Starting phenix.real_space_refine on Fri Mar 15 19:24:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krp_23009/03_2024/7krp_23009_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krp_23009/03_2024/7krp_23009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krp_23009/03_2024/7krp_23009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krp_23009/03_2024/7krp_23009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krp_23009/03_2024/7krp_23009_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7krp_23009/03_2024/7krp_23009_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.003 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 75 5.49 5 Mg 1 5.21 5 S 83 5.16 5 C 7700 2.51 5 N 2111 2.21 5 O 2589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12561 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1416 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 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: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} 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: "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: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 769 Classifications: {'RNA': 36} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna3p': 35} 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: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 24.703 58.884 80.276 1.00 23.18 S ATOM 2495 SG CYS A 306 25.136 60.110 83.908 1.00 20.09 S ATOM 2527 SG CYS A 310 25.698 56.441 82.999 1.00 17.07 S ATOM 3935 SG CYS A 487 27.719 72.698 66.042 1.00 28.42 S ATOM 5188 SG CYS A 645 27.788 75.074 69.011 1.00 32.11 S ATOM 5194 SG CYS A 646 26.236 71.615 69.477 1.00 29.89 S Time building chain proxies: 7.40, per 1000 atoms: 0.59 Number of scatterers: 12561 At special positions: 0 Unit cell: (95.85, 161.88, 142.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 83 16.00 P 75 15.00 Mg 1 11.99 O 2589 8.00 N 2111 7.00 C 7700 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: 5.62 Conformation dependent library (CDL) restraints added in 2.0 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 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " 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 " Number of angles added : 6 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 11 sheets defined 46.8% alpha, 9.9% beta 33 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 5.97 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 143 through 148 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: 3.838A pdb=" N ALA A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.320A 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 235 through 247 removed outlier: 3.857A pdb=" N SER A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 4.048A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) 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 286 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: 3.584A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.527A 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 446 through 458 removed outlier: 4.077A pdb=" N ALA A 449 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 450 " --> pdb=" O ASN A 447 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP A 452 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 453 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.487A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.200A 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 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 517 Processing helix chain 'A' and resid 521 through 531 removed outlier: 3.649A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 581 removed outlier: 4.162A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 688 through 709 Processing helix chain 'A' and resid 718 through 731 removed outlier: 3.717A 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 790 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 834 through 842 removed outlier: 3.790A pdb=" N LEU A 838 " --> pdb=" O PRO A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 859 through 871 Proline residue: A 868 - end of helix removed outlier: 4.786A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 4.054A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.880A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 32 through 96 removed outlier: 3.761A pdb=" N ARG B 75 " --> pdb=" O TYR B 71 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.701A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.535A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.536A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 74 removed outlier: 3.729A 