Starting phenix.real_space_refine on Mon Mar 11 07:28:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktv_23031/03_2024/7ktv_23031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktv_23031/03_2024/7ktv_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_23031/03_2024/7ktv_23031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktv_23031/03_2024/7ktv_23031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktv_23031/03_2024/7ktv_23031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ktv_23031/03_2024/7ktv_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-dev-5265/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: 4.55, per 1000 atoms: 0.60 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: 2.93 Conformation dependent library (CDL) restraints added in 1.4 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: 0.89 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: 2.33 Time building geometry restraints manager: 3.19 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 3.880 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.260 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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: 32.100 ------------------------------------------------------------------------------- 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 : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8437 (tp30) REVERT: A 74 MET cc_start: 0.9029 (tpt) cc_final: 0.8609 (tpt) REVERT: A 82 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8774 (mt-10) REVERT: A 94 MET cc_start: 0.9550 (mtt) cc_final: 0.9131 (mtp) REVERT: A 107 TYR cc_start: 0.8572 (m-10) cc_final: 0.8035 (m-10) REVERT: A 168 MET cc_start: 0.9358 (ttt) cc_final: 0.9074 (tpp) REVERT: A 170 LYS cc_start: 0.9568 (mmtm) cc_final: 0.9355 (mmtm) REVERT: A 196 ASN cc_start: 0.9308 (m110) cc_final: 0.8737 (m110) REVERT: A 244 ILE cc_start: 0.9664 (pt) cc_final: 0.9428 (mm) REVERT: A 382 GLN cc_start: 0.9520 (mp-120) cc_final: 0.9113 (mp10) REVERT: A 388 ILE cc_start: 0.8854 (pt) cc_final: 0.8446 (mm) REVERT: A 485 ARG cc_start: 0.8363 (mmp80) cc_final: 0.8110 (mmm160) REVERT: A 503 TRP cc_start: 0.8460 (t60) cc_final: 0.8136 (t60) REVERT: A 639 LYS cc_start: 0.8958 (pttt) cc_final: 0.8684 (pttp) REVERT: A 643 THR cc_start: 0.9491 (p) cc_final: 0.8983 (p) REVERT: A 659 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9040 (mm-30) REVERT: A 698 MET cc_start: 0.9642 (mmp) cc_final: 0.9422 (mmm) REVERT: A 708 LYS cc_start: 0.9483 (ttpt) cc_final: 0.9247 (ptmt) REVERT: A 792 LYS cc_start: 0.9379 (mmtt) cc_final: 0.9015 (pttp) REVERT: A 835 PHE cc_start: 0.8810 (m-80) cc_final: 0.8561 (m-80) REVERT: A 1018 CYS cc_start: 0.9270 (t) cc_final: 0.8970 (m) REVERT: A 1059 ILE cc_start: 0.8877 (mm) cc_final: 0.8534 (mm) REVERT: A 1090 MET cc_start: 0.8943 (mmt) cc_final: 0.8619 (mmt) REVERT: A 1096 GLN cc_start: 0.9245 (tm-30) cc_final: 0.9001 (tm-30) outliers start: 1 outliers final: 1 residues processed: 224 average time/residue: 0.2506 time to fit residues: 70.9822 Evaluate side-chains 148 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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: 1.9990 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN A 399 ASN A 474 GLN A 506 ASN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7654 Z= 0.197 Angle : 0.673 7.742 10325 Z= 0.355 Chirality : 0.041 0.169 1215 Planarity : 0.006 0.072 1358 Dihedral : 6.407 22.731 1060 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: -3.50 (0.23), residues: 991 helix: -2.01 (0.15), residues: 775 sheet: None (None), residues: 0 loop : -2.71 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 394 HIS 0.004 0.001 HIS A 636 PHE 0.026 0.002 PHE A 633 TYR 0.022 0.002 TYR A 822 ARG 0.013 