Starting phenix.real_space_refine on Fri Dec 8 07:01:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktv_23031/12_2023/7ktv_23031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktv_23031/12_2023/7ktv_23031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktv_23031/12_2023/7ktv_23031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktv_23031/12_2023/7ktv_23031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktv_23031/12_2023/7ktv_23031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktv_23031/12_2023/7ktv_23031.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 4671 2.51 5 N 1373 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A TYR 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A ARG 975": "NH1" <-> "NH2" Residue "A ARG 1055": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7577 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7577 Classifications: {'peptide': 995} Link IDs: {'PTRANS': 35, 'TRANS': 959} Chain breaks: 1 Time building chain proxies: 4.23, per 1000 atoms: 0.56 Number of scatterers: 7577 At special positions: 0 Unit cell: (84.15, 102.3, 129.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1490 8.00 N 1373 7.00 C 4671 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: 3.03 Conformation dependent library (CDL) restraints added in 1.3 seconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 0 sheets defined 84.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 6 through 22 Proline residue: A 15 - end of helix removed outlier: 3.530A pdb=" N GLN A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN A 19 " --> pdb=" O PRO A 15 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.742A pdb=" N GLU A 28 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU A 29 " --> pdb=" O ILE A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 65 removed outlier: 3.537A pdb=" N ASN A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 96 removed outlier: 3.661A pdb=" N ASP A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Proline residue: A 75 - end of helix removed outlier: 3.531A pdb=" N ALA A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 Processing helix chain 'A' and resid 107 through 131 removed outlier: 3.850A pdb=" N GLY A 111 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.280A pdb=" N ARG A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 151 removed outlier: 3.965A pdb=" N VAL A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 151' Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.600A pdb=" N THR A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 removed outlier: 3.551A pdb=" N LEU A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 214 removed outlier: 3.712A pdb=" N SER A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Proline residue: A 203 - end of helix Processing helix chain 'A' and resid 224 through 248 removed outlier: 3.536A pdb=" N ASN A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 261 Processing helix chain 'A' and resid 262 through 274 removed outlier: 3.651A pdb=" N LYS A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 287 through 290 removed outlier: 3.821A pdb=" N SER A 290 " --> pdb=" O PRO A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.660A pdb=" N GLN A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 306 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 326 removed outlier: 3.709A pdb=" N ARG A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 338 removed outlier: 3.886A pdb=" N VAL A 335 " --> pdb=" O MET A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.684A pdb=" N GLN A 354 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 389 removed outlier: 3.738A pdb=" N ASP A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 362 " --> pdb=" O GLN A 358 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 376 " --> pdb=" O ARG A 372 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 381 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN A 382 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 407 through 422 removed outlier: 3.565A pdb=" N LEU A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 446 removed outlier: 3.790A pdb=" N ARG A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.935A pdb=" N LYS A 453 " --> pdb=" O ARG A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.715A pdb=" N LEU A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 483 removed outlier: 4.016A pdb=" N LYS A 476 " --> pdb=" O ASN A 472 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 505 removed outlier: 4.235A pdb=" N GLN A 499 " --> pdb=" O GLY A 495 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TRP A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 534 through 558 removed outlier: 3.626A pdb=" N GLN A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 573 removed outlier: 3.704A pdb=" N LEU A 572 " --> pdb=" O GLN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 597 removed outlier: 3.671A pdb=" N LEU A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 586 " --> pdb=" O ASP A 582 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 597 " --> pdb=" O GLN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.881A pdb=" N ILE A 606 " --> pdb=" O THR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 650 removed outlier: 3.931A pdb=" N GLU A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU A 624 " --> pdb=" O PRO A 620 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 626 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 685 removed outlier: 3.705A pdb=" N GLN A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Proline residue: A 673 - end of helix Processing helix chain 'A' and resid 688 through 717 removed outlier: 4.058A pdb=" N ASN A 705 " --> pdb=" O GLN A 701 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 743 removed outlier: 3.961A pdb=" N ASP A 724 " --> pdb=" O LYS A 720 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 