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 33 through 62 removed outlier: 3.744A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 81 removed outlier: 4.292A pdb=" N SER D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 98 removed outlier: 4.012A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 111 Processing helix chain 'D' and resid 135 through 141 removed outlier: 3.623A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 7.104A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (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 202 through 204 removed outlier: 6.463A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= F, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= G, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.295A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= I, first strand: chain 'A' and resid 815 through 822 Processing sheet with id= J, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.056A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.437A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 5.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3662 1.34 - 1.46: 2591 1.46 - 1.57: 6398 1.57 - 1.69: 197 1.69 - 1.81: 130 Bond restraints: 12978 Sorted by residual: bond pdb=" C17 1N7 A1005 " pdb=" C18 1N7 A1005 " ideal model delta sigma weight residual 1.528 1.638 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C17 1N7 D 201 " pdb=" C18 1N7 D 201 " ideal model delta sigma weight residual 1.528 1.633 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C17 1N7 A1006 " pdb=" C18 1N7 A1006 " ideal model delta sigma weight residual 1.528 1.630 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C24 1N7 A1005 " pdb=" N1 1N7 A1005 " ideal model delta sigma weight residual 1.346 1.441 -0.095 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C24 1N7 D 201 " pdb=" N1 1N7 D 201 " ideal model delta sigma weight residual 1.346 1.440 -0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 12973 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.69: 564 105.69 - 113.28: 7304 113.28 - 120.87: 6334 120.87 - 128.47: 3618 128.47 - 136.06: 147 Bond angle restraints: 17967 Sorted by residual: angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C4 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C9 1N7 A1005 " ideal model delta sigma weight residual 117.60 105.50 12.10 3.00e+00 1.11e-01 1.63e+01 angle pdb=" O3' C P 25 " pdb=" C3' C P 25 " pdb=" C2' C P 25 " ideal model delta sigma weight residual 113.70 118.97 -5.27 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C23 1N7 A1005 " pdb=" C24 1N7 A1005 " pdb=" N1 1N7 A1005 " ideal model delta sigma weight residual 115.43 125.06 -9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C23 1N7 D 201 " pdb=" C24 1N7 D 201 " pdb=" N1 1N7 D 201 " ideal model delta sigma weight residual 115.43 125.03 -9.60 3.00e+00 1.11e-01 1.02e+01 ... (remaining 17962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.57: 7630 30.57 - 61.15: 311 61.15 - 91.72: 65 91.72 - 122.29: 20 122.29 - 152.87: 5 Dihedral angle restraints: 8031 sinusoidal: 3950 harmonic: 4081 Sorted by residual: dihedral pdb=" CA SER D 31 " pdb=" C SER D 31 " pdb=" N GLU D 32 " pdb=" CA GLU D 32 " ideal model delta harmonic sigma weight residual 0.00 -31.31 31.31 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" C22 1N7 A1005 " pdb=" C23 1N7 A1005 " pdb=" C24 1N7 A1005 " pdb=" N1 1N7 A1005 " ideal model delta sinusoidal sigma weight residual 227.30 74.43 152.87 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA SER A 759 " pdb=" C SER A 759 " pdb=" N ASP A 760 " pdb=" CA ASP A 760 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 8028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.025: 2099 1.025 - 2.051: 0 2.051 - 3.076: 0 3.076 - 4.101: 0 4.101 - 5.127: 2 Chirality restraints: 2101 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 2.70 -5.13 2.00e-01 2.50e+01 6.57e+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 -2.56 5.09 2.00e-01 2.50e+01 6.48e+02 chirality pdb=" C17 1N7 A1006 " pdb=" C16 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" O3 1N7 A1006 " both_signs ideal model delta sigma weight residual False 2.40 2.82 -0.42 2.00e-01 2.50e+01 4.37e+00 ... (remaining 2098 not shown) Planarity restraints: 2007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 338 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO A 339 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 93 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO A 94 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 338 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C VAL A 338 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL A 338 " -0.010 2.00e-02 