0.001 ARG A1044 *********************** 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 200 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8701 (tp30) REVERT: A 74 MET cc_start: 0.8811 (tpt) cc_final: 0.8469 (tpt) REVERT: A 94 MET cc_start: 0.9366 (mtt) cc_final: 0.8824 (mtp) REVERT: A 107 TYR cc_start: 0.8522 (m-10) cc_final: 0.8051 (m-10) REVERT: A 174 MET cc_start: 0.9276 (mtm) cc_final: 0.8415 (mtm) REVERT: A 180 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8731 (mm-40) REVERT: A 196 ASN cc_start: 0.9296 (m110) cc_final: 0.9054 (m-40) REVERT: A 244 ILE cc_start: 0.9569 (pt) cc_final: 0.9298 (mm) REVERT: A 246 ARG cc_start: 0.8567 (tpt170) cc_final: 0.8143 (tpt170) REVERT: A 266 MET cc_start: 0.7552 (ttm) cc_final: 0.6748 (tmm) REVERT: A 377 MET cc_start: 0.8555 (ttt) cc_final: 0.7880 (ppp) REVERT: A 382 GLN cc_start: 0.9572 (mp10) cc_final: 0.9047 (mp10) REVERT: A 388 ILE cc_start: 0.8864 (pt) cc_final: 0.8489 (mm) REVERT: A 474 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8429 (pp30) REVERT: A 545 CYS cc_start: 0.9160 (m) cc_final: 0.8687 (t) REVERT: A 563 GLU cc_start: 0.9294 (pm20) cc_final: 0.8979 (pp20) REVERT: A 669 ARG cc_start: 0.8877 (ttm110) cc_final: 0.8545 (ptp-110) REVERT: A 703 ILE cc_start: 0.8537 (mt) cc_final: 0.8283 (mt) REVERT: A 708 LYS cc_start: 0.9363 (ttpt) cc_final: 0.9124 (ptmt) REVERT: A 792 LYS cc_start: 0.9370 (mmtt) cc_final: 0.9034 (pptt) REVERT: A 835 PHE cc_start: 0.8798 (m-80) cc_final: 0.8598 (m-80) REVERT: A 1001 MET cc_start: 0.9137 (ptt) cc_final: 0.8233 (ppp) REVERT: A 1018 CYS cc_start: 0.9243 (t) cc_final: 0.8916 (m) REVERT: A 1059 ILE cc_start: 0.9019 (mm) cc_final: 0.8735 (mm) REVERT: A 1090 MET cc_start: 0.8898 (mmt) cc_final: 0.8548 (mmm) REVERT: A 1096 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8901 (tm-30) outliers start: 3 outliers final: 0 residues processed: 199 average time/residue: 0.2438 time to fit residues: 61.7963 Evaluate side-chains 144 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 61 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 355 GLN 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3754 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= 0.178 Angle : 0.604 6.672 10325 Z= 0.317 Chirality : 0.040 0.129 1215 Planarity : 0.005 0.066 1358 Dihedral : 5.774 21.070 1060 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.25 % Allowed : 3.08 % Favored : 96.67 % 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: -2.35 (0.25), residues: 991 helix: -1.12 (0.17), residues: 787 sheet: None (None), residues: 0 loop : -2.66 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 394 HIS 0.005 0.001 HIS A 636 PHE 0.020 0.002 PHE A 817 TYR 0.020 0.002 TYR A 822 ARG 0.004 0.000 ARG A 669 *********************** 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 204 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.9298 (mtt) cc_final: 0.8947 (mtp) REVERT: A 107 TYR cc_start: 0.8510 (m-10) cc_final: 0.8231 (m-10) REVERT: A 115 ILE cc_start: 0.8840 (mm) cc_final: 0.8600 (mm) REVERT: A 173 LYS cc_start: 0.9549 (pptt) cc_final: 0.9194 (tptt) REVERT: A 177 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9224 (tp30) REVERT: A 244 ILE cc_start: 0.9495 (pt) cc_final: 0.9226 (mm) REVERT: A 246 ARG cc_start: 0.8567 (tpt170) cc_final: 0.8186 (tpt170) REVERT: A 320 GLU cc_start: 0.9228 (pt0) cc_final: 0.8993 (pt0) REVERT: A 377 MET cc_start: 0.8404 (ttt) cc_final: 0.7700 (ppp) REVERT: A 382 GLN cc_start: 0.9568 (mp10) cc_final: 0.9105 (mp10) REVERT: A 388 ILE cc_start: 0.8871 (pt) cc_final: 0.8548 (mm) REVERT: A 545 CYS cc_start: 0.9152 (m) cc_final: 0.8818 (t) REVERT: A 563 GLU cc_start: 0.9294 (pm20) cc_final: 0.9019 (pp20) REVERT: A 633 PHE cc_start: 0.8816 (t80) cc_final: 