Starting phenix.real_space_refine on Tue Mar 3 17:26:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ktv_23031/03_2026/7ktv_23031.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ktv_23031/03_2026/7ktv_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/cci-nas-00/data/ceres_data/7ktv_23031/03_2026/7ktv_23031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ktv_23031/03_2026/7ktv_23031.map" model { file = "/net/cci-nas-00/data/ceres_data/7ktv_23031/03_2026/7ktv_23031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ktv_23031/03_2026/7ktv_23031.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.60, per 1000 atoms: 0.21 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 - 3.00 Amino acid : True - 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: 0.72 Conformation dependent library (CDL) restraints added in 253.7 milliseconds 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: 0.21 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: 0.99 Time building geometry restraints manager: 0.96 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: 0.00 - 2.21: 9855 2.21 - 4.42: 391 4.42 - 6.64: 57 6.64 - 8.85: 19 8.85 - 11.06: 3 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 3.040 nonbonded pdb=" O HIS A 974 " pdb=" OG1 THR A 978 " model vdw 2.249 3.040 nonbonded pdb=" O ASP A 361 " pdb=" OG1 THR A 364 " model vdw 2.256 3.040 nonbonded pdb=" O HIS A 694 " pdb=" OG1 THR A 697 " model vdw 2.276 3.040 nonbonded pdb=" O VAL A 598 " pdb=" OG1 THR A 602 " model vdw 2.277 3.040 ... (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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.140 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.330 ------------------------------------------------------------------------------- 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= 0.293 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.012 0.001 ARG A 409 TYR 0.016 0.003 TYR A 160 PHE 0.023 0.004 PHE A 78 TRP 0.038 0.004 TRP A 394 HIS 0.009 0.003 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00629 ( 7654) covalent geometry : angle 1.05511 (10325) hydrogen bonds : bond 0.31291 ( 490) hydrogen bonds : angle 9.75266 ( 1464) *********************** 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 to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.224 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: 0.1061 time to fit residues: 30.1714 Evaluate side-chains 148 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 550 GLN A 554 GLN A 632 ASN A 694 HIS ** A1048 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.087637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.068346 restraints weight = 37836.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.070001 restraints weight = 29515.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.071256 restraints weight = 24306.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.072194 restraints weight = 20817.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.072959 restraints weight = 18465.768| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7654 Z= 0.195 Angle : 0.733 8.086 10325 Z= 0.391 Chirality : 0.043 0.180 1215 Planarity : 0.007 0.066 1358 Dihedral : 6.568 24.902 1060 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.23), residues: 991 helix: -2.02 (0.15), residues: 771 sheet: None (None), residues: 0 loop : -2.42 (0.44), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 832 TYR 0.022 0.002 TYR A 822 PHE 0.028 0.003 PHE A 633 TRP 0.034 0.002 TRP A 394 HIS 0.004 0.001 HIS A 694 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 7654) covalent geometry : angle 0.73253 (10325) hydrogen bonds : bond 0.06091 ( 490) hydrogen bonds : angle 6.22856 ( 1464) *********************** 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 199 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 0.261 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: 0.9162 (mm-30) cc_final: 0.8689 (tp30) REVERT: A 74 MET cc_start: 0.8928 (tpt) cc_final: 0.8523 (tpt) REVERT: A 94 MET cc_start: 0.9398 (mtt) cc_final: 0.8872 (mtp) REVERT: A 107 TYR cc_start: 0.8596 (m-10) cc_final: 0.8128 (m-10) REVERT: A 131 VAL cc_start: 0.9589 (m) cc_final: 0.9316 (m) REVERT: A 156 ASP cc_start: 0.9070 (t70) cc_final: 0.8649 (p0) REVERT: A 170 LYS cc_start: 0.9464 (mmtm) cc_final: 0.9199 (mmtm) REVERT: A 196 ASN cc_start: 0.9349 (m110) cc_final: 0.9114 (m110) REVERT: A 244 ILE cc_start: 0.9586 (pt) cc_final: 0.9262 (mm) REVERT: A 377 MET cc_start: 0.8807 (ttt) cc_final: 0.7886 (ppp) REVERT: A 382 GLN cc_start: 0.9579 (mp10) cc_final: 0.9152 (mp10) REVERT: A 388 ILE cc_start: 0.8930 (pt) cc_final: 0.8567 (mm) REVERT: A 465 GLN cc_start: 0.9507 (mt0) cc_final: 0.9287 (mt0) REVERT: A 501 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7959 (tm-30) REVERT: A 503 TRP cc_start: 0.8750 (t60) cc_final: 0.8471 (t60) REVERT: A 563 GLU cc_start: 0.9441 (pm20) cc_final: 0.9099 (pp20) REVERT: A 659 GLU cc_start: 0.9370 (mm-30) cc_final: 0.9108 (mm-30) REVERT: A 703 ILE cc_start: 0.8608 (mt) cc_final: 0.8317 (mt) REVERT: A 708 LYS cc_start: 0.9504 (ttpt) cc_final: 0.9280 (ptmt) REVERT: A 792 LYS cc_start: 0.9394 (mmtt) cc_final: 0.9067 (pptt) REVERT: A 1001 MET cc_start: 0.9176 (ptt) cc_final: 0.8471 (ppp) REVERT: A 1018 CYS cc_start: 0.9278 (t) cc_final: 0.8983 (m) REVERT: A 1059 ILE cc_start: 0.9067 (mm) cc_final: 0.8789 (mm) REVERT: A 1090 MET cc_start: 0.8956 (mmt) cc_final: 0.8612 (mmm) REVERT: A 1096 GLN cc_start: 0.9202 (tm-30) cc_final: 0.8907 (tm-30) outliers start: 3 outliers final: 0 residues processed: 198 average time/residue: 0.0945 time to fit residues: 24.1632 Evaluate side-chains 142 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 60 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN A 399 ASN ** A 506 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.091931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.071892 restraints weight = 36423.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.073701 restraints weight = 28119.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.075122 restraints weight = 22902.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.076192 restraints weight = 19369.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.077058 restraints weight = 17045.747| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3915 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= 0.134 Angle : 0.633 6.998 10325 Z= 0.333 Chirality : 0.041 0.132 1215 Planarity : 0.006 0.066 1358 Dihedral : 5.816 18.984 1060 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.25 % Allowed : 3.69 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.24), residues: 991 helix: -1.24 (0.16), residues: 775 sheet: None (None), residues: 0 loop : -2.32 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 832 TYR 0.021 0.002 TYR A 822 PHE 0.026 0.003 PHE A 633 TRP 0.033 0.002 TRP A 394 HIS 0.005 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7654) covalent geometry : angle 0.63324 (10325) hydrogen bonds : bond 0.04342 ( 490) hydrogen bonds : angle 5.41224 ( 1464) *********************** 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 209 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 207 time to evaluate : 0.272 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 74 MET cc_start: 0.8658 (tpt) cc_final: 0.8293 (tpt) REVERT: A 94 MET cc_start: 0.9367 (mtt) cc_final: 0.9021 (mtp) REVERT: A 107 TYR cc_start: 0.8510 (m-10) cc_final: 0.8308 (m-10) REVERT: A 115 ILE cc_start: 0.8912 (mm) cc_final: 0.8648 (mm) REVERT: A 173 LYS cc_start: 0.9571 (pptt) cc_final: 0.9223 (tptt) REVERT: A 177 GLU cc_start: 0.9530 (mm-30) cc_final: 0.9249 (tp30) REVERT: A 244 ILE cc_start: 0.9530 (pt) cc_final: 0.9245 (mm) REVERT: A 246 ARG cc_start: 0.8706 (tpt170) cc_final: 0.8418 (tpt170) REVERT: A 341 ARG cc_start: 0.7127 (tmt-80) cc_final: 0.6548 (ptt90) REVERT: A 377 MET cc_start: 0.8684 (ttt) cc_final: 0.7848 (ppp) REVERT: A 382 GLN cc_start: 0.9583 (mp10) cc_final: 0.9249 (mp10) REVERT: A 388 ILE cc_start: 0.8926 (pt) cc_final: 0.8604 (mm) REVERT: A 545 CYS cc_start: 0.9260 (m) cc_final: 0.8874 (t) REVERT: A 547 ARG cc_start: 0.8509 (tpt170) cc_final: 0.8236 (tpm170) REVERT: A 563 GLU cc_start: 0.9386 (pm20) cc_final: 0.9078 (pp20) REVERT: A 659 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9131 (mm-30) REVERT: A 698 MET cc_start: 0.9527 (mmp) cc_final: 0.9006 (mmm) REVERT: A 708 LYS cc_start: 0.9431 (ttpt) cc_final: 0.9117 (ptmt) REVERT: A 792 LYS cc_start: 0.9408 (mmtt) cc_final: 0.9020 (mmmm) REVERT: A 1001 MET cc_start: 0.8964 (ptt) cc_final: 0.8525 (ptt) REVERT: A 1018 CYS cc_start: 0.9251 (t) cc_final: 0.8908 (m) REVERT: A 1078 ASN cc_start: 0.8484 (p0) cc_final: 0.8022 (p0) REVERT: A 1090 MET cc_start: 0.8845 (mmt) cc_final: 0.8463 (mmt) REVERT: A 1096 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8828 (tm-30) outliers start: 2 outliers final: 0 residues processed: 208 average time/residue: 0.0985 time to fit residues: 26.3984 Evaluate side-chains 151 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS A 838 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.093190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.072893 restraints weight = 37114.