cc_start: 0.7321 (m-80) cc_final: 0.6443 (m-80) REVERT: F 62 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.6634 (pp30) REVERT: F 68 MET cc_start: 0.7560 (pmm) cc_final: 0.7253 (mtp) REVERT: F 161 ARG cc_start: 0.5363 (ttp-110) cc_final: 0.4671 (mmm160) REVERT: F 274 MET cc_start: 0.6653 (mmt) cc_final: 0.6311 (mmp) REVERT: F 329 LYS cc_start: 0.3941 (OUTLIER) cc_final: 0.3151 (mttt) REVERT: F 394 LYS cc_start: 0.8421 (mptt) cc_final: 0.7512 (tppt) REVERT: F 395 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7608 (m90) REVERT: F 436 MET cc_start: 0.6660 (mtt) cc_final: 0.6287 (mtm) REVERT: F 447 GLU cc_start: 0.5484 (OUTLIER) cc_final: 0.4204 (pm20) REVERT: F 534 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7028 (t70) outliers start: 127 outliers final: 99 residues processed: 299 average time/residue: 0.3410 time to fit residues: 160.5614 Evaluate side-chains 295 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 179 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 542 ASP Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 534 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 10.0000 chunk 240 optimal weight: 20.0000 chunk 219 optimal weight: 8.9990 chunk 233 optimal weight: 0.7980 chunk 140 optimal weight: 0.4980 chunk 101 optimal weight: 0.5980 chunk 183 optimal weight: 0.0870 chunk 71 optimal weight: 0.9990 chunk 211 optimal weight: 0.0020 chunk 220 optimal weight: 0.9980 chunk 232 optimal weight: 0.7980 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN A 791 ASN D 179 ASN E 548 GLN F 265 ASN F 268 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22622 Z= 0.145 Angle : 0.547 13.720 31122 Z= 0.271 Chirality : 0.039 0.214 3616 Planarity : 0.004 0.083 3649 Dihedral : 13.859 124.968 4349 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.08 % Favored : 94.61 % Rotamer: Outliers : 4.45 % Allowed : 22.00 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2541 helix: 0.53 (0.17), residues: 1001 sheet: -0.56 (0.30), residues: 321 loop : -1.31 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 182 HIS 0.005 0.001 HIS A 309 PHE 0.031 0.001 PHE E 475 TYR 0.021 0.001 TYR F 324 ARG 0.008 0.000 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 194 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8393 (tp40) REVERT: A 555 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7540 (ptp90) REVERT: A 610 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7192 (mm-30) REVERT: A 615 MET cc_start: 0.6772 (tpp) cc_final: 0.6093 (ttt) REVERT: A 633 MET cc_start: 0.8247 (tmm) cc_final: 0.7673 (tmm) REVERT: A 750 ARG cc_start: 0.8000 (mmm-85) cc_final: 0.7364 (mtp85) REVERT: A 911 ASN cc_start: 0.8200 (t0) cc_final: 0.7830 (t0) REVERT: B 60 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6471 (tm-30) REVERT: B 96 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7753 (ttm-80) REVERT: E 62 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7338 (pp30) REVERT: E 109 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7809 (mp) REVERT: E 235 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8570 (pp) REVERT: E 325 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7528 (mp) REVERT: E 347 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7713 (ptmm) REVERT: E 369 ASP cc_start: 0.8512 (t70) cc_final: 0.8207 (t70) REVERT: E 532 THR cc_start: 0.7087 (OUTLIER) cc_final: 0.6793 (t) REVERT: E 543 TYR cc_start: 0.7300 (m-80) cc_final: 0.6484 (m-80) REVERT: F 62 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.6689 (pp30) REVERT: F 161 ARG cc_start: 0.5335 (ttp-110) cc_final: 0.4664 (mmm160) REVERT: F 274 MET cc_start: 0.6606 (mmt) cc_final: 0.6246 (mmp) REVERT: F 291 PHE cc_start: 0.6728 (t80) cc_final: 0.6206 (t80) REVERT: F 329 LYS cc_start: 0.3743 (OUTLIER) cc_final: 0.3112 (mttt) REVERT: F 394 LYS cc_start: 0.8347 (mptt) cc_final: 0.7423 (tppt) REVERT: F 395 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7739 (m90) REVERT: F 436 MET cc_start: 0.6460 (mtt) cc_final: 0.6020 (mtm) REVERT: F 447 GLU cc_start: 0.5506 (OUTLIER) cc_final: 0.4242 (pm20) REVERT: F 534 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.6838 (t70) outliers start: 99 outliers final: 69 residues processed: 278 average time/residue: 0.3304 time to fit residues: 144.9567 Evaluate side-chains 265 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 182 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 542 ASP Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 534 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 8.9990 chunk 246 