0.8339 (t80) REVERT: A 659 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8903 (mm-30) REVERT: A 669 ARG cc_start: 0.8841 (ttm110) cc_final: 0.8532 (ptp-110) REVERT: A 708 LYS cc_start: 0.9317 (ttpt) cc_final: 0.9023 (ptmt) REVERT: A 719 THR cc_start: 0.8894 (m) cc_final: 0.8605 (m) REVERT: A 792 LYS cc_start: 0.9402 (mmtt) cc_final: 0.9013 (mmmm) REVERT: A 835 PHE cc_start: 0.8746 (m-80) cc_final: 0.8515 (m-80) REVERT: A 1001 MET cc_start: 0.9031 (ptt) cc_final: 0.8517 (ptt) REVERT: A 1018 CYS cc_start: 0.9224 (t) cc_final: 0.8838 (m) REVERT: A 1059 ILE cc_start: 0.9018 (mm) cc_final: 0.8749 (mm) REVERT: A 1090 MET cc_start: 0.8742 (mmt) cc_final: 0.8398 (mmt) REVERT: A 1096 GLN cc_start: 0.9275 (tm-30) cc_final: 0.9001 (tm-30) outliers start: 2 outliers final: 0 residues processed: 203 average time/residue: 0.2245 time to fit residues: 59.1497 Evaluate side-chains 150 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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: 10.0000 chunk 67 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN 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 ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7654 Z= 0.187 Angle : 0.615 6.138 10325 Z= 0.320 Chirality : 0.041 0.242 1215 Planarity : 0.005 0.064 1358 Dihedral : 5.435 20.418 1060 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 22.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.37 % Allowed : 3.45 % Favored : 96.18 % 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: -1.60 (0.26), residues: 991 helix: -0.58 (0.18), residues: 790 sheet: None (None), residues: 0 loop : -2.47 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 394 HIS 0.003 0.001 HIS A 694 PHE 0.015 0.002 PHE A 817 TYR 0.011 0.001 TYR A 822 ARG 0.004 0.000 ARG A 823 *********************** 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 205 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 202 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8619 (mt-10) REVERT: A 94 MET cc_start: 0.9255 (mtt) cc_final: 0.8913 (mtp) REVERT: A 107 TYR cc_start: 0.8563 (m-10) cc_final: 0.8313 (m-10) REVERT: A 115 ILE cc_start: 0.8890 (mm) cc_final: 0.8656 (mm) REVERT: A 135 ILE cc_start: 0.9207 (pt) cc_final: 0.8995 (pt) REVERT: A 173 LYS cc_start: 0.9537 (pptt) cc_final: 0.9053 (pptt) REVERT: A 174 MET cc_start: 0.9035 (mtm) cc_final: 0.8301 (mtm) REVERT: A 244 ILE cc_start: 0.9497 (pt) cc_final: 0.9195 (mm) REVERT: A 246 ARG cc_start: 0.8555 (tpt170) cc_final: 0.8186 (tpt170) REVERT: A 247 VAL cc_start: 0.9475 (t) cc_final: 0.9261 (t) REVERT: A 308 LYS cc_start: 0.8973 (mmpt) cc_final: 0.8706 (mmtm) REVERT: A 377 MET cc_start: 0.8435 (ttt) cc_final: 0.7723 (ppp) REVERT: A 382 GLN cc_start: 0.9588 (mp10) cc_final: 0.9126 (mp10) REVERT: A 388 ILE cc_start: 0.8888 (pt) cc_final: 0.8578 (mm) REVERT: A 501 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 545 CYS cc_start: 0.9129 (m) cc_final: 0.8844 (t) REVERT: A 547 ARG cc_start: 0.8548 (tpt170) cc_final: 0.8303 (mmp80) REVERT: A 563 GLU cc_start: 0.9312 (pm20) cc_final: 0.9033 (pp20) REVERT: A 591 MET cc_start: 0.9356 (tpt) cc_final: 0.9073 (tpt) REVERT: A 593 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8817 (tp40) REVERT: A 633 PHE cc_start: 0.8836 (t80) cc_final: 0.8372 (t80) REVERT: A 659 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8911 (mm-30) REVERT: A 669 ARG cc_start: 0.8823 (ttm110) cc_final: 0.8595 (ptp-110) REVERT: A 698 MET cc_start: 0.9443 (mmp) cc_final: 0.8815 (mmm) REVERT: A 708 LYS cc_start: 0.9337 (ttpt) cc_final: 0.9133 (ptmt) REVERT: A 719 THR cc_start: 0.8880 (m) cc_final: 0.8651 (m) REVERT: A 737 CYS cc_start: 0.9261 (t) cc_final: 0.8937 (t) REVERT: A 792 LYS cc_start: 0.9419 (mmtt) cc_final: 0.9006 (mmmm) REVERT: A 818 LEU cc_start: 0.9655 (mm) cc_final: 0.9424 (mm) REVERT: A 1001 MET cc_start: 0.8860 (ptt) cc_final: 0.8649 (ppp) REVERT: A 1018 CYS cc_start: 0.9290 (t) cc_final: 0.8928 (m) REVERT: A 1090 MET cc_start: 0.8722 (mmt) cc_final: 0.8372 (mmt) REVERT: A 1096 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8967 (tm-30) outliers start: 3 outliers final: 0 residues processed: 203 average time/residue: 0.2223 time to fit residues: 58.9225 Evaluate side-chains 159 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7654 Z= 0.163 Angle : 0.598 7.415 10325 Z= 0.305 Chirality : 0.040 0.199 1215 Planarity : 0.005 0.064 1358 Dihedral : 5.176 18.340 1060 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.37 % Allowed : 1.60 % Favored : 98.03 % 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: -1.13 (0.26), residues: 991 helix: -0.26 (0.18), residues: 795 sheet: None (None), residues: 0 loop : -2.33 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 394 HIS 0.003 0.001 HIS A 636 PHE 0.030 0.003 PHE A 599 TYR 0.008 0.001 TYR A 822 ARG 0.003 0.000 ARG A 113 *********************** 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 206 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8611 (mt-10) REVERT: A 94 MET cc_start: 0.9228 (mtt) cc_final: 0.8889 (mtp) REVERT: A 115 ILE cc_start: 0.8801 (mm) cc_final: 0.8549 (mm) REVERT: A 132 ARG cc_start: 0.9133 (mtm-85) cc_final: 0.7929 (mtm-85) REVERT: A 173 LYS cc_start: 0.9534 (pptt) cc_final: 0.8782 (tptt) REVERT: A 177 GLU cc_start: 0.9529 (mm-30) cc_final: 0.8971 (mm-30) REVERT: A 190 MET cc_start: 0.8484 (ptp) cc_final: 0.8235 (ptp) REVERT: A 201 LEU cc_start: 0.9479 (mp) cc_final: 0.9223 (mt) REVERT: A 244 ILE cc_start: 0.9486 (pt) cc_final: 0.9269 (mm) REVERT: A 246 ARG cc_start: 0.8479 (tpt170) cc_final: 0.8190 (tpt170) REVERT: A 247 VAL cc_start: 0.9299 (t) cc_final: 0.9087 (t) REVERT: A 377 MET cc_start: 0.8235 (ttt) cc_final: 0.7546 (ppp) REVERT: A 382 GLN cc_start: 0.9567 (mp10) cc_final: 0.9226 (mp10) REVERT: A 388 ILE cc_start: 0.8874 (pt) cc_final: 0.8555 (mm) REVERT: A 501 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 547 ARG cc_start: 0.8526 (tpt170) cc_final: 0.8291 (mmp80) REVERT: A 563 GLU cc_start: 0.9289 (pm20) cc_final: 0.9045 (pp20) REVERT: A 591 MET cc_start: 0.9162 (tpt) cc_final: 0.8895 (tpt) REVERT: A 599 PHE cc_start: 0.8385 (m-10) cc_final: 0.7750 (m-10) REVERT: A 633 PHE cc_start: 0.8777 (t80) cc_final: 0.8341 (t80) REVERT: A 634 GLU cc_start: 0.9596 (pt0) cc_final: 0.9319 (pp20) REVERT: A 635 ASN cc_start: 0.9760 (t0) cc_final: 0.9553 (t0) REVERT: A 669 ARG cc_start: 0.8812 (ttm110) cc_final: 0.8584 (ptp-110) REVERT: A 708 LYS cc_start: 0.9321 (ttpt) cc_final: 0.8932 (ptmm) REVERT: A 748 MET cc_start: 0.9157 (mmm) cc_final: 0.8820 (mmm) REVERT: A 754 THR cc_start: 0.9256 (p) cc_final: 0.8695 (p) REVERT: A 792 LYS cc_start: 0.9388 (mmtt) cc_final: 0.8989 (mmmt) REVERT: A 1018 CYS cc_start: 0.9198 (t) cc_final: 0.8839 (m) REVERT: A 1038 LYS cc_start: 0.9041 (pptt) cc_final: 0.8791 (ptpt) REVERT: A 1078 ASN cc_start: 0.8458 (p0) cc_final: 0.8189 (p0) REVERT: A 1090 MET cc_start: 0.8705 (mmt) cc_final: 0.8406 (mmt) outliers start: 3 outliers final: 0 residues processed: 204 average time/residue: 0.2498 time to fit residues: 65.9817 Evaluate side-chains 167 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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: 7.9990 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 354 GLN ** 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 636 HIS ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5029 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= 0.172 Angle : 0.605 7.323 10325 Z= 0.312 Chirality : 0.041 0.148 1215 Planarity : 0.005 