Starting phenix.real_space_refine on Fri Sep 11 23:09:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ppj_20440/09_2026/6ppj_20440.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ppj_20440/09_2026/6ppj_20440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ppj_20440/09_2026/6ppj_20440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ppj_20440/09_2026/6ppj_20440.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ppj_20440/09_2026/6ppj_20440.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ppj_20440/09_2026/6ppj_20440.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ppj_20440/09_2026/6ppj_20440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ppj_20440/09_2026/6ppj_20440.cif" } resolution = 3.5 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 3 5.49 5 S 37 5.16 5 C 7621 2.51 5 N 2230 2.21 5 O 2109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12004 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1102 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 8, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 962 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'UNK:plan-1': 11, 'ARG:plan': 3, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2675 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 18, 'TRANS': 375} Chain breaks: 11 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'UNK:plan-1': 16, 'ARG:plan': 11, 'ASN:plan1': 2, 'HIS:plan': 3, 'ASP:plan': 16, 'GLU:plan': 16, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 218 Chain: "B" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 932 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain breaks: 5 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 138 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'UNK:plan-1': 33, 'HIS:plan': 3, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 6209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 901, 6209 Classifications: {'peptide': 901} Incomplete info: {'truncation_to_alanine': 164} Link IDs: {'PTRANS': 54, 'TRANS': 846} Chain breaks: 25 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 611 Unresolved non-hydrogen angles: 764 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLU:plan': 34, 'ASN:plan1': 6, 'ASP:plan': 40, 'GLN:plan1': 11, 'ARG:plan': 27, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 465 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'ANP': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.89, per 1000 atoms: 0.24 Number of scatterers: 12004 At special positions: 0 Unit cell: (144.698, 99.9108, 109.385, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 37 16.00 P 3 15.00 O 2109 8.00 N 2230 7.00 C 7621 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 Links applied TRANS " UNK B 195 " - " ARG B 194 " " UNK B1063 " - " GLY B1062 " Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 617.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1101 " pdb="FE3 SF4 A1101 " - pdb=" SG CYS A1027 " pdb="FE4 SF4 A1101 " - pdb=" SG CYS A 807 " pdb="FE2 SF4 A1101 " - pdb=" SG CYS A1036 " pdb="FE1 SF4 A1101 " - pdb=" SG CYS A1030 " Number of angles added : 12 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3272 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 9 sheets defined 51.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 31 through 36 removed outlier: 3.820A pdb=" N ALA B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 56 through 67 removed outlier: 3.819A pdb=" N VAL B 60 " --> pdb=" O MET B 56 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 66 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 removed outlier: 3.645A pdb=" N ALA B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 119 through 130 removed outlier: 4.326A pdb=" N GLY B 124 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 148 through 153 Processing helix chain 'B' and resid 172 through 180 removed outlier: 3.575A pdb=" N LEU B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 191 through 205 No H-bonds generated for 'chain 'B' and resid 191 through 205' Processing helix chain 'B' and resid 226 through 231 Processing helix chain 'B' and resid 232 through 234 No H-bonds generated for 'chain 'B' and resid 232 through 234' Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.539A pdb=" N ALA B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 3.805A pdb=" N ALA B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 268 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 4.197A pdb=" N GLY B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.662A pdb=" N ASP B 289 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.730A pdb=" N GLN B 320 " --> pdb=" O ASP B 317 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 317 through 321' Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 376 removed outlier: 3.607A pdb=" N UNK B 370 " --> pdb=" O UNK B 366 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N UNK B 371 " --> pdb=" O UNK B 367 