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.074789 restraints weight = 28557.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.076285 restraints weight = 23191.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.077430 restraints weight = 19581.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.078335 restraints weight = 17101.087| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4537 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= 0.134 Angle : 0.634 9.219 10325 Z= 0.328 Chirality : 0.042 0.238 1215 Planarity : 0.005 0.063 1358 Dihedral : 5.434 18.637 1060 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.37 % Allowed : 3.08 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.25), residues: 991 helix: -0.75 (0.17), residues: 796 sheet: None (None), residues: 0 loop : -2.19 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 669 TYR 0.010 0.001 TYR A 822 PHE 0.015 0.002 PHE A 633 TRP 0.030 0.002 TRP A 394 HIS 0.003 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7654) covalent geometry : angle 0.63404 (10325) hydrogen bonds : bond 0.03855 ( 490) hydrogen bonds : angle 5.08596 ( 1464) *********************** 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 207 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 0.196 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 82 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8625 (mt-10) REVERT: A 94 MET cc_start: 0.9340 (mtt) cc_final: 0.8997 (mtp) REVERT: A 115 ILE cc_start: 0.8900 (mm) cc_final: 0.8641 (mm) REVERT: A 136 ARG cc_start: 0.9322 (mpt90) cc_final: 0.9055 (mmt90) REVERT: A 173 LYS cc_start: 0.9530 (pptt) cc_final: 0.9016 (pptt) REVERT: A 205 LEU cc_start: 0.9674 (mm) cc_final: 0.9456 (mm) REVERT: A 244 ILE cc_start: 0.9525 (pt) cc_final: 0.9292 (mm) REVERT: A 246 ARG cc_start: 0.8705 (tpt170) cc_final: 0.8400 (tpt170) REVERT: A 377 MET cc_start: 0.8606 (ttt) cc_final: 0.7748 (ppp) REVERT: A 382 GLN cc_start: 0.9572 (mp10) cc_final: 0.9279 (mp10) REVERT: A 388 ILE cc_start: 0.8938 (pt) cc_final: 0.8656 (mm) REVERT: A 545 CYS cc_start: 0.9207 (m) cc_final: 0.8849 (t) REVERT: A 547 ARG cc_start: 0.8556 (tpt170) cc_final: 0.8210 (tpm170) REVERT: A 563 GLU cc_start: 0.9365 (pm20) cc_final: 0.9067 (pp20) REVERT: A 633 PHE cc_start: 0.8960 (t80) cc_final: 0.8740 (t80) REVERT: A 659 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9132 (mm-30) REVERT: A 669 ARG cc_start: 0.9283 (ttm110) cc_final: 0.8905 (ptp-110) REVERT: A 708 LYS cc_start: 0.9437 (ttpt) cc_final: 0.9188 (ptmt) REVERT: A 737 CYS cc_start: 0.9279 (t) cc_final: 0.8993 (t) REVERT: A 792 LYS cc_start: 0.9425 (mmtt) cc_final: 0.9009 (mmmt) REVERT: A 1018 CYS cc_start: 0.9245 (t) cc_final: 0.8961 (m) REVERT: A 1090 MET cc_start: 0.8794 (mmt) cc_final: 0.8426 (mmt) outliers start: 3 outliers final: 0 residues processed: 205 average time/residue: 0.0944 time to fit residues: 25.2185 Evaluate side-chains 155 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 ASN ** 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 A1097 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.094169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.073859 restraints weight = 37205.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.075719 restraints weight = 28928.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.077152 restraints weight = 23627.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.078240 restraints weight = 20082.