2.50e+03 pdb=" N PRO A 339 " -0.009 2.00e-02 2.50e+03 ... (remaining 2004 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 38 2.41 - 3.03: 7156 3.03 - 3.65: 19553 3.65 - 4.28: 29670 4.28 - 4.90: 48437 Nonbonded interactions: 104854 Sorted by model distance: nonbonded pdb="MG MG A1003 " pdb=" O2A ADP A1004 " model vdw 1.784 2.170 nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1003 " model vdw 2.048 2.170 nonbonded pdb=" OD2 ASP A 218 " pdb="MG MG A1003 " model vdw 2.065 2.170 nonbonded pdb="MG MG A1003 " pdb=" O1B ADP A1004 " model vdw 2.074 2.170 nonbonded pdb=" O TYR A 915 " pdb=" OH TYR A 921 " model vdw 2.227 2.440 ... (remaining 104849 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 \ 31 or (resid 32 and (name N or name CA or name C or name O or name CB )) or resi \ d 33 through 38 or (resid 39 and (name N or name CA or name C or name O or name \ CB )) or resid 40 through 191)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 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: 0.000 Extract box with map and model: 7.410 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 43.390 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 12978 Z= 0.376 Angle : 0.691 12.105 17967 Z= 0.371 Chirality : 0.165 5.127 2101 Planarity : 0.003 0.042 2007 Dihedral : 17.525 152.867 5389 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.18 % Allowed : 6.95 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.51 (0.22), residues: 1365 helix: -0.49 (0.20), residues: 672 sheet: -1.31 (0.44), residues: 136 loop : -1.41 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 PHE 0.013 0.002 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.003 0.000 ARG A 726 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 344 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.7637 (m-10) cc_final: 0.7386 (m-10) REVERT: A 450 ILE cc_start: 0.7102 (tp) cc_final: 0.6844 (tp) REVERT: A 481 ASP cc_start: 0.6962 (OUTLIER) cc_final: 0.6739 (t0) REVERT: A 666 MET cc_start: 0.6076 (OUTLIER) cc_final: 0.5429 (mtt) REVERT: A 755 MET cc_start: 0.6677 (ttm) cc_final: 0.6449 (ttp) REVERT: A 768 SER cc_start: 0.5726 (m) cc_final: 0.5466 (m) REVERT: B 165 LYS cc_start: 0.5807 (mptt) cc_final: 0.5396 (tmtt) REVERT: D 176 ASN cc_start: 0.5391 (OUTLIER) cc_final: 0.4996 (t0) outliers start: 50 outliers final: 13 residues processed: 379 average time/residue: 0.2446 time to fit residues: 131.0071 Evaluate side-chains 228 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 113 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 599 HIS A 611 ASN A 613 HIS A 703 ASN A 767 ASN A 789 GLN B 157 GLN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12978 Z= 0.387 Angle : 0.785 11.912 17967 Z= 0.395 Chirality : 0.047 0.270 2101 Planarity : 0.005 0.061 2007 Dihedral : 15.983 166.196 2868 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.77 % Allowed : 12.47 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.22), residues: 1365 helix: -0.28 (0.20), residues: 686 sheet: -1.59 (0.42), residues: 132 loop : -1.58 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 598 HIS 0.008 0.002 HIS A 362 PHE 0.032 0.003 PHE D 92 TYR 0.043 0.002 TYR A 32 ARG 0.010 0.001 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 173 time to evaluate : 1.304 Fit side-chains revert: symmetry clash REVERT: A 57 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7754 (tp40) REVERT: A 261 LEU cc_start: 0.8320 (mt) cc_final: 0.8118 (mt) REVERT: A 633 MET cc_start: 0.7186 (ttp) cc_final: 0.6901 (ttp) REVERT: A 668 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6458 (tmm) REVERT: A 703 ASN cc_start: 0.8327 (m-40) cc_final: 0.8073 (m110) REVERT: A 723 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8026 (tp) REVERT: B 90 MET cc_start: 0.8206 (tmm) cc_final: 0.7885 (ttp) REVERT: B 165 LYS cc_start: 0.7066 (mptt) cc_final: 0.6396 (tttm) REVERT: D 62 MET cc_start: 0.6647 (tpp) cc_final: 0.6412 (ttm) outliers start: 57 outliers final: 23 residues processed: 220 average time/residue: 0.2036 time to fit residues: 68.5993 Evaluate side-chains 159 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 157 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.1980 chunk 39 optimal weight: 0.4980 chunk 106 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 128 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 114 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 GLN A 300 ASN A 497 ASN A 613 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 158 GLN D 176 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12978 Z= 0.178 Angle : 0.523 8.621 17967 Z= 0.266 Chirality : 0.038 0.185 2101 Planarity : 0.003 0.051 2007 Dihedral : 15.297 136.371 2852 