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N UNK B 374 " --> pdb=" O UNK B 370 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N UNK B 375 " --> pdb=" O UNK B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.023A pdb=" N ASP B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TRP B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 413 " --> pdb=" O TRP B 409 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 417 " --> pdb=" O HIS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 440 Processing helix chain 'B' and resid 441 through 450 removed outlier: 3.766A pdb=" N GLU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 481 removed outlier: 3.965A pdb=" N MET B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 493 removed outlier: 3.723A pdb=" N VAL B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 493 " --> pdb=" O MET B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 514 removed outlier: 3.554A pdb=" N ALA B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 506 " --> pdb=" O ARG B 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 removed outlier: 3.851A pdb=" N VAL B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 528' Processing helix chain 'B' and resid 558 through 572 removed outlier: 3.550A pdb=" N GLU B 567 " --> pdb=" O ALA B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 577 removed outlier: 4.525A pdb=" N GLY B 576 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 590 removed outlier: 3.888A pdb=" N ARG B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 589 " --> pdb=" O GLU B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 598 removed outlier: 3.538A pdb=" N ALA B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 597 " --> pdb=" O ASP B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 Processing helix chain 'B' and resid 636 through 642 removed outlier: 4.047A pdb=" N GLU B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 Processing helix chain 'B' and resid 735 through 742 Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.984A pdb=" N ASP B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 759 removed outlier: 3.519A pdb=" N THR B 759 " --> pdb=" O TYR B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 794 removed outlier: 4.083A pdb=" N THR B 791 " --> pdb=" O CYS B 787 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 853 removed outlier: 3.648A pdb=" N GLY B 843 " --> pdb=" O HIS B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 876 removed outlier: 3.620A pdb=" N ASP B 869 " --> pdb=" O ALA B 865 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA B 873 " --> pdb=" O ASP B 869 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 876 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 898 Processing helix chain 'B' and resid 903 through 911 removed outlier: 4.079A pdb=" N UNK B 911 " --> pdb=" O UNK B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 935 removed outlier: 4.212A pdb=" N THR B 925 " --> pdb=" O ALA B 921 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 927 " --> pdb=" O LEU B 923 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP B 930 " --> pdb=" O THR B 926 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN B 932 " --> pdb=" O HIS B 928 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 933 " --> pdb=" O GLU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 972 removed outlier: 3.667A pdb=" N SER B 972 " --> pdb=" O ALA B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1043 removed outlier: 4.128A pdb=" N GLN B1033 " --> pdb=" O HIS B1029 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B1034 " --> pdb=" O ALA B1030 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL B1036 " --> pdb=" O VAL B1032 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B1037 " --> pdb=" O GLN B1033 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TRP B1041 " --> pdb=" O TYR B1037 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1080 Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.808A pdb=" N VAL A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A 41 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 45 " --> pdb=" O ASP A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.554A pdb=" N ALA A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 106 removed outlier: 3.838A pdb=" N ALA A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 106 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 124 removed outlier: 3.658A pdb=" N GLN A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.513A pdb=" N ASP A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.869A pdb=" N ALA A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 165 " --> pdb=" O LEU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.722A pdb=" N GLY A 172 " --> pdb=" O THR A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.582A pdb=" N GLN A 179 " --> pdb=" O PRO A 175 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG A 180 