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.079140 restraints weight = 17670.775| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7654 Z= 0.125 Angle : 0.625 7.161 10325 Z= 0.321 Chirality : 0.042 0.237 1215 Planarity : 0.005 0.063 1358 Dihedral : 5.222 18.126 1060 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.12 % Allowed : 1.97 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.26), residues: 991 helix: -0.31 (0.18), residues: 797 sheet: None (None), residues: 0 loop : -2.04 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 669 TYR 0.009 0.001 TYR A 822 PHE 0.029 0.002 PHE A 599 TRP 0.036 0.002 TRP A 394 HIS 0.003 0.001 HIS A 694 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 7654) covalent geometry : angle 0.62488 (10325) hydrogen bonds : bond 0.03488 ( 490) hydrogen bonds : angle 4.85111 ( 1464) *********************** 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 205 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.309 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 82 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8605 (mt-10) REVERT: A 94 MET cc_start: 0.9347 (mtt) cc_final: 0.8942 (mtp) REVERT: A 115 ILE cc_start: 0.8880 (mm) cc_final: 0.8625 (mm) REVERT: A 134 ILE cc_start: 0.9366 (mp) cc_final: 0.9143 (pt) REVERT: A 135 ILE cc_start: 0.9481 (pt) cc_final: 0.9235 (pt) REVERT: A 136 ARG cc_start: 0.9328 (mpt90) cc_final: 0.9114 (mpt-90) REVERT: A 173 LYS cc_start: 0.9397 (pptt) cc_final: 0.8959 (pptt) REVERT: A 177 GLU cc_start: 0.9100 (mp0) cc_final: 0.8225 (mp0) REVERT: A 244 ILE cc_start: 0.9553 (pt) cc_final: 0.9334 (mm) REVERT: A 246 ARG cc_start: 0.8705 (tpt170) cc_final: 0.8409 (tpt170) REVERT: A 253 TRP cc_start: 0.6113 (m100) cc_final: 0.5466 (m100) REVERT: A 377 MET cc_start: 0.8577 (ttt) cc_final: 0.7710 (ppp) REVERT: A 382 GLN cc_start: 0.9558 (mp10) cc_final: 0.9270 (mp10) REVERT: A 388 ILE cc_start: 0.8919 (pt) cc_final: 0.8638 (mm) REVERT: A 545 CYS cc_start: 0.9190 (m) cc_final: 0.8849 (t) REVERT: A 547 ARG cc_start: 0.8527 (tpt170) cc_final: 0.8173 (tpm170) REVERT: A 563 GLU cc_start: 0.9396 (pm20) cc_final: 0.9092 (pp20) REVERT: A 599 PHE cc_start: 0.8252 (m-10) cc_final: 0.7977 (m-10) REVERT: A 633 PHE cc_start: 0.8883 (t80) cc_final: 0.8585 (t80) REVERT: A 634 GLU cc_start: 0.9642 (pt0) cc_final: 0.9360 (pp20) REVERT: A 635 ASN cc_start: 0.9767 (t0) cc_final: 0.9540 (t0) REVERT: A 659 GLU cc_start: 0.9361 (mm-30) cc_final: 0.9134 (mm-30) REVERT: A 669 ARG cc_start: 0.9293 (ttm110) cc_final: 0.8966 (ptp-110) REVERT: A 708 LYS cc_start: 0.9420 (ttpt) cc_final: 0.9169 (ptmt) REVERT: A 723 LEU cc_start: 0.8592 (mp) cc_final: 0.8283 (mp) REVERT: A 741 MET cc_start: 0.8983 (mmp) cc_final: 0.8738 (mmm) REVERT: A 748 MET cc_start: 0.9299 (mmm) cc_final: 0.8888 (mmm) REVERT: A 792 LYS cc_start: 0.9404 (mmtt) cc_final: 0.8984 (mmmt) REVERT: A 998 MET cc_start: 0.7820 (mmt) cc_final: 0.7181 (mmt) REVERT: A 1018 CYS cc_start: 0.9152 (t) cc_final: 0.8919 (m) REVERT: A 1038 LYS cc_start: 0.9000 (pptt) cc_final: 0.8739 (ptpt) REVERT: A 1078 ASN cc_start: 0.8394 (p0) cc_final: 0.8081 (p0) REVERT: A 1090 MET cc_start: 0.8763 (mmt) cc_final: 0.8399 (mmt) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.1008 time to fit residues: 26.4336 Evaluate side-chains 166 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 HIS A1039 GLN A1097 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.090275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.070672 restraints weight = 38443.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.072426 restraints weight = 30016.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.073811 restraints weight = 24608.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.074837 restraints weight = 20968.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.075695 restraints weight = 18449.609| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7654 Z= 0.174 Angle : 0.674 8.868 10325 Z= 0.348 Chirality : 0.043 0.213 1215 Planarity : 0.005 0.066 1358 Dihedral : 5.294 17.740 1060 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.26), residues: 991 helix: -0.22 (0.18), residues: 793 sheet: None (None), residues: 0 loop : -1.67 (0.49), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 669 TYR 0.011 0.001 TYR A 822 PHE 0.022 0.003 PHE A 599 TRP 0.039 0.002 TRP A 394 HIS 0.004 0.001 HIS A 694 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7654) covalent geometry : angle 0.67396 (10325) hydrogen bonds : bond 0.03799 ( 490) hydrogen bonds : angle 4.94402 ( 1464) *********************** 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 196 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8010 (pmm) cc_final: 0.7730 (pmm) REVERT: A 82 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8665 (mt-10) REVERT: A 94 MET cc_start: 0.9272 (mtt) cc_final: 0.8854 (mtp) REVERT: A 115 ILE cc_start: 0.8926 (mm) cc_final: 0.8713 (mm) REVERT: A 136 ARG cc_start: 0.9305 (mpt90) cc_final: 