731 " --> pdb=" O GLU A 727 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASP A 735 " --> pdb=" O LYS A 731 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LYS A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS A 737 " --> pdb=" O ASP A 733 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 774 removed outlier: 3.576A pdb=" N GLY A 752 " --> pdb=" O MET A 748 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 767 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU A 772 " --> pdb=" O LYS A 768 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A 773 " --> pdb=" O ARG A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 805 removed outlier: 5.316A pdb=" N ALA A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL A 783 " --> pdb=" O PHE A 779 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 787 " --> pdb=" O VAL A 783 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 788 " --> pdb=" O LYS A 784 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER A 795 " --> pdb=" O SER A 791 " (cutoff:3.500A) Proline residue: A 796 - end of helix Processing helix chain 'A' and resid 812 through 836 removed outlier: 3.881A pdb=" N LEU A 818 " --> pdb=" O GLN A 814 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA A 829 " --> pdb=" O LEU A 825 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS A 830 " --> pdb=" O GLY A 826 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 835 " --> pdb=" O VAL A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 978 removed outlier: 4.805A pdb=" N GLU A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1005 removed outlier: 3.558A pdb=" N ALA A 990 " --> pdb=" O ASP A 986 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 995 " --> pdb=" O ALA A 991 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A1002 " --> pdb=" O MET A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1007 No H-bonds generated for 'chain 'A' and resid 1006 through 1007' Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1011 through 1040 removed outlier: 3.525A pdb=" N LEU A1015 " --> pdb=" O THR A1011 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A1022 " --> pdb=" O CYS A1018 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A1024 " --> pdb=" O LYS A1020 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A1039 " --> pdb=" O GLU A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1054 removed outlier: 4.337A pdb=" N GLU A1054 " --> pdb=" O LEU A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1074 removed outlier: 3.981A pdb=" N THR A1058 " --> pdb=" O GLU A1054 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A1059 " --> pdb=" O ARG A1055 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR A1061 " --> pdb=" O PRO A1057 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A1062 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A1068 " --> pdb=" O LYS A1064 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A1069 " --> pdb=" O ILE A1065 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A1070 " --> pdb=" O LEU A1066 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A1071 " --> pdb=" O SER A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1114 removed outlier: 3.671A pdb=" N GLN A1086 " --> pdb=" O GLU A1082 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A1095 " --> pdb=" O LEU A1091 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A1109 " --> pdb=" O THR A1105 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A1110 " --> pdb=" O VAL A1106 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A1114 " --> pdb=" O GLU A1110 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 3.29 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: 2583 1.34 - 1.46: 899 1.46 - 1.57: 4096 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 7654 Sorted by residual: bond pdb=" CB ILE A1056 " pdb=" CG2 ILE A1056 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 bond pdb=" CB PHE A 835 " pdb=" CG PHE A 835 " ideal model delta sigma weight residual 1.502 1.464 0.038 2.30e-02 1.89e+03 2.70e+00 bond pdb=" CG LEU A 250 " pdb=" CD2 LEU A 250 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CB GLN A1062 " pdb=" CG GLN A1062 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.44e+00 bond pdb=" C PRO A 75 " pdb=" N PRO A 76 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.19e-02 7.06e+03 2.43e+00 ... (remaining 7649 not shown) Histogram of bond angle deviations from ideal: 97.63 - 104.89: 138 104.89 - 112.16: 3742 112.16 - 119.43: 2962 119.43 - 126.69: 3414 126.69 - 133.96: 69 Bond angle restraints: 10325 Sorted by residual: angle pdb=" N GLN A 185 " pdb=" CA GLN A 185 " pdb=" C GLN A 185 " ideal model delta sigma weight residual 113.18 107.94 5.24 1.33e+00 5.65e-01 1.55e+01 angle pdb=" CA GLN A 185 " pdb=" C GLN A 185 " pdb=" N GLU A 186 " ideal model delta sigma weight residual 118.22 114.41 3.81 1.03e+00 9.43e-01 1.37e+01 angle pdb=" N GLY A 535 " pdb=" CA GLY A 535 " pdb=" C GLY A 535 " ideal model delta sigma weight residual 112.34 119.86 -7.52 2.04e+00 2.40e-01 1.36e+01 angle pdb=" C ARG A1076 " pdb=" N THR A1077 " pdb=" CA THR A1077 " ideal model delta sigma weight residual 121.54 128.37 -6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" C LEU A 967 " pdb=" N ALA A 968 " pdb=" CA ALA A 968 " ideal model delta sigma weight residual 125.66 131.99 -6.33 1.85e+00 2.92e-01 1.17e+01 ... (remaining 10320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 4396 15.29 - 30.58: 345 30.58 - 45.87: 88 45.87 - 61.16: 7 61.16 - 76.45: 8 Dihedral angle restraints: 4844 sinusoidal: 1958 harmonic: 2886 Sorted by residual: dihedral pdb=" CA ASP A 447 " pdb=" C ASP A 447 " pdb=" N LEU A 448 " pdb=" CA LEU A 448 " ideal model delta harmonic sigma weight residual 180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA ALA A 490 " pdb=" C ALA A 490 " pdb=" N VAL A 491 " pdb=" CA VAL A 491 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA VAL A 658 " pdb=" C VAL A 658 " pdb=" N GLU A 659 " pdb=" CA GLU A 659 " ideal model delta harmonic sigma weight residual 180.00 152.74 27.26 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 4841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 871 0.059 - 0.119: 286 0.119 - 0.178: 45 0.178 - 0.238: 10 0.238 - 0.297: 3 Chirality restraints: 1215 Sorted by residual: chirality pdb=" CB ILE A 730 " pdb=" CA ILE A 730 " pdb=" CG1 ILE A 730 " pdb=" CG2 ILE A 730 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE A1016 " pdb=" CA ILE A1016 " pdb=" CG1 ILE A1016 " pdb=" CG2 ILE A1016 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE A 20 " pdb=" CA ILE A 20 " pdb=" CG1 ILE A 20 " pdb=" CG2 ILE A 20 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1212 not shown) Planarity restraints: 1358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 964 " -0.051 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO A 965 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 965 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 965 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 165 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO A 166 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 166 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 166 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 42 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO A 43 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.036 5.00e-02 4.00e+02 ... (remaining 1355 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1347 2.76 - 3.29: 8566 3.29 - 3.83: 13692 3.83 - 4.36: 17066 4.36 - 4.90: 24489 Nonbonded interactions: 65160 Sorted by model distance: nonbonded pdb=" OD1 ASP A 601 " pdb=" OG1 THR A 604 " model vdw 2.221 2.440 nonbonded pdb=" O HIS A 974 " pdb=" OG1 THR A 978 " model vdw 2.249 2.440 nonbonded pdb=" O ASP A 361 " pdb=" OG1 THR A 364 " model vdw 2.256 2.440 nonbonded pdb=" O HIS A 694 " pdb=" OG1 THR A 697 " model vdw 2.276 2.440 nonbonded pdb=" O VAL A 598 " pdb=" OG1 THR A 602 " model vdw 2.277 2.440 ... (remaining 65155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.010 Extract box with map and model: 3.900 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 23.480 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 0.069 7654 Z= 0.409 Angle : 1.055 11.062 10325 Z= 0.567 Chirality : 0.060 0.297 1215 Planarity : 0.008 0.077 1358 Dihedral : 12.504 76.451 2958 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 0.12 % Allowed : 4.19 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.20 (0.19), residues: 991 helix: -3.52 (0.12), residues: 713 sheet: None (None), residues: 0 loop : -2.51 (0.35), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP A 394 HIS 0.009 0.003 HIS A 27 PHE 0.023 0.004 PHE A 78 TYR 0.016 0.003 TYR A 160 ARG 0.012 0.001 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 224 average time/residue: 0.2591 time to fit residues: 73.6303 Evaluate side-chains 138 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0768 time to fit residues: 1.4234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 632 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 HIS A1093 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7654 Z= 0.229 Angle : 0.711 7.548 10325 Z= 0.379 Chirality : 0.042 0.176 1215 Planarity : 0.006 0.070 1358 Dihedral : 6.445 23.527 1060 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.37 % Allowed : 3.69 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.23), residues: 991 helix: -1.87 (0.16), residues: 771 sheet: None (None), residues: 0 loop : -2.56 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 394 HIS 0.005 0.001 HIS A 636 PHE 0.025 0.002 PHE A 633 TYR 0.023 0.002 TYR A 822 ARG 0.008 0.001 ARG A 669 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 193 average time/residue: 0.2392 time to fit residues: 59.5593 Evaluate side-chains 133 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 30.0000 chunk 24 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN A 399 ASN A 474 GLN ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7654 Z= 0.175 Angle : 0.615 6.747 10325 Z= 0.323 Chirality : 0.041 0.126 1215 Planarity : 0.005 0.064 1358 Dihedral : 5.792 20.968 1060 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.25 % Allowed : 3.94 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.25), residues: 991 helix: -1.10 (0.17), residues: 794 sheet: None (None), residues: 0 loop : -2.50 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 394 HIS 0.004 0.001 HIS A 636 PHE 0.018 0.002 PHE A 817 TYR 0.018 0.002 TYR A 822 ARG 0.003 0.000 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 196 average time/residue: 0.2409 time to fit residues: 60.8009 Evaluate side-chains 141 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 0.1980 chunk 47 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7654 Z= 0.287 Angle : 0.736 9.211 10325 Z= 0.387 Chirality : 0.045 0.223 1215 Planarity : 0.006 0.066 1358 Dihedral : 5.830 22.718 1060 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 33.