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 201 removed outlier: 4.056A pdb=" N LEU A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 removed outlier: 4.772A pdb=" N GLY A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.562A pdb=" N ASN A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.674A pdb=" N HIS A 259 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 319 through 327 removed outlier: 3.780A pdb=" N THR A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.749A pdb=" N GLY A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 415 through 418 removed outlier: 3.585A pdb=" N ARG A 418 " --> pdb=" O PRO A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 418' Processing helix chain 'A' and resid 419 through 435 removed outlier: 4.403A pdb=" N LEU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 466 removed outlier: 3.867A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 486 removed outlier: 4.171A pdb=" N VAL A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 removed outlier: 3.981A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 removed outlier: 3.575A pdb=" N GLN A 526 " --> pdb=" O TYR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 549 through 559 removed outlier: 3.718A pdb=" N ASP A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 removed outlier: 3.815A pdb=" N ASP A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.091A pdb=" N ARG A 586 " --> pdb=" O ASP A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 669 through 677 removed outlier: 3.912A pdb=" N LEU A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.980A pdb=" N SER A 708 " --> pdb=" O CYS A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 736 removed outlier: 3.546A pdb=" N VAL A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 734 " --> pdb=" O ALA A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.981A pdb=" N CYS A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 807 Processing helix chain 'A' and resid 807 through 816 removed outlier: 3.671A pdb=" N LEU A 812 " --> pdb=" O PRO A 808 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 815 " --> pdb=" O TRP A 811 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 837 removed outlier: 3.751A pdb=" N HIS A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.751A pdb=" N LYS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 854 " --> pdb=" O LEU A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 887 removed outlier: 3.569A pdb=" N SER A 865 " --> pdb=" O ALA A 861 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN A 867 " --> pdb=" O TRP A 863 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A 871 " --> pdb=" O ASN A 867 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 877 " --> pdb=" O ARG A 873 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 879 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 884 " --> pdb=" O THR A 880 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP A 885 " --> pdb=" O ARG A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 1000 through 1011 removed outlier: 4.154A pdb=" N THR A1006 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1015 removed outlier: 3.714A pdb=" N ALA A1015 " --> pdb=" O ALA A1012 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1012 through 1015' Processing sheet with id=AA1, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.061A pdb=" N VAL B 74 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N SER B 117 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLY B 76 " --> pdb=" O SER B 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 141 through 142 removed outlier: 5.904A pdb=" N ARG B 141 " --> pdb=" O MET B 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 395 through 399 removed outlier: 6.008A pdb=" N ARG B 396 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N GLY B 769 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA B 398 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER B 768 " --> pdb=" O VAL B 677 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA B 432 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA B 431 " --> pdb=" O GLN B 660 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N LEU B 662 " --> pdb=" O ALA B 431 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL B 433 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AA5, first strand: chain 'B' and resid 984 through 989 removed outlier: 3.731A pdb=" N PHE B 986 " --> pdb=" O GLY B 997 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY B 997 " --> pdb=" O PHE B 986 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 279 Processing sheet with id=AA7, first strand: chain 'A' and resid 91 through 92 removed outlier: 5.713A pdb=" N LEU A 58 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 354 removed outlier: 3.505A pdb=" N ALA A 688 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 604 " --> pdb=" O MET A 382 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 895 through 897 removed