0.064 1358 Dihedral : 5.022 17.427 1060 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.12 % Allowed : 2.22 % Favored : 97.66 % 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: -0.80 (0.27), residues: 991 helix: -0.06 (0.18), residues: 795 sheet: None (None), residues: 0 loop : -2.07 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 394 HIS 0.005 0.001 HIS A 694 PHE 0.013 0.002 PHE A 599 TYR 0.010 0.001 TYR A 822 ARG 0.006 0.000 ARG A 136 *********************** 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 202 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8140 (pmm) cc_final: 0.7882 (pmm) REVERT: A 82 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8617 (mt-10) REVERT: A 94 MET cc_start: 0.9230 (mtt) cc_final: 0.8505 (mtt) REVERT: A 115 ILE cc_start: 0.8754 (mm) cc_final: 0.8499 (mm) REVERT: A 244 ILE cc_start: 0.9488 (pt) cc_final: 0.9286 (mm) REVERT: A 247 VAL cc_start: 0.9336 (t) cc_final: 0.9108 (t) REVERT: A 377 MET cc_start: 0.8343 (ttt) cc_final: 0.7639 (ppp) REVERT: A 382 GLN cc_start: 0.9565 (mp10) cc_final: 0.9249 (mp10) REVERT: A 388 ILE cc_start: 0.8849 (pt) cc_final: 0.8539 (mm) REVERT: A 501 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 547 ARG cc_start: 0.8533 (tpt170) cc_final: 0.8289 (mmp80) REVERT: A 563 GLU cc_start: 0.9285 (pm20) cc_final: 0.9026 (pp20) REVERT: A 599 PHE cc_start: 0.8575 (m-10) cc_final: 0.8152 (m-10) REVERT: A 633 PHE cc_start: 0.8734 (t80) cc_final: 0.8327 (t80) REVERT: A 634 GLU cc_start: 0.9584 (pt0) cc_final: 0.9320 (pp20) REVERT: A 659 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8890 (mm-30) REVERT: A 669 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8589 (ptp-110) REVERT: A 694 HIS cc_start: 0.9518 (m90) cc_final: 0.9305 (m-70) REVERT: A 708 LYS cc_start: 0.9310 (ttpt) cc_final: 0.9070 (ptmt) REVERT: A 741 MET cc_start: 0.8991 (mmp) cc_final: 0.8782 (mmm) REVERT: A 792 LYS cc_start: 0.9388 (mmtt) cc_final: 0.8946 (mmmm) REVERT: A 799 MET cc_start: 0.9545 (ptp) cc_final: 0.9258 (ptp) REVERT: A 818 LEU cc_start: 0.9608 (mm) cc_final: 0.9329 (mm) REVERT: A 1018 CYS cc_start: 0.9318 (t) cc_final: 0.8864 (m) REVERT: A 1078 ASN cc_start: 0.8481 (p0) cc_final: 0.8257 (p0) REVERT: A 1090 MET cc_start: 0.8622 (mmt) cc_final: 0.8292 (mmt) REVERT: A 1096 GLN cc_start: 0.9377 (pm20) cc_final: 0.9131 (pm20) outliers start: 1 outliers final: 0 residues processed: 202 average time/residue: 0.2238 time to fit residues: 58.4721 Evaluate side-chains 163 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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: 2.9990 chunk 10 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 506 ASN ** 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 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7654 Z= 0.217 Angle : 0.636 7.347 10325 Z= 0.330 Chirality : 0.042 0.134 1215 Planarity : 0.005 0.066 1358 Dihedral : 5.107 17.923 1060 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 24.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.12 % Allowed : 2.22 % Favored : 97.66 % 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: -0.78 (0.27), residues: 991 helix: -0.04 (0.18), residues: 782 sheet: None (None), residues: 0 loop : -1.93 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 253 HIS 0.005 0.001 HIS A 527 PHE 0.020 0.002 PHE A 599 TYR 0.011 0.001 TYR A 822 ARG 0.005 0.001 ARG A 113 *********************** 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 192 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8180 (pmm) cc_final: 0.7836 (pmm) REVERT: A 82 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8632 (mt-10) REVERT: A 94 MET cc_start: 0.9116 (mtt) cc_final: 0.8851 (mtt) REVERT: A 244 ILE cc_start: 0.9528 (pt) cc_final: 