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.01 % Allowed : 15.15 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.22), residues: 1365 helix: 0.27 (0.20), residues: 687 sheet: -1.21 (0.44), residues: 129 loop : -1.30 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.007 0.001 HIS A 613 PHE 0.014 0.001 PHE A 741 TYR 0.013 0.001 TYR A 515 ARG 0.003 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8084 (p0) cc_final: 0.7820 (p0) REVERT: A 666 MET cc_start: 0.7362 (mtt) cc_final: 0.6934 (mtt) REVERT: A 703 ASN cc_start: 0.7908 (m-40) cc_final: 0.7467 (m110) REVERT: A 922 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7102 (tt0) REVERT: B 90 MET cc_start: 0.8102 (tmm) cc_final: 0.7772 (ttp) REVERT: B 165 LYS cc_start: 0.7326 (mptt) cc_final: 0.6903 (tttm) REVERT: C 4 SER cc_start: 0.8796 (t) cc_final: 0.8356 (m) REVERT: D 50 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6141 (m-30) REVERT: D 164 SER cc_start: 0.7486 (m) cc_final: 0.6936 (t) outliers start: 36 outliers final: 22 residues processed: 164 average time/residue: 0.2065 time to fit residues: 52.0340 Evaluate side-chains 151 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASN Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 50 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 HIS ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.7232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12978 Z= 0.242 Angle : 0.541 8.616 17967 Z= 0.275 Chirality : 0.039 0.185 2101 Planarity : 0.003 0.048 2007 Dihedral : 14.943 169.697 2851 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.68 % Allowed : 14.98 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1365 helix: 0.48 (0.20), residues: 684 sheet: -1.20 (0.43), residues: 129 loop : -1.26 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 182 HIS 0.005 0.001 HIS A 309 PHE 0.017 0.001 PHE D 92 TYR 0.017 0.001 TYR A 32 ARG 0.004 0.001 ARG A 889 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8263 (p0) cc_final: 0.7912 (p0) REVERT: B 165 LYS cc_start: 0.7576 (mptt) cc_final: 0.7221 (tttm) REVERT: C 21 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7375 (tpp-160) REVERT: C 38 ASP cc_start: 0.7595 (m-30) cc_final: 0.7372 (m-30) REVERT: D 50 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6321 (m-30) REVERT: D 70 MET cc_start: 0.7000 (mmm) cc_final: 0.6759 (ttm) outliers start: 44 outliers final: 25 residues processed: 156 average time/residue: 0.2243 time to fit residues: 51.7954 Evaluate side-chains 140 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 408 GLN A 496 ASN A 703 ASN D 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.8649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12978 Z= 0.333 Angle : 0.598 8.325 17967 Z= 0.309 Chirality : 0.042 0.187 2101 Planarity : 0.004 0.049 2007 Dihedral : 15.149 176.571 2848 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.60 % Allowed : 15.23 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.22), residues: 1365 helix: 0.32 (0.20), residues: 683 sheet: -1.38 (0.41), residues: 138 loop : -1.27 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 916 HIS 0.007 0.001 HIS A 309 PHE 0.018 0.002 PHE A 741 TYR 0.018 0.002 TYR A 32 ARG 0.008 0.001 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 134 time to evaluate : 1.390 Fit side-chains revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8377 (p0) cc_final: 0.8021 (p0) REVERT: A 268 TRP cc_start: 0.8363 (OUTLIER) cc_final: 0.6167 (m-90) REVERT: A 431 GLU cc_start: 0.6928 (tp30) cc_final: 0.6540 (tt0) REVERT: A 553 ARG cc_start: 0.7808 (ttm110) cc_final: 0.7514 (mtm-85) REVERT: A 638 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 883 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7677 (tp) REVERT: B 67 MET cc_start: 0.5861 (tpp) cc_final: 0.4924 (tmm) REVERT: B 82 LYS cc_start: 0.7846 (mptt) cc_final: 0.7530 (mptt) REVERT: B 165 LYS cc_start: 0.7764 (mptt) cc_final: 0.7257 (mtpp) REVERT: D 50 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6773 (m-30) REVERT: D 78 ASP cc_start: 0.7851 (t70) cc_final: 0.7487 (t0) REVERT: D 96 ARG cc_start: 0.7077 (mtt180) cc_final: 0.5890 (mpt180) REVERT: D 164 SER cc_start: 0.7643 (m) cc_final: 0.7123 (t) outliers start: 55 outliers final: 34 residues processed: 176 average time/residue: 0.2426 time to fit residues: 62.8579 Evaluate side-chains 157 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 HIS A 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.8776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12978 Z= 0.206 Angle : 0.510 6.642 17967 Z= 0.261 Chirality : 0.038 0.183 2101 Planarity : 0.003 0.044 2007 Dihedral : 14.996 177.025 2847 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.77 % Allowed : 17.24 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.22), residues: 1365 helix: 0.70 (0.20), residues: 679 sheet: -1.18 (0.41), residues: 137 loop : -1.25 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.015 0.001 TYR A 788 ARG 0.004 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 120 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8447 (p0) cc_final: 0.8114 (p0) REVERT: A 249 ARG cc_start: 0.7981 (ttp-110) cc_final: 0.7773 (mtp180) REVERT: A 268 TRP cc_start: 0.8402 (OUTLIER) cc_final: 0.6134 (m-90) REVERT: A 332 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7866 (ttmm) REVERT: A 360 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7250 (m-40) REVERT: A 431 GLU cc_start: 0.6903 (tp30) cc_final: 0.6574 (tt0) REVERT: A 450 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8168 (tp) REVERT: A 553 ARG cc_start: 0.7805 (ttm110) cc_final: 0.7585 (mtm-85) REVERT: B 67 MET cc_start: 0.5821 (tpp) cc_final: 0.4953 (tmm) REVERT: D 50 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.6990 (m-30) REVERT: D 78 ASP cc_start: 0.7872 (t70) cc_final: 0.7498 (t0) REVERT: D 94 MET cc_start: 0.8425 (mtm) cc_final: 0.8149 (mtp) REVERT: D 164 SER cc_start: 0.7650 (m) cc_final: 0.7173 (t) outliers start: 45 outliers final: 30 residues processed: 153 average time/residue: 0.2206 time to fit residues: 52.2465 Evaluate side-chains 153 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.0970 chunk 77 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.8916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12978 Z= 0.248 Angle : 0.524 6.508 17967 Z= 0.269 Chirality : 0.039 0.184 2101 Planarity : 0.003 0.046 2007 Dihedral : 14.961 170.103 2847 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.93 % Allowed : 17.82 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1365 helix: 0.79 (0.20), residues: 676 sheet: -1.14 (0.41), residues: 135 loop : -1.18 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.016 0.001 PHE A 741 TYR 0.014 0.001 TYR A 32 ARG 0.005 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 119 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8400 (p0) cc_final: 0.8030 (p0) REVERT: A 360 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7304 (m-40) REVERT: A 431 GLU cc_start: 0.6862 (tp30) cc_final: 0.6524 (tt0) REVERT: A 553 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7629 (mtm-85) REVERT: A 883 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7667 (tp) REVERT: B 67 MET cc_start: 0.5753 (tpp) cc_final: 0.4990 (tmm) REVERT: D 50 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: D 78 ASP cc_start: 0.8018 (t70) cc_final: 0.7660 (t0) REVERT: D 94 MET cc_start: 0.8444 (mtm) cc_final: 0.8216 (mtp) REVERT: D 164 SER cc_start: 0.7635 (m) cc_final: 0.7173 (t) outliers start: 47 outliers final: 34 residues processed: 156 average time/residue: 0.2158 time to fit residues: 51.8642 Evaluate side-chains 156 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 119 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.9136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12978 Z= 0.300 Angle : 0.555 6.682 17967 Z= 0.284 Chirality : 0.041 0.185 2101 Planarity : 0.003 0.047 2007 Dihedral : 14.985 151.571 2847 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.68 % Allowed : 18.58 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.22), residues: 1365 helix: 0.69 (0.20), residues: 678 sheet: -1.29 (0.41), residues: 135 loop : -1.17 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.017 0.002 PHE A 741 TYR 0.015 0.001 TYR A 80 ARG 0.004 0.000 ARG A 750 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 121 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8482 (p0) cc_final: 0.8103 (p0) REVERT: A 268 TRP cc_start: 0.8376 (OUTLIER) cc_final: 0.6222 (m-90) REVERT: A 360 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7317 (m-40) REVERT: A 431 GLU cc_start: 0.6921 (tp30) cc_final: 0.6605 (tt0) REVERT: A 883 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7701 (tp) REVERT: B 67 MET cc_start: 0.5910 (tpp) cc_final: 0.5166 (tmm) REVERT: D 50 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: D 78 ASP cc_start: 0.8133 (t70) cc_final: 0.7777 (t0) REVERT: D 96 ARG cc_start: 0.7062 (mtt180) cc_final: 0.5955 (mpt180) REVERT: D 164 SER cc_start: 0.7591 (m) cc_final: 0.7046 (t) outliers start: 44 outliers final: 37 residues processed: 153 average time/residue: 0.2111 time to fit residues: 49.1322 Evaluate side-chains 158 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 117 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 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 613 HIS D 