outlier: 7.095A pdb=" N THR A 895 " --> pdb=" O ARG A 921 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG A 921 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 923 " --> pdb=" O VAL A 931 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 932 " --> pdb=" O LYS A 975 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1152 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: 1.93 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 4856 1.43 - 1.64: 7272 1.64 - 1.85: 53 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 12193 Sorted by residual: bond pdb=" N3B ANP A1102 " pdb=" PG ANP A1102 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.03e+01 bond pdb=" O3A ANP A1102 " pdb=" PB ANP A1102 " ideal model delta sigma weight residual 1.700 1.598 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" N VAL B 970 " pdb=" CA VAL B 970 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.83e+01 bond pdb=" N VAL B 677 " pdb=" CA VAL B 677 " ideal model delta sigma weight residual 1.460 1.491 -0.031 7.50e-03 1.78e+04 1.74e+01 bond pdb=" N TRP B 830 " pdb=" CA TRP B 830 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.22e+01 ... (remaining 12188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15549 2.07 - 4.14: 981 4.14 - 6.21: 136 6.21 - 8.29: 34 8.29 - 10.36: 20 Bond angle restraints: 16720 Sorted by residual: angle pdb=" N ARG A 918 " pdb=" CA ARG A 918 " pdb=" C ARG A 918 " ideal model delta sigma weight residual 111.17 121.42 -10.25 1.41e+00 5.03e-01 5.28e+01 angle pdb=" N PRO B 678 " pdb=" CA PRO B 678 " pdb=" C PRO B 678 " ideal model delta sigma weight residual 113.47 123.53 -10.06 1.43e+00 4.89e-01 4.95e+01 angle pdb=" C GLY A 917 " pdb=" N ARG A 918 " pdb=" CA ARG A 918 " ideal model delta sigma weight residual 122.82 129.74 -6.92 1.42e+00 4.96e-01 2.37e+01 angle pdb=" CA ARG A 918 " pdb=" C ARG A 918 " pdb=" O ARG A 918 " ideal model delta sigma weight residual 122.27 116.71 5.56 1.16e+00 7.43e-01 2.30e+01 angle pdb=" N VAL A 960 " pdb=" CA VAL A 960 " pdb=" C VAL A 960 " ideal model delta sigma weight residual 110.42 105.92 4.50 9.60e-01 1.09e+00 2.20e+01 ... (remaining 16715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 7128 35.78 - 71.56: 40 71.56 - 107.34: 2 107.34 - 143.12: 0 143.12 - 178.90: 2 Dihedral angle restraints: 7172 sinusoidal: 2180 harmonic: 4992 Sorted by residual: dihedral pdb=" C LEU B 701 " pdb=" N LEU B 701 " pdb=" CA LEU B 701 " pdb=" CB LEU B 701 " ideal model delta harmonic sigma weight residual -122.60 -137.12 14.52 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" CA VAL B 982 " pdb=" C VAL B 982 " pdb=" N GLU B 983 " pdb=" CA GLU B 983 " ideal model delta harmonic sigma weight residual -180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA GLY A 274 " pdb=" C GLY A 274 " pdb=" N THR A 275 " pdb=" CA THR A 275 " ideal model delta harmonic sigma weight residual 180.00 151.43 28.57 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 7169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1899 0.098 - 0.196: 200 0.196 - 0.294: 16 0.294 - 0.392: 5 0.392 - 0.490: 1 Chirality restraints: 2121 Sorted by residual: chirality pdb=" CA LEU B 701 " pdb=" N LEU B 701 " pdb=" C LEU B 701 " pdb=" CB LEU B 701 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CA PRO B 678 " pdb=" N PRO B 678 " pdb=" C PRO B 678 " pdb=" CB PRO B 678 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ARG A 918 " pdb=" N ARG A 918 " pdb=" C ARG A 918 " pdb=" CB ARG A 918 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 2118 not shown) Planarity restraints: 2117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 917 " 0.019 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C GLY A 917 " -0.068 2.00e-02 2.50e+03 pdb=" O GLY A 917 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG A 918 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 113 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.75e+00 pdb=" C SER B 113 " -0.054 2.00e-02 2.50e+03 pdb=" O SER B 113 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA B 114 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 576 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.65e+00 pdb=" C GLY B 576 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY B 576 " 0.020 2.00e-02 2.50e+03 pdb=" N HIS B 577 " 0.019 2.00e-02 2.50e+03 ... (remaining 2114 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1296 2.74 - 3.28: 10621 3.28 - 3.82: 17736 3.82 - 4.36: 20717 4.36 - 4.90: 35729 Nonbonded interactions: 86099 Sorted by model distance: nonbonded pdb=" NE1 TRP A 787 " pdb=" CA ALA A1015 " model vdw 2.202 3.550 nonbonded pdb=" OG SER A 312 " pdb=" O THR A 340 " model vdw 2.243 3.040 nonbonded pdb=" O THR A 33 " pdb=" O2A ANP A1102 " model vdw 2.272 3.040 nonbonded pdb=" O THR B 165 " pdb=" ND2 ASN A 867 " model vdw 2.294 3.120 nonbonded pdb=" O GLY B 863 " pdb=" NH2 ARG A 724 " model vdw 2.356 3.120 ... (remaining 86094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.010 