0.9281 (mm) REVERT: A 246 ARG cc_start: 0.8491 (tpt170) cc_final: 0.8158 (tpt170) REVERT: A 377 MET cc_start: 0.8357 (ttt) cc_final: 0.7427 (ppp) REVERT: A 380 SER cc_start: 0.9405 (m) cc_final: 0.9159 (p) REVERT: A 388 ILE cc_start: 0.8862 (pt) cc_final: 0.8515 (mm) REVERT: A 501 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 547 ARG cc_start: 0.8542 (tpt170) cc_final: 0.8269 (mmp80) REVERT: A 563 GLU cc_start: 0.9398 (pm20) cc_final: 0.9071 (pp20) REVERT: A 588 GLN cc_start: 0.8847 (mt0) cc_final: 0.8641 (mp10) REVERT: A 633 PHE cc_start: 0.8768 (t80) cc_final: 0.8332 (t80) REVERT: A 634 GLU cc_start: 0.9603 (pt0) cc_final: 0.9330 (pp20) REVERT: A 635 ASN cc_start: 0.9781 (t0) cc_final: 0.9579 (t0) REVERT: A 669 ARG cc_start: 0.8879 (ttm110) cc_final: 0.8506 (ptp-110) REVERT: A 694 HIS cc_start: 0.9477 (m90) cc_final: 0.9252 (m-70) REVERT: A 708 LYS cc_start: 0.9342 (ttpt) cc_final: 0.9101 (ptmt) REVERT: A 737 CYS cc_start: 0.9292 (t) cc_final: 0.8947 (t) REVERT: A 792 LYS cc_start: 0.9391 (mmtt) cc_final: 0.8951 (mmmm) REVERT: A 797 MET cc_start: 0.8644 (ppp) cc_final: 0.8288 (ppp) REVERT: A 818 LEU cc_start: 0.9623 (mm) cc_final: 0.9417 (mm) REVERT: A 1018 CYS cc_start: 0.9365 (t) cc_final: 0.8955 (m) REVERT: A 1078 ASN cc_start: 0.8525 (p0) cc_final: 0.8246 (p0) REVERT: A 1090 MET cc_start: 0.8707 (mmt) cc_final: 0.8394 (mmt) outliers start: 1 outliers final: 0 residues processed: 192 average time/residue: 0.2167 time to fit residues: 54.2910 Evaluate side-chains 152 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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: 0.4980 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 354 GLN ** 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 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7654 Z= 0.165 Angle : 0.615 6.835 10325 Z= 0.315 Chirality : 0.041 0.149 1215 Planarity : 0.004 0.065 1358 Dihedral : 4.955 19.784 1060 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.12 % Allowed : 1.23 % Favored : 98.65 % 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: -0.53 (0.27), residues: 991 helix: 0.09 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -1.76 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 253 HIS 0.003 0.001 HIS A 636 PHE 0.007 0.001 PHE A 126 TYR 0.010 0.001 TYR A 822 ARG 0.004 0.000 ARG A 136 *********************** 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 197 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.9103 (mtt) cc_final: 0.8597 (mtt) REVERT: A 115 ILE cc_start: 0.8717 (mm) cc_final: 0.8478 (mm) REVERT: A 135 ILE cc_start: 0.9282 (pt) cc_final: 0.8942 (pt) REVERT: A 136 ARG cc_start: 0.8850 (mpp-170) cc_final: 0.8581 (mpt180) REVERT: A 154 MET cc_start: 0.8759 (tpt) cc_final: 0.7561 (mpp) REVERT: A 192 VAL cc_start: 0.9297 (m) cc_final: 0.9094 (p) REVERT: A 246 ARG cc_start: 0.8473 (tpt170) cc_final: 0.8170 (tpt170) REVERT: A 253 TRP cc_start: 0.5418 (m100) cc_final: 0.5162 (m100) REVERT: A 377 MET cc_start: 0.8283 (ttt) cc_final: 0.7348 (ppp) REVERT: A 380 SER cc_start: 0.9391 (m) cc_final: 0.9166 (p) REVERT: A 388 ILE cc_start: 0.8905 (pt) cc_final: 0.8564 (mm) REVERT: A 501 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 547 ARG cc_start: 0.8497 (tpt170) cc_final: 0.8252 (mmp80) REVERT: A 563 GLU cc_start: 0.9342 (pm20) cc_final: 0.9045 (pp20) REVERT: A 588 GLN cc_start: 0.8851 (mt0) cc_final: 0.8635 (mp10) REVERT: A 628 GLU cc_start: 0.9528 (mp0) cc_final: 0.9288 (pm20) REVERT: A 633 PHE cc_start: 0.8689 (t80) cc_final: 0.8284 (t80) REVERT: A 634 GLU cc_start: 0.9596 (pt0) cc_final: 0.9352 (pp20) REVERT: A 640 LEU cc_start: 0.8558 (mp) cc_final: 0.8349 (mp) REVERT: A 669 ARG cc_start: 0.8857 (ttm110) cc_final: 0.8510 (ptp-110) REVERT: A 694 HIS