optimal weight: 30.0000 chunk 150 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 259 optimal weight: 20.0000 chunk 238 optimal weight: 20.0000 chunk 206 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 46 ASN F 46 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 22622 Z= 0.467 Angle : 0.674 13.114 31122 Z= 0.340 Chirality : 0.045 0.239 3616 Planarity : 0.004 0.095 3649 Dihedral : 14.028 125.078 4347 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.91 % Favored : 91.77 % Rotamer: Outliers : 4.72 % Allowed : 22.22 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.12 % 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: -1.08 (0.17), residues: 2541 helix: 0.23 (0.17), residues: 1004 sheet: -0.75 (0.29), residues: 335 loop : -1.51 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 182 HIS 0.009 0.001 HIS E 290 PHE 0.018 0.002 PHE D 92 TYR 0.025 0.002 TYR A 748 ARG 0.007 0.001 ARG F 497 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 182 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8342 (tp40) REVERT: A 280 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8118 (mt) REVERT: A 610 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7108 (mm-30) REVERT: A 615 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6464 (ttt) REVERT: A 633 MET cc_start: 0.8373 (tmm) cc_final: 0.7800 (tmm) REVERT: A 911 ASN cc_start: 0.8255 (t0) cc_final: 0.7853 (t0) REVERT: B 60 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6389 (tm-30) REVERT: E 62 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7291 (pp30) REVERT: E 235 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8718 (pp) REVERT: E 325 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7665 (mp) REVERT: E 347 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7768 (ptmm) REVERT: E 532 THR cc_start: 0.7187 (OUTLIER) cc_final: 0.6921 (t) REVERT: E 534 ASP cc_start: 0.7824 (m-30) cc_final: 0.7084 (t0) REVERT: E 543 TYR cc_start: 0.7373 (m-80) cc_final: 0.6466 (m-80) REVERT: F 62 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.6655 (pp30) REVERT: F 161 ARG cc_start: 0.5323 (ttp-110) cc_final: 0.4665 (mmm160) REVERT: F 274 MET cc_start: 0.6656 (mmt) cc_final: 0.6329 (mmp) REVERT: F 329 LYS cc_start: 0.3925 (OUTLIER) cc_final: 0.3407 (mttt) REVERT: F 357 PHE cc_start: 0.7008 (m-80) cc_final: 0.6598 (m-80) REVERT: F 394 LYS cc_start: 0.8547 (mptt) cc_final: 0.7667 (tppt) REVERT: F 395 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7738 (m90) REVERT: F 436 MET cc_start: 0.6891 (mtt) cc_final: 0.6454 (mtm) REVERT: F 447 GLU cc_start: 0.5426 (OUTLIER) cc_final: 0.4295 (pm20) REVERT: F 534 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7118 (t70) outliers start: 105 outliers final: 77 residues processed: 273 average time/residue: 0.3195 time to fit residues: 138.5898 Evaluate side-chains 266 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 175 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 397 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 60 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 GLU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 542 ASP Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 447 GLU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 534 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.8980 chunk 219 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 190 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 206 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 212 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.101344 restraints weight = 32848.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.099199 restraints weight = 39861.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100423 restraints weight = 43768.973| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.174 22622 Z= 0.415 Angle : 0.808 59.199 31122 Z= 0.441 Chirality : 0.045 0.831 3616 Planarity : 0.005 0.095 3649 Dihedral : 14.026 125.150 4345 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.83 % Favored : 91.85 % Rotamer: Outliers : 4.41 % Allowed : 22.18 % Favored : 73.41 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.17), residues: 2541 helix: 0.24 (0.17), residues: 1004 sheet: -0.76 (0.29), residues: 335 loop : -1.53 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 182 HIS 0.008 0.001 HIS E 290 PHE 0.019 0.002 PHE A 652 TYR 0.097 0.002 TYR B 22 ARG 0.005 0.000 ARG F 497 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4469.56 seconds wall clock time: 82 minutes 0.35 seconds (4920.35 seconds total)