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 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 : 0.017 0.789 12199 Z= 0.613 Angle : 1.319 38.232 16738 Z= 0.669 Chirality : 0.065 0.490 2121 Planarity : 0.008 0.072 2115 Dihedral : 10.690 178.898 3894 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.82 % Allowed : 6.16 % Favored : 92.03 % Cbeta Deviations : 0.12 % 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: -5.81 (0.15), residues: 1580 helix: -4.55 (0.09), residues: 801 sheet: -1.48 (0.47), residues: 132 loop : -3.21 (0.19), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 597 TYR 0.030 0.003 TYR A 864 PHE 0.024 0.003 PHE A 477 TRP 0.045 0.004 TRP A 616 HIS 0.014 0.002 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00882 / 0.45 (12193) covalent geometry : angle 1.15161 / 0.67 (16720) hydrogen bonds : bond 0.34104 / 23.16 ( 399) hydrogen bonds : angle 10.36186 / 7.24 ( 1152) metal coordination : bond 0.77570 / 36.54 ( 4) metal coordination : angle 24.00936 / 13.83 ( 12) link_TRANS : bond 0.00425 / 0.22 ( 2) link_TRANS : angle 1.07448 / 0.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 249 time to evaluate : 0.441 Fit side-chains REVERT: B 225 MET cc_start: 0.7703 (tmt) cc_final: 0.7409 (tmm) REVERT: B 612 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8908 (mt) REVERT: B 1013 LEU cc_start: 0.9034 (tm) cc_final: 0.8703 (tp) REVERT: A 284 PRO cc_start: 0.9030 (Cg_endo) cc_final: 0.8685 (Cg_exo) REVERT: A 313 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: A 568 TYR cc_start: 0.8268 (t80) cc_final: 0.7937 (t80) REVERT: A 964 LEU cc_start: 0.6105 (OUTLIER) cc_final: 0.5077 (tp) REVERT: A 1000 ARG cc_start: 0.7035 (tmm-80) cc_final: 0.6685 (tpp-160) outliers start: 18 outliers final: 7 residues processed: 262 average time/residue: 0.1711 time to fit residues: 58.0386 Evaluate side-chains 155 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 0.0060 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 HIS A 259 HIS A 263 GLN A 311 GLN A 342 ASN A 816 HIS A 848 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.132033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114790 restraints weight = 18278.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.113774 restraints weight = 16706.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.114363 restraints weight = 15811.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114891 restraints weight = 12846.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115201 restraints weight = 11279.294| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12199 Z= 0.122 Angle : 0.764 29.209 16738 Z= 0.321 Chirality : 0.041 0.137 2121 Planarity : 0.005 0.053 2115 Dihedral : 8.248 175.524 1846 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.43 % Allowed : 11.30 % Favored : 85.27 % 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: -4.58 (0.17), residues: 1580 helix: -3.49 (0.13), residues: 812 sheet: -0.77 (0.53), residues: 106 loop : -2.63 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 614 TYR 0.018 0.002 TYR B 755 PHE 0.009 0.001 PHE A 196 TRP 0.019 0.001 TRP B 497 HIS 0.008 0.001 HIS A 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (12193) covalent geometry : angle 0.63904 / 0.32 (16720) hydrogen bonds : bond 0.04207 / 2.93 ( 399) hydrogen bonds : angle 4.95673 / 3.51 ( 1152) metal coordination : bond 0.02135 / 0.96 ( 4) metal coordination : angle 15.62487 / 9.07 ( 12) link_TRANS : bond 0.00022 / 0.01 ( 2) link_TRANS : angle 0.31925 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: B 225 MET cc_start: 0.7677 (tmt) cc_final: 0.7421 (tmm) REVERT: B 290 THR cc_start: 0.8645 (m) cc_final: 0.8301 (p) REVERT: B 412 ASP cc_start: 0.7625 (m-30) cc_final: 0.7388 (m-30) REVERT: B 679 HIS cc_start: 0.6779 (p90) cc_final: 0.6505 (p-80) REVERT: B 1013 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8880 (tp) REVERT: A 126 ILE cc_start: 0.8822 (mm) cc_final: 0.8552 (mm) REVERT: A 568 TYR cc_start: 0.8496 (t80) cc_final: 0.8147 (t80) REVERT: A 685 MET cc_start: 0.8324 (ttm) cc_final: 0.8039 (ttt) REVERT: A 964 LEU cc_start: 0.5990 (OUTLIER) cc_final: 0.5153 (tt) REVERT: A 1000 ARG cc_start: 0.7247 (tmm-80) cc_final: 0.6932 (tpp-160) outliers start: 34 outliers final: 17 residues processed: 180 average time/residue: 0.1458 time to fit residues: 35.4636 Evaluate side-chains 144 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 787 TRP Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1027 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 93 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 HIS A 419 GLN A 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.127443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110187 restraints weight = 18539.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110084 restraints weight = 21169.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.111000 restraints weight = 18321.