cc_start: 0.9445 (m90) cc_final: 0.9214 (m-70) REVERT: A 708 LYS cc_start: 0.9322 (ttpt) cc_final: 0.9035 (ptmt) REVERT: A 712 LEU cc_start: 0.9277 (mm) cc_final: 0.8799 (tp) REVERT: A 737 CYS cc_start: 0.9317 (t) cc_final: 0.8823 (t) REVERT: A 741 MET cc_start: 0.8954 (mmp) cc_final: 0.8725 (mmm) REVERT: A 748 MET cc_start: 0.9147 (mmm) cc_final: 0.8896 (mmm) REVERT: A 792 LYS cc_start: 0.9387 (mmtt) cc_final: 0.8951 (mmmm) REVERT: A 797 MET cc_start: 0.8475 (ppp) cc_final: 0.8154 (ppp) REVERT: A 818 LEU cc_start: 0.9619 (mm) cc_final: 0.9401 (mm) REVERT: A 1018 CYS cc_start: 0.9237 (t) cc_final: 0.8841 (m) REVERT: A 1090 MET cc_start: 0.8785 (mmt) cc_final: 0.8479 (mmt) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2274 time to fit residues: 58.1971 Evaluate side-chains 153 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.859 ------------------------------------------------------------------------------- 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: 10.0000 chunk 91 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 506 ASN ** 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** A1039 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.5661 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= 0.171 Angle : 0.626 7.675 10325 Z= 0.319 Chirality : 0.041 0.160 1215 Planarity : 0.004 0.065 1358 Dihedral : 4.876 20.737 1060 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % 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: -0.31 (0.27), residues: 991 helix: 0.23 (0.19), residues: 797 sheet: None (None), residues: 0 loop : -1.61 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 394 HIS 0.004 0.001 HIS A 636 PHE 0.014 0.002 PHE A 599 TYR 0.010 0.001 TYR A 822 ARG 0.003 0.000 ARG A 136 *********************** 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 194 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8516 (mt-10) REVERT: A 94 MET cc_start: 0.9067 (mtt) cc_final: 0.8556 (mtt) REVERT: A 154 MET cc_start: 0.8819 (tpt) cc_final: 0.7634 (mpp) REVERT: A 192 VAL cc_start: 0.9353 (m) cc_final: 0.9136 (p) REVERT: A 237 MET cc_start: 0.8395 (mmt) cc_final: 0.8150 (mmm) REVERT: A 246 ARG cc_start: 0.8414 (tpt170) cc_final: 0.8094 (tpt170) REVERT: A 247 VAL cc_start: 0.9350 (t) cc_final: 0.9108 (t) REVERT: A 253 TRP cc_start: 0.5478 (m100) cc_final: 0.5100 (m100) REVERT: A 377 MET cc_start: 0.8106 (ttt) cc_final: 0.7258 (ppp) REVERT: A 380 SER cc_start: 0.9391 (m) cc_final: 0.9174 (p) REVERT: A 388 ILE cc_start: 0.8925 (pt) cc_final: 0.8561 (mm) REVERT: A 501 GLN cc_start: 0.7999 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 533 MET cc_start: 0.7939 (mpp) cc_final: 0.7709 (mpp) REVERT: A 547 ARG cc_start: 0.8532 (tpt170) cc_final: 0.8247 (mmp80) REVERT: A 563 GLU cc_start: 0.9329 (pm20) cc_final: 0.9038 (pp20) REVERT: A 634 GLU cc_start: 0.9593 (pt0) cc_final: 0.9369 (pp20) REVERT: A 669 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8454 (ttm110) REVERT: A 694 HIS cc_start: 0.9440 (m90) cc_final: 0.9214 (m-70) REVERT: A 708 LYS cc_start: 0.9321 (ttpt) cc_final: 0.8905 (ptmm) REVERT: A 712 LEU cc_start: 0.9274 (mm) cc_final: 0.8830 (tp) REVERT: A 737 CYS cc_start: 0.9302 (t) cc_final: 0.9004 (t) REVERT: A 741 MET cc_start: 0.8944 (mmp) cc_final: 0.8701 (mmm) REVERT: A 748 MET cc_start: 0.9182 (mmm) cc_final: 0.8917 (mmm) REVERT: A 797 MET cc_start: 0.8465 (ppp) cc_final: 0.8201 (ppp) REVERT: A 818 LEU cc_start: 0.9613 (mm) cc_final: 0.9405 (mm) REVERT: A 1090 MET cc_start: 0.8775 (mmt) cc_final: 0.8511 (mmt) REVERT: A 1096 GLN cc_start: 0.9390 (pm20) cc_final: 0.9067 (pm20) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.2211 time to fit residues: 55.7661 Evaluate side-chains 153 