0.9065 (mmt90) REVERT: A 173 LYS cc_start: 0.9425 (pptt) cc_final: 0.9120 (pptt) REVERT: A 176 ASP cc_start: 0.9591 (m-30) cc_final: 0.9387 (m-30) REVERT: A 244 ILE cc_start: 0.9564 (pt) cc_final: 0.9343 (mm) REVERT: A 246 ARG cc_start: 0.8749 (tpt170) cc_final: 0.8279 (tpt170) REVERT: A 249 GLN cc_start: 0.9366 (mt0) cc_final: 0.9127 (mt0) REVERT: A 377 MET cc_start: 0.8635 (ttt) cc_final: 0.7721 (ppp) REVERT: A 382 GLN cc_start: 0.9573 (mp10) cc_final: 0.9190 (mp10) REVERT: A 388 ILE cc_start: 0.9106 (pt) cc_final: 0.8774 (mm) REVERT: A 545 CYS cc_start: 0.9237 (m) cc_final: 0.8869 (t) REVERT: A 547 ARG cc_start: 0.8497 (tpt170) cc_final: 0.8041 (tpm170) REVERT: A 563 GLU cc_start: 0.9503 (pm20) cc_final: 0.9165 (pp20) REVERT: A 633 PHE cc_start: 0.8919 (t80) cc_final: 0.8488 (t80) REVERT: A 634 GLU cc_start: 0.9632 (pt0) cc_final: 0.9358 (pt0) REVERT: A 659 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9147 (mm-30) REVERT: A 669 ARG cc_start: 0.9322 (ttm110) cc_final: 0.8949 (ptp-110) REVERT: A 694 HIS cc_start: 0.9503 (m90) cc_final: 0.9295 (m-70) REVERT: A 708 LYS cc_start: 0.9446 (ttpt) cc_final: 0.9208 (ptmt) REVERT: A 737 CYS cc_start: 0.9155 (t) cc_final: 0.8676 (t) REVERT: A 741 MET cc_start: 0.9019 (mmp) cc_final: 0.8818 (mmm) REVERT: A 792 LYS cc_start: 0.9405 (mmtt) cc_final: 0.8951 (mmmm) REVERT: A 799 MET cc_start: 0.9537 (ptp) cc_final: 0.9258 (ptp) REVERT: A 818 LEU cc_start: 0.9568 (mm) cc_final: 0.9290 (mm) REVERT: A 1018 CYS cc_start: 0.9350 (t) cc_final: 0.9022 (m) REVERT: A 1078 ASN cc_start: 0.8455 (p0) cc_final: 0.8216 (p0) REVERT: A 1090 MET cc_start: 0.8789 (mmt) cc_final: 0.8450 (mmt) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.0930 time to fit residues: 23.7159 Evaluate side-chains 152 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 65 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 0.0980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN A 506 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.093882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.073907 restraints weight = 37798.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.075772 restraints weight = 29369.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.077241 restraints weight = 23946.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.078363 restraints weight = 20306.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.079256 restraints weight = 17766.112| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7654 Z= 0.138 Angle : 0.655 6.466 10325 Z= 0.339 Chirality : 0.042 0.163 1215 Planarity : 0.005 0.066 1358 Dihedral : 5.213 18.127 1060 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.27), residues: 991 helix: -0.06 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -1.65 (0.49), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 268 TYR 0.010 0.001 TYR A 822 PHE 0.021 0.002 PHE A 599 TRP 0.034 0.002 TRP A 394 HIS 0.002 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7654) covalent geometry : angle 0.65453 (10325) hydrogen bonds : bond 0.03471 ( 490) hydrogen bonds : angle 4.89405 ( 1464) *********************** 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 203 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8621 (mt-10) REVERT: A 94 MET cc_start: 0.9268 (mtt) cc_final: 0.8824 (mtt) REVERT: A 115 ILE cc_start: 0.8848 (mm) cc_final: 0.8618 (mm) REVERT: A 136 ARG cc_start: 0.9310 (mpt90) cc_final: 0.9086 (mpt-90) REVERT: A 154 MET cc_start: 0.8652 (tpt) cc_final: 0.7501 (mpp) REVERT: A 173 LYS cc_start: 0.9494 (pptt) cc_final: 0.9207 (pptt) REVERT: A 174 MET cc_start: 0.9069 (mtm) cc_final: 0.8325 (ptt) REVERT: A 177 GLU cc_start: 0.9194 (mp0) cc_final: 0.8531 (mp0) REVERT: A 377 MET cc_start: 0.8510 (ttt) cc_final: 0.7403 (ppp) REVERT: A 382 GLN cc_start: 0.9558 (mp10) cc_final: 0.9286 (mp10) REVERT: A 388 ILE cc_start: 0.9032 (pt) cc_final: 0.8656 (mm) REVERT: A 545 CYS cc_start: 0.9176 (m) cc_final: 0.8834 (t) REVERT: A 547 ARG cc_start: 0.8515 (tpt170) cc_final: 0.8133 (tpm170) REVERT: A 563 GLU cc_start: 0.9472 (pm20) cc_final: 0.9137 (pp20) REVERT: A 633 PHE cc_start: 0.8797 (t80) cc_final: 0.8462 (t80) REVERT: A 634 GLU cc_start: 0.9610 (pt0) cc_final: 0.9335 (pp20) REVERT: A 635 ASN cc_start: 0.9779 (t0) cc_final: 0.9533 (t0) REVERT: A 659 GLU cc_start: 0.9348 (mm-30) cc_final: 0.9147 (mm-30) REVERT: A 669 ARG cc_start: 0.9260 (ttm110) cc_final: 0.8833 (ptp-110) REVERT: A 694 HIS cc_start: 0.9478 (m90) cc_final: 0.9244 (m-70) REVERT: A 708 LYS cc_start: 0.9445 (ttpt) cc_final: 0.9177 (ptmt) REVERT: A 712 LEU cc_start: 0.9383 (mm) cc_final: 0.8898 (tp) REVERT: A 748 MET cc_start: 0.9347 (mmm) cc_final: 0.8971 (mmm) REVERT: A 792 LYS cc_start: 0.9380 (mmtt) cc_final: 0.8944 (mmmm) REVERT: A 797 MET cc_start: 0.8534 (ppp) cc_final: 0.8159 (ppp) REVERT: A 818 LEU cc_start: 0.9555 (mm) cc_final: 0.9306 (mm) REVERT: A 998 MET cc_start: 0.7485 (mmt) cc_final: 0.6977 (mmt) REVERT: A 1038 LYS cc_start: 0.9016 (pptt) cc_final: 0.8688 (ptpt) REVERT: A 1090 MET cc_start: 0.8756 (mmt) cc_final: 0.8379 (mmt) REVERT: A 1099 MET cc_start: 0.8457 (mmt) cc_final: 0.8242 (mmm) REVERT: A 1101 SER cc_start: 0.9633 (m) cc_final: 0.9408 (p) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.0982 time to fit residues: 25.8598 Evaluate side-chains 158 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN A 506 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.092318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.072627 restraints weight = 37916.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.074496 restraints weight = 29283.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.075932 restraints weight = 23824.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.077043 restraints weight = 20164.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.077905 restraints weight = 17637.318| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7654 Z= 0.150 Angle : 0.669 7.320 10325 Z= 0.344 Chirality : 0.042 0.146 1215 Planarity : 0.005 0.066 1358 Dihedral : 5.096 17.823 1060 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.27), residues: 991 helix: 0.08 (0.18), residues: 791 sheet: None (None), residues: 0 loop : -1.54 (0.50), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 268 TYR 0.010 0.001 TYR A 822 PHE 0.019 0.002 PHE A 599 TRP 0.035 0.002 TRP A 394 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 7654) covalent geometry : angle 0.66856 (10325) hydrogen bonds : bond 0.03535 ( 490) hydrogen bonds : angle 4.79818 ( 1464) *********************** 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 194 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.278 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: 0.9168 (mt-10) cc_final: 0.8626 (mt-10) REVERT: A 94 MET cc_start: 0.9186 (mtt) cc_final: 0.8776 (mtt) REVERT: A 115 ILE cc_start: 0.8852 (mm) cc_final: 0.8613 (mm) REVERT: A 135 ILE cc_start: 0.9455 (pt) cc_final: 0.9223 (pt) REVERT: A 136 ARG cc_start: 0.9316 (mpt90) cc_final: 0.9055 (mmt90) REVERT: A 173 LYS cc_start: 0.9469 (pptt) cc_final: 0.9240 (pptt) REVERT: A 174 MET cc_start: 0.9055 (mtm) cc_final: 0.8224 (ptt) REVERT: A 302 ILE cc_start: 0.7129 (mm) cc_final: 0.6708 (mm) REVERT: A 377 MET cc_start: 0.8491 (ttt) cc_final: 0.7581 (ppp) REVERT: A 382 GLN cc_start: 0.9561 (mp10) cc_final: 0.9290 (mp10) REVERT: A 388 ILE cc_start: 0.8945 (pt) cc_final: 0.8530 (mm) REVERT: A 545 CYS cc_start: 0.9168 (m) cc_final: 0.8834 (t) REVERT: A 563 GLU cc_start: 0.9510 (pm20) cc_final: 0.9162 (pp20) REVERT: A 633 PHE cc_start: 0.8820 (t80) cc_final: 0.8434 (t80) REVERT: A 634 GLU cc_start: 0.9599 (pt0) cc_final: 0.9320 (pp20) REVERT: A 635 ASN cc_start: 0.9775 (t0) cc_final: 0.9540 (t0) REVERT: A 645 GLU cc_start: 0.9543 (mt-10) cc_final: 0.9131 (mt-10) REVERT: A 659 GLU cc_start: 0.9362 (mm-30) cc_final: 0.9150 (mm-30) REVERT: A 669 ARG cc_start: 0.9224 (ttm110) cc_final: 0.8841 (ptp-110) REVERT: A 694 HIS cc_start: 0.9483 (m90) cc_final: 0.9243 (m-70) REVERT: A 708 LYS cc_start: 0.9445 (ttpt) cc_final: 0.9181 (ptmt) REVERT: A 737 CYS cc_start: 0.9141 (t) cc_final: 0.8706 (t) REVERT: A 741 MET cc_start: 0.9095 (mmp) cc_final: 0.8815 (mmm) REVERT: A 792 LYS cc_start: 0.9346 (mmtt) cc_final: 0.8899 (mmmm) REVERT: A 797 MET cc_start: 0.8613 (ppp) cc_final: 0.8294 (ppp) REVERT: A 1018 CYS cc_start: 0.9400 (m) cc_final: 0.9168 (m) REVERT: A 1078 ASN cc_start: 0.8439 (p0) cc_final: 0.8182 (p0) REVERT: A 1090 MET cc_start: 0.8829 (mmt) cc_final: 0.8492 (mmt) REVERT: A 1099 MET cc_start: 0.8441 (mmt) cc_final: 0.8170 (mmm) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.0903 time to fit residues: 22.8681 Evaluate side-chains 149 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN ** A 636 HIS ** 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 = 0.3956 r_free = 0.3956 target = 0.092034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.072463 restraints weight = 37638.