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110863 restraints weight = 13415.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111063 restraints weight = 12744.124| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12199 Z= 0.153 Angle : 0.719 25.131 16738 Z= 0.303 Chirality : 0.042 0.140 2121 Planarity : 0.005 0.044 2115 Dihedral : 7.794 175.742 1836 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.05 % Allowed : 11.20 % Favored : 83.75 % 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: -3.75 (0.18), residues: 1580 helix: -2.58 (0.16), residues: 808 sheet: -0.92 (0.49), residues: 119 loop : -2.49 (0.21), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 588 TYR 0.018 0.002 TYR A 864 PHE 0.012 0.001 PHE A 618 TRP 0.019 0.001 TRP B 497 HIS 0.007 0.001 HIS A 775 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (12193) covalent geometry : angle 0.60995 / 0.30 (16720) hydrogen bonds : bond 0.03743 / 2.59 ( 399) hydrogen bonds : angle 4.32091 / 3.09 ( 1152) metal coordination : bond 0.01623 / 0.65 ( 4) metal coordination : angle 14.21539 / 8.29 ( 12) link_TRANS : bond 0.00012 / 0.01 ( 2) link_TRANS : angle 0.35750 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 0.443 Fit side-chains REVERT: B 225 MET cc_start: 0.7779 (tmt) cc_final: 0.7420 (tmm) REVERT: B 290 THR cc_start: 0.8600 (m) cc_final: 0.8288 (p) REVERT: B 872 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8341 (mm) REVERT: B 1013 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8853 (tp) REVERT: A 126 ILE cc_start: 0.8786 (mm) cc_final: 0.8530 (mm) REVERT: A 568 TYR cc_start: 0.8568 (t80) cc_final: 0.8160 (t80) REVERT: A 685 MET cc_start: 0.8361 (ttm) cc_final: 0.8064 (ttt) REVERT: A 964 LEU cc_start: 0.5962 (OUTLIER) cc_final: 0.5109 (tt) outliers start: 50 outliers final: 27 residues processed: 166 average time/residue: 0.1298 time to fit residues: 30.2564 Evaluate side-chains 147 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 886 THR Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 81 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 61 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 126 optimal weight: 0.3980 chunk 2 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.112928 restraints weight = 18294.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112124 restraints weight = 18829.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112462 restraints weight = 19141.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112782 restraints weight = 16891.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.113304 restraints weight = 13594.219| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12199 Z= 0.104 Angle : 0.652 23.683 16738 Z= 0.272 Chirality : 0.040 0.174 2121 Planarity : 0.004 0.038 2115 Dihedral : 7.434 172.517 1836 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.34 % Allowed : 12.31 % Favored : 83.35 % 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: -3.06 (0.19), residues: 1580 helix: -1.92 (0.17), residues: 819 sheet: -0.72 (0.46), residues: 129 loop : -2.31 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 614 TYR 0.014 0.001 TYR B 755 PHE 0.011 0.001 PHE A 618 TRP 0.016 0.001 TRP B 497 HIS 0.004 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (12193) covalent geometry : angle 0.55155 / 0.27 (16720) hydrogen bonds : bond 0.02762 / 1.93 ( 399) hydrogen bonds : angle 3.83284 / 2.73 ( 1152) metal coordination : bond 0.01204 / 0.49 ( 4) metal coordination : angle 12.97920 / 7.66 ( 12) link_TRANS : bond 0.00024 / 0.01 ( 2) link_TRANS : angle 0.28738 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.397 Fit side-chains REVERT: B 225 MET cc_start: 0.7737 (tmt) cc_final: 0.7440 (tmm) REVERT: B 290 THR cc_start: 0.8525 (m) cc_final: 0.8261 (p) REVERT: B 872 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8323 (mm) REVERT: B 1013 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8872 (tp) REVERT: A 86 VAL cc_start: 0.8812 (p) cc_final: 0.8524 (m) REVERT: A 126 ILE cc_start: 0.8741 (mm) cc_final: 0.8499 (mm) REVERT: A 568 TYR cc_start: 0.8561 (t80) cc_final: 0.8323 (t80) REVERT: A 685 MET cc_start: 0.8333 (ttm) cc_final: 0.8108 (ttm) REVERT: A 964 LEU cc_start: 0.6096 (OUTLIER) cc_final: 0.4983 (tp) outliers start: 43 outliers final: 29 residues processed: 162 average time/residue: 0.1305 time to fit residues: 29.4904 Evaluate side-chains 150 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 0.0970 chunk 155 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 123 optimal weight: 0.0670 chunk 108 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106265 restraints weight = 18482.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.105785 restraints weight = 23260.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106794 restraints weight = 21341.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.106750 restraints weight = 16277.