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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: 5.9990 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 506 ASN ** 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** A1039 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5731 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= 0.208 Angle : 0.649 7.540 10325 Z= 0.333 Chirality : 0.043 0.177 1215 Planarity : 0.004 0.065 1358 Dihedral : 4.930 21.451 1060 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.12 % Allowed : 0.25 % Favored : 99.63 % 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: -0.33 (0.27), residues: 991 helix: 0.20 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -1.53 (0.49), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 702 HIS 0.004 0.001 HIS A 636 PHE 0.013 0.002 PHE A 599 TYR 0.008 0.001 TYR A 822 ARG 0.004 0.000 ARG A 136 ********************** 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 185 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.9060 (mtt) cc_final: 0.8769 (mtt) REVERT: A 135 ILE cc_start: 0.9336 (pt) cc_final: 0.8905 (pt) REVERT: A 136 ARG cc_start: 0.8903 (mpp-170) cc_final: 0.8587 (mpt180) REVERT: A 192 VAL cc_start: 0.9360 (m) cc_final: 0.9133 (p) REVERT: A 253 TRP cc_start: 0.5682 (m100) cc_final: 0.5216 (m100) REVERT: A 377 MET cc_start: 0.8156 (ttt) cc_final: 0.7269 (ppp) REVERT: A 380 SER cc_start: 0.9409 (m) cc_final: 0.9184 (p) REVERT: A 388 ILE cc_start: 0.8896 (pt) cc_final: 0.8508 (mm) REVERT: A 501 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7560 (tm-30) REVERT: A 547 ARG cc_start: 0.8526 (tpt170) cc_final: 0.8210 (mmp80) REVERT: A 563 GLU cc_start: 0.9411 (pm20) cc_final: 0.9084 (pp20) REVERT: A 659 GLU cc_start: 0.8819 (mp0) cc_final: 0.8364 (mp0) REVERT: A 669 ARG cc_start: 0.8885 (ttm110) cc_final: 0.8507 (ptp-110) REVERT: A 694 HIS cc_start: 0.9437 (m90) cc_final: 0.9210 (m-70) REVERT: A 708 LYS cc_start: 0.9338 (ttpt) cc_final: 0.9104 (ptmt) REVERT: A 748 MET cc_start: 0.9185 (mmm) cc_final: 0.8920 (mmm) REVERT: A 792 LYS cc_start: 0.9371 (mmtt) cc_final: 0.9034 (pttp) REVERT: A 799 MET cc_start: 0.9491 (ptp) cc_final: 0.9105 (ppp) REVERT: A 1096 GLN cc_start: 0.9391 (pm20) cc_final: 0.9155 (pm20) outliers start: 1 outliers final: 0 residues processed: 185 average time/residue: 0.2061 time to fit residues: 50.2945 Evaluate side-chains 143 residues out of total 812 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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: 0.8980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 56 optimal weight: 20.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 506 ASN ** 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** A1039 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.092914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.073623 restraints weight = 43516.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.075174 restraints weight = 35091.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.076374 restraints weight = 29740.590| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7654 Z= 0.196 Angle : 0.646 8.616 10325 Z= 0.328 Chirality : 0.042 0.173 1215 Planarity : 0.004 0.065 1358 Dihedral : 4.882 20.265 1060 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.12 % Allowed : 0.25 % Favored : 99.63 % 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: -0.33 (0.27), residues: 991 helix: 0.22 (0.18), residues: 802 sheet: None (None), residues: 0 loop : -1.67 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 394 HIS 0.004 0.001 HIS A 636 PHE 0.013 0.002 PHE A 599 TYR 0.008 0.001 TYR A 822 ARG 0.003 0.000 ARG A 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1940.63 seconds wall clock time: 35 minutes 54.18 seconds (2154.18 seconds total)