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.074300 restraints weight = 29267.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.075708 restraints weight = 23783.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.076814 restraints weight = 20128.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.077682 restraints weight = 17584.188| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7654 Z= 0.160 Angle : 0.671 7.194 10325 Z= 0.346 Chirality : 0.043 0.142 1215 Planarity : 0.005 0.067 1358 Dihedral : 5.178 19.812 1060 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.27), residues: 991 helix: 0.11 (0.18), residues: 789 sheet: None (None), residues: 0 loop : -1.32 (0.51), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 975 TYR 0.009 0.002 TYR A 822 PHE 0.013 0.002 PHE A 835 TRP 0.015 0.002 TRP A 394 HIS 0.005 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7654) covalent geometry : angle 0.67059 (10325) hydrogen bonds : bond 0.03607 ( 490) hydrogen bonds : angle 4.86022 ( 1464) *********************** 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 189 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8635 (mt-10) REVERT: A 94 MET cc_start: 0.9172 (mtt) cc_final: 0.8762 (mtt) REVERT: A 136 ARG cc_start: 0.9338 (mpt90) cc_final: 0.9031 (mmt90) REVERT: A 154 MET cc_start: 0.8730 (tpt) cc_final: 0.7398 (mpp) REVERT: A 173 LYS cc_start: 0.9464 (pptt) cc_final: 0.9124 (pptt) REVERT: A 174 MET cc_start: 0.9093 (mtm) cc_final: 0.8400 (ptt) REVERT: A 177 GLU cc_start: 0.9174 (mp0) cc_final: 0.8433 (mp0) REVERT: A 377 MET cc_start: 0.8483 (ttt) cc_final: 0.7583 (ppp) REVERT: A 382 GLN cc_start: 0.9562 (mp10) cc_final: 0.9299 (mp10) REVERT: A 388 ILE cc_start: 0.8894 (pt) cc_final: 0.8423 (mm) REVERT: A 465 GLN cc_start: 0.9503 (mt0) cc_final: 0.9209 (mm110) REVERT: A 501 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7542 (tm-30) REVERT: A 545 CYS cc_start: 0.9159 (m) cc_final: 0.8864 (t) REVERT: A 563 GLU cc_start: 0.9542 (pm20) cc_final: 0.9338 (pm20) REVERT: A 633 PHE cc_start: 0.8904 (t80) cc_final: 0.8484 (t80) REVERT: A 634 GLU cc_start: 0.9601 (pt0) cc_final: 0.9326 (pp20) REVERT: A 635 ASN cc_start: 0.9795 (t0) cc_final: 0.9551 (t0) REVERT: A 645 GLU cc_start: 0.9566 (mt-10) cc_final: 0.9196 (mt-10) REVERT: A 659 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9151 (mm-30) REVERT: A 694 HIS cc_start: 0.9513 (m90) cc_final: 0.9267 (m-70) REVERT: A 708 LYS cc_start: 0.9476 (ttpt) cc_final: 0.9232 (ptmt) REVERT: A 741 MET cc_start: 0.9044 (mmp) cc_final: 0.8720 (mmm) REVERT: A 748 MET cc_start: 0.9336 (mmm) cc_final: 0.8920 (mmm) REVERT: A 792 LYS cc_start: 0.9361 (mmtt) cc_final: 0.8913 (mmmm) REVERT: A 799 MET cc_start: 0.9505 (ptp) cc_final: 0.9148 (ptp) REVERT: A 1018 CYS cc_start: 0.9329 (m) cc_final: 0.9107 (m) REVERT: A 1034 LYS cc_start: 0.9019 (mmtm) cc_final: 0.8670 (mmtt) REVERT: A 1078 ASN cc_start: 0.8496 (p0) cc_final: 0.8222 (p0) REVERT: A 1090 MET cc_start: 0.8843 (mmt) cc_final: 0.8503 (mmt) REVERT: A 1099 MET cc_start: 0.8440 (mmt) cc_final: 0.8008 (mmm) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.0920 time to fit residues: 22.8998 Evaluate side-chains 143 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 34 optimal weight: 0.0470 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN ** 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 = 0.4537 r_free = 0.4537 target = 0.146970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.134327 restraints weight = 42228.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.136267 restraints weight = 27481.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.137624 restraints weight = 19661.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.138611 restraints weight = 15036.