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.107200 restraints weight = 16245.868| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12199 Z= 0.246 Angle : 0.785 25.329 16738 Z= 0.340 Chirality : 0.046 0.165 2121 Planarity : 0.005 0.049 2115 Dihedral : 7.859 177.250 1836 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 6.36 % Allowed : 12.31 % Favored : 81.33 % 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: -2.97 (0.20), residues: 1580 helix: -1.75 (0.17), residues: 824 sheet: -1.13 (0.45), residues: 138 loop : -2.30 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 998 TYR 0.022 0.002 TYR A 864 PHE 0.017 0.002 PHE B 336 TRP 0.019 0.002 TRP B 497 HIS 0.011 0.001 HIS A 775 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.25 (12193) covalent geometry : angle 0.68686 / 0.34 (16720) hydrogen bonds : bond 0.04028 / 2.80 ( 399) hydrogen bonds : angle 4.30058 / 3.07 ( 1152) metal coordination : bond 0.01684 / 0.73 ( 4) metal coordination : angle 14.20351 / 8.42 ( 12) link_TRANS : bond 0.00054 / 0.03 ( 2) link_TRANS : angle 0.42188 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 122 time to evaluate : 0.463 Fit side-chains REVERT: B 225 MET cc_start: 0.7909 (tmt) cc_final: 0.7547 (tmm) REVERT: B 290 THR cc_start: 0.8651 (m) cc_final: 0.8408 (p) REVERT: B 872 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8378 (mm) REVERT: B 1013 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8895 (tp) REVERT: A 86 VAL cc_start: 0.8842 (p) cc_final: 0.8590 (m) REVERT: A 254 VAL cc_start: 0.9076 (OUTLIER) cc_final: 0.8682 (t) REVERT: A 685 MET cc_start: 0.8426 (ttm) cc_final: 0.8075 (ttt) REVERT: A 964 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.4795 (tp) outliers start: 63 outliers final: 42 residues processed: 175 average time/residue: 0.1295 time to fit residues: 31.5413 Evaluate side-chains 165 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1017 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 837 SER Chi-restraints excluded: chain A residue 964 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 9 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.128974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111915 restraints weight = 18406.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.111267 restraints weight = 20447.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112392 restraints weight = 18790.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112430 restraints weight = 13087.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112835 restraints weight = 12587.468| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12199 Z= 0.100 Angle : 0.653 23.423 16738 Z= 0.273 Chirality : 0.040 0.168 2121 Planarity : 0.004 0.039 2115 Dihedral : 7.422 176.177 1836 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.04 % Allowed : 14.83 % Favored : 81.13 % 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: -2.34 (0.20), residues: 1580 helix: -1.16 (0.18), residues: 810 sheet: -1.11 (0.43), residues: 138 loop : -2.03 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 998 TYR 0.016 0.001 TYR B 755 PHE 0.026 0.001 PHE B 254 TRP 0.015 0.001 TRP B 497 HIS 0.004 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (12193) covalent geometry : angle 0.55175 / 0.27 (16720) hydrogen bonds : bond 0.02539 / 1.77 ( 399) hydrogen bonds : angle 3.68390 / 2.62 ( 1152) metal coordination : bond 0.00844 / 0.35 ( 4) metal coordination : angle 13.07914 / 7.56 ( 12) link_TRANS : bond 0.00035 / 0.02 ( 2) link_TRANS : angle 0.31078 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.468 Fit side-chains REVERT: B 225 MET cc_start: 0.7788 (tmt) cc_final: 0.7536 (tmm) REVERT: B 290 THR cc_start: 0.8571 (m) cc_final: 0.8337 (p) REVERT: B 872 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8352 (mm) REVERT: B 1013 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8887 (tp) REVERT: A 86 VAL cc_start: 0.8793 (p) cc_final: 0.8513 (m) REVERT: A 390 PRO cc_start: 0.7418 (Cg_exo) cc_final: 0.6870 (Cg_endo) REVERT: A 685 MET cc_start: 0.8349 (ttm) cc_final: 0.8102 (ttm) REVERT: A 964 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.4863 (tp) outliers start: 40 outliers final: 32 residues processed: 154 average time/residue: 0.1311 time to fit residues: 28.2654 Evaluate side-chains 154 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 153 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 102 optimal weight: 0.0770 chunk 67 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.110835 restraints weight = 18199.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110272 restraints weight = 21201.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.111277 restraints weight = 19904.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.111325 restraints weight = 13905.