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.9215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12978 Z= 0.219 Angle : 0.515 7.062 17967 Z= 0.263 Chirality : 0.039 0.183 2101 Planarity : 0.003 0.044 2007 Dihedral : 14.861 134.216 2847 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.77 % Allowed : 18.33 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1365 helix: 0.83 (0.20), residues: 673 sheet: -1.25 (0.42), residues: 135 loop : -1.14 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.005 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 122 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 161 ASP cc_start: 0.8405 (p0) cc_final: 0.8034 (p0) REVERT: A 268 TRP cc_start: 0.8374 (OUTLIER) cc_final: 0.6259 (m-90) REVERT: A 332 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8130 (ttmm) REVERT: A 360 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7293 (m-40) REVERT: A 372 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8559 (tp) REVERT: A 431 GLU cc_start: 0.6932 (tp30) cc_final: 0.6709 (tt0) REVERT: B 67 MET cc_start: 0.5893 (tpp) cc_final: 0.5185 (tmm) REVERT: D 50 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: D 78 ASP cc_start: 0.8143 (t70) cc_final: 0.7795 (t0) REVERT: D 96 ARG cc_start: 0.7080 (mtt180) cc_final: 0.5962 (mpt180) REVERT: D 164 SER cc_start: 0.7411 (m) cc_final: 0.7050 (t) REVERT: D 166 ILE cc_start: 0.6428 (mm) cc_final: 0.6139 (tp) outliers start: 45 outliers final: 32 residues processed: 155 average time/residue: 0.2259 time to fit residues: 52.4771 Evaluate side-chains 157 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 613 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.9346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12978 Z= 0.348 Angle : 0.587 8.764 17967 Z= 0.300 Chirality : 0.042 0.186 2101 Planarity : 0.004 0.050 2007 Dihedral : 14.977 125.581 2846 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.68 % Allowed : 18.58 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.22), residues: 1365 helix: 0.65 (0.20), residues: 672 sheet: -1.41 (0.41), residues: 135 loop : -1.14 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.018 0.002 PHE A 741 TYR 0.016 0.002 TYR A 80 ARG 0.005 0.000 ARG A 750 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 123 time to evaluate : 1.372 Fit side-chains REVERT: A 161 ASP cc_start: 0.8495 (p0) cc_final: 0.8102 (p0) REVERT: A 268 TRP cc_start: 0.8437 (OUTLIER) cc_final: 0.6344 (m-90) REVERT: A 360 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7479 (m-40) REVERT: A 431 GLU cc_start: 0.6974 (tp30) cc_final: 0.6744 (tt0) REVERT: A 883 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7734 (tp) REVERT: B 67 MET cc_start: 0.5871 (tpp) cc_final: 0.5190 (tmm) REVERT: B 82 LYS cc_start: 0.7850 (mptt) cc_final: 0.7544 (mptt) REVERT: B 165 LYS cc_start: 0.7727 (mptt) cc_final: 0.7256 (mtpp) REVERT: D 32 GLU cc_start: 0.1694 (OUTLIER) cc_final: 0.1183 (pt0) REVERT: D 50 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: D 78 ASP cc_start: 0.8123 (t70) cc_final: 0.7745 (t0) REVERT: D 94 MET cc_start: 0.8398 (mtp) cc_final: 0.8168 (mtt) REVERT: D 96 ARG cc_start: 0.7108 (mtt180) cc_final: 0.5991 (mpt180) REVERT: D 164 SER cc_start: 0.7556 (m) cc_final: 0.7125 (t) REVERT: D 166 ILE cc_start: 0.6634 (mm) cc_final: 0.6411 (tp) outliers start: 44 outliers final: 36 residues processed: 159 average time/residue: 0.2487 time to fit residues: 58.7345 Evaluate side-chains 162 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 121 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 813 CYS Chi-restraints excluded: chain A residue 824 ASP Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 185 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 112 optimal weight: 0.3980 chunk 46 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113702 restraints weight = 14652.382| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.44 r_work: 0.3084 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.9386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12978 Z= 0.164 Angle : 0.505 8.777 17967 Z= 0.257 Chirality : 0.038 0.181 2101 Planarity : 0.003 0.040 2007 Dihedral : 14.784 125.287 2846 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.85 % Allowed : 19.50 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.23), residues: 1365 helix: 0.94 (0.21), residues: 668 sheet: -1.26 (0.41), residues: 135 loop : -1.06 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.041 0.001 PHE D 15 TYR 0.015 0.001 TYR A 788 ARG 0.004 0.000 ARG B 96 =============================================================================== Job complete usr+sys time: 2717.03 seconds wall clock time: 50 minutes 4.10 seconds (3004.10 seconds total)