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.139240 restraints weight = 12117.083| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7654 Z= 0.129 Angle : 0.669 7.605 10325 Z= 0.340 Chirality : 0.042 0.151 1215 Planarity : 0.005 0.066 1358 Dihedral : 4.936 17.145 1060 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.27), residues: 991 helix: 0.18 (0.18), residues: 798 sheet: None (None), residues: 0 loop : -1.17 (0.53), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 586 TYR 0.020 0.002 TYR A 144 PHE 0.008 0.001 PHE A 599 TRP 0.011 0.001 TRP A 394 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7654) covalent geometry : angle 0.66887 (10325) hydrogen bonds : bond 0.03314 ( 490) hydrogen bonds : angle 4.70108 ( 1464) ********************** 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 196 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.279 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: A 1 MET cc_start: 0.7923 (pmm) cc_final: 0.7675 (pmm) REVERT: A 82 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8465 (mt-10) REVERT: A 94 MET cc_start: 0.9142 (mtt) cc_final: 0.8579 (mtt) REVERT: A 115 ILE cc_start: 0.8793 (mm) cc_final: 0.8552 (mm) REVERT: A 132 ARG cc_start: 0.9248 (mtm-85) cc_final: 0.7985 (mtm-85) REVERT: A 136 ARG cc_start: 0.9315 (mpt90) cc_final: 0.9108 (mmt90) REVERT: A 154 MET cc_start: 0.8283 (tpt) cc_final: 0.7204 (mpp) REVERT: A 173 LYS cc_start: 0.9470 (pptt) cc_final: 0.9062 (pptt) REVERT: A 177 GLU cc_start: 0.9159 (mp0) cc_final: 0.8368 (mp0) REVERT: A 247 VAL cc_start: 0.9401 (t) cc_final: 0.9112 (t) REVERT: A 253 TRP cc_start: 0.5922 (m100) cc_final: 0.5337 (m100) REVERT: A 377 MET cc_start: 0.8297 (ttt) cc_final: 0.7459 (ppp) REVERT: A 382 GLN cc_start: 0.9517 (mp10) cc_final: 0.9265 (mp10) REVERT: A 388 ILE cc_start: 0.8876 (pt) cc_final: 0.8411 (mm) REVERT: A 465 GLN cc_start: 0.9468 (mt0) cc_final: 0.9156 (mm110) REVERT: A 533 MET cc_start: 0.8109 (mpp) cc_final: 0.7655 (mpp) REVERT: A 534 MET cc_start: 0.8301 (mmp) cc_final: 0.7547 (pmm) REVERT: A 545 CYS cc_start: 0.8987 (m) cc_final: 0.8784 (t) REVERT: A 547 ARG cc_start: 0.8462 (tpt170) cc_final: 0.8052 (tpm170) REVERT: A 563 GLU cc_start: 0.9404 (pm20) cc_final: 0.9033 (pp20) REVERT: A 609 LEU cc_start: 0.9527 (mt) cc_final: 0.9320 (mt) REVERT: A 626 PHE cc_start: 0.8033 (t80) cc_final: 0.7246 (t80) REVERT: A 628 GLU cc_start: 0.9570 (mp0) cc_final: 0.9332 (pm20) REVERT: A 633 PHE cc_start: 0.8750 (t80) cc_final: 0.8348 (t80) REVERT: A 634 GLU cc_start: 0.9556 (pt0) cc_final: 0.9255 (pp20) REVERT: A 635 ASN cc_start: 0.9752 (t0) cc_final: 0.9485 (t0) REVERT: A 645 GLU cc_start: 0.9513 (mt-10) cc_final: 0.9019 (mt-10) REVERT: A 659 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9184 (mm-30) REVERT: A 669 ARG cc_start: 0.9350 (ptp-110) cc_final: 0.8841 (ptt-90) REVERT: A 694 HIS cc_start: 0.9408 (m90) cc_final: 0.9096 (m-70) REVERT: A 708 LYS cc_start: 0.9464 (ttpt) cc_final: 0.9233 (ptmt) REVERT: A 737 CYS cc_start: 0.9094 (t) cc_final: 0.8476 (t) REVERT: A 741 MET cc_start: 0.8988 (mmp) cc_final: 0.8721 (mmm) REVERT: A 792 LYS cc_start: 0.9364 (mmtt) cc_final: 0.8922 (mmmm) REVERT: A 799 MET cc_start: 0.9463 (ptp) cc_final: 0.9076 (ptp) REVERT: A 818 LEU cc_start: 0.9550 (mm) cc_final: 0.9336 (mm) REVERT: A 1034 LYS cc_start: 0.8869 (mmtm) cc_final: 0.8349 (mmtt) REVERT: A 1090 MET cc_start: 0.8763 (mmt) cc_final: 0.8427 (mmt) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.0971 time to fit residues: 24.4359 Evaluate side-chains 157 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN ** A 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 GLN ** 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 = 0.4015 r_free = 0.4015 target = 0.094970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.075274 restraints weight = 36808.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.077084 restraints weight = 28688.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.078531 restraints weight = 23480.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.079677 restraints weight = 19864.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.080571 restraints weight = 17338.595| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7654 Z= 0.142 Angle : 0.671 7.663 10325 Z= 0.344 Chirality : 0.043 0.145 1215 Planarity : 0.005 0.064 1358 Dihedral : 4.916 19.077 1060 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.27), residues: 991 helix: 0.19 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -1.21 (0.54), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 300 TYR 0.021 0.002 TYR A 144 PHE 0.021 0.002 PHE A 599 TRP 0.011 0.001 TRP A 394 HIS 0.004 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 7654) covalent geometry : angle 0.67148 (10325) hydrogen bonds : bond 0.03423 ( 490) hydrogen bonds : angle 4.77722 ( 1464) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1344.75 seconds wall clock time: 24 minutes 1.13 seconds (1441.13 seconds total)