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.25 % Allowed : 3.69 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.25), residues: 991 helix: -0.78 (0.18), residues: 789 sheet: None (None), residues: 0 loop : -2.40 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 394 HIS 0.004 0.001 HIS A 527 PHE 0.020 0.003 PHE A 835 TYR 0.010 0.002 TYR A 822 ARG 0.005 0.001 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 178 average time/residue: 0.2252 time to fit residues: 52.5060 Evaluate side-chains 131 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 550 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7654 Z= 0.193 Angle : 0.653 6.181 10325 Z= 0.338 Chirality : 0.042 0.163 1215 Planarity : 0.005 0.065 1358 Dihedral : 5.548 20.262 1060 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.49 % Allowed : 2.34 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.26), residues: 991 helix: -0.43 (0.18), residues: 793 sheet: None (None), residues: 0 loop : -2.34 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 394 HIS 0.004 0.001 HIS A 694 PHE 0.015 0.002 PHE A 599 TYR 0.008 0.001 TYR A 822 ARG 0.004 0.000 ARG A 669 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 190 average time/residue: 0.2323 time to fit residues: 57.8696 Evaluate side-chains 139 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1163 time to fit residues: 1.4953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 0.5980 chunk 18 optimal weight: 0.0470 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS A1039 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7654 Z= 0.191 Angle : 0.651 6.797 10325 Z= 0.336 Chirality : 0.042 0.132 1215 Planarity : 0.005 0.065 1358 Dihedral : 5.387 20.136 1060 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.12 % Allowed : 2.83 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 991 helix: -0.26 (0.18), residues: 793 sheet: None (None), residues: 0 loop : -2.27 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 394 HIS 0.004 0.001 HIS A 694 PHE 0.013 0.002 PHE A 835 TYR 0.009 0.001 TYR A 822 ARG 0.008 0.001 ARG A 669 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 190 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.2309 time to fit residues: 57.5626 Evaluate side-chains 136 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 492 HIS ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7654 Z= 0.215 Angle : 0.676 7.440 10325 Z= 0.351 Chirality : 0.043 0.217 1215 Planarity : 0.005 0.065 1358 Dihedral : 5.411 19.589 1060 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 25.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.12 % Allowed : 2.09 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.26), residues: 991 helix: -0.18 (0.18), residues: 789 sheet: None (None), residues: 0 loop : -2.16 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 394 HIS 0.005 0.001 HIS A 694 PHE 0.013 0.002 PHE A 835 TYR 0.008 0.001 TYR A 822 ARG 0.011 0.001 ARG A 669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.2180 time to fit residues: 52.2645 Evaluate side-chains 133 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.833 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 0.0970 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN A 474 GLN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7654 Z= 0.199 Angle : 0.676 7.861 10325 Z= 0.347 Chirality : 0.043 0.159 1215 Planarity : 0.005 0.065 1358 Dihedral : 5.288 19.107 1060 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 23.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.12 % Allowed : 0.86 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.27), residues: 991 helix: -0.14 (0.18), residues: 794 sheet: None (None), residues: 0 loop : -1.94 (0.46), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 394 HIS 0.005 0.001 HIS A 694 PHE 0.010 0.002 PHE A 633 TYR 0.011 0.001 TYR A 822 ARG 0.009 0.001 ARG A 832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.2162 time to fit residues: 53.7883 Evaluate side-chains 137 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.953 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 84 optimal weight: 0.0270 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN A 474 GLN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7654 Z= 0.189 Angle : 0.703 11.265 10325 Z= 0.353 Chirality : 0.043 0.177 1215 Planarity : 0.005 0.062 1358 Dihedral : 5.248 26.365 1060 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.12 % Allowed : 1.35 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.27), residues: 991 helix: -0.06 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -2.00 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 394 HIS 0.006 0.001 HIS A 694 PHE 0.010 0.001 PHE A 633 TYR 0.008 0.001 TYR A 822 ARG 0.012 0.001 ARG A 669 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 187 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.2468 time to fit residues: 60.2553 Evaluate side-chains 150 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 0.0020 chunk 62 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7654 Z= 0.196 Angle : 0.717 13.374 10325 Z= 0.357 Chirality : 0.044 0.311 1215 Planarity : 0.005 0.063 1358 Dihedral : 5.085 18.935 1060 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.27), residues: 991 helix: 0.03 (0.18), residues: 794 sheet: None (None), residues: 0 loop : -1.82 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 253 HIS 0.002 0.001 HIS A 22 PHE 0.017 0.002 PHE A 599 TYR 0.008 0.001 TYR A 822 ARG 0.010 0.001 ARG A 759 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.2186 time to fit residues: 53.4039 Evaluate side-chains 139 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 GLN ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS A1039 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.150991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.133416 restraints weight = 44439.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.135336 restraints weight = 29478.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.136703 restraints weight = 21277.533| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7654 Z= 0.185 Angle : 0.686 8.547 10325 Z= 0.344 Chirality : 0.042 0.208 1215 Planarity : 0.005 0.060 1358 Dihedral : 4.976 18.817 1060 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.12 % Allowed : 0.99 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.27), residues: 991 helix: 0.18 (0.19), residues: 795 sheet: None (None), residues: 0 loop : -1.79 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 253 HIS 0.006 0.001 HIS A 694 PHE 0.013 0.001 PHE A 599 TYR 0.008 0.001 TYR A 822 ARG 0.013 0.001 ARG A 669 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1921.86 seconds wall clock time: 35 minutes 34.85 seconds (2134.85 seconds total)