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111485 restraints weight = 13864.667| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12199 Z= 0.101 Angle : 0.636 21.914 16738 Z= 0.267 Chirality : 0.040 0.165 2121 Planarity : 0.004 0.049 2115 Dihedral : 7.302 177.758 1836 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.94 % Allowed : 14.83 % Favored : 80.22 % 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: -1.78 (0.21), residues: 1580 helix: -0.67 (0.19), residues: 800 sheet: -0.60 (0.46), residues: 120 loop : -1.86 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 998 TYR 0.021 0.001 TYR A 568 PHE 0.024 0.001 PHE B 254 TRP 0.016 0.001 TRP B 497 HIS 0.004 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (12193) covalent geometry : angle 0.54628 / 0.27 (16720) hydrogen bonds : bond 0.02483 / 1.73 ( 399) hydrogen bonds : angle 3.60594 / 2.59 ( 1152) metal coordination : bond 0.00904 / 0.36 ( 4) metal coordination : angle 12.14587 / 7.12 ( 12) link_TRANS : bond 0.00026 / 0.01 ( 2) link_TRANS : angle 0.28533 / 0.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 0.469 Fit side-chains REVERT: B 225 MET cc_start: 0.7773 (tmt) cc_final: 0.7550 (tmm) REVERT: B 290 THR cc_start: 0.8584 (m) cc_final: 0.8358 (p) REVERT: B 872 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8322 (mm) REVERT: B 1013 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8849 (tp) REVERT: A 86 VAL cc_start: 0.8740 (p) cc_final: 0.8467 (m) REVERT: A 390 PRO cc_start: 0.7491 (Cg_exo) cc_final: 0.6961 (Cg_endo) REVERT: A 685 MET cc_start: 0.8352 (ttm) cc_final: 0.8116 (ttm) REVERT: A 964 LEU cc_start: 0.6152 (OUTLIER) cc_final: 0.4900 (tp) outliers start: 49 outliers final: 33 residues processed: 159 average time/residue: 0.1240 time to fit residues: 27.9469 Evaluate side-chains 152 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 36 optimal weight: 0.0870 chunk 85 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 144 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114508 restraints weight = 18181.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113925 restraints weight = 20577.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115813 restraints weight = 18712.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115427 restraints weight = 12817.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115613 restraints weight = 11628.142| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12199 Z= 0.084 Angle : 0.608 20.243 16738 Z= 0.253 Chirality : 0.039 0.161 2121 Planarity : 0.004 0.045 2115 Dihedral : 7.074 178.695 1834 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.34 % Allowed : 15.94 % Favored : 79.72 % 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: -1.29 (0.21), residues: 1580 helix: -0.21 (0.19), residues: 802 sheet: -0.38 (0.43), residues: 137 loop : -1.74 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 998 TYR 0.018 0.001 TYR A 568 PHE 0.022 0.001 PHE B 254 TRP 0.009 0.001 TRP B 497 HIS 0.003 0.000 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.08 (12193) covalent geometry : angle 0.52485 / 0.25 (16720) hydrogen bonds : bond 0.02100 / 1.48 ( 399) hydrogen bonds : angle 3.37641 / 2.37 ( 1152) metal coordination : bond 0.00808 / 0.33 ( 4) metal coordination : angle 11.44504 / 6.62 ( 12) link_TRANS : bond 0.00032 / 0.02 ( 2) link_TRANS : angle 0.23674 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: B 872 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8321 (mm) REVERT: B 1013 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8775 (tp) REVERT: A 86 VAL cc_start: 0.8684 (p) cc_final: 0.8388 (m) REVERT: A 390 PRO cc_start: 0.7548 (Cg_exo) cc_final: 0.7032 (Cg_endo) REVERT: A 625 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7448 (mt0) outliers start: 43 outliers final: 30 residues processed: 157 average time/residue: 0.1282 time to fit residues: 28.2699 Evaluate side-chains 152 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 140 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 131 optimal weight: 0.0670 chunk 86 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.128370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.111613 restraints weight = 18164.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.111021 restraints weight = 20591.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.111900 restraints weight = 19289.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111577 restraints weight = 14952.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.111748 restraints weight = 13635.140| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12199 Z= 0.110 Angle : 0.629 20.104 16738 Z= 0.263 Chirality : 0.040 0.156 2121 Planarity : 0.004 0.056 2115 Dihedral : 7.014 178.189 1832 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 3.73 % Allowed : 16.85 % Favored : 79.41 % 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: -1.16 (0.21), residues: 1580 helix: -0.04 (0.19), residues: 806 sheet: -0.38 (0.43), residues: 138 loop : -1.75 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 998 TYR 0.017 0.001 TYR A 568 PHE 0.020 0.001 PHE B 254 TRP 0.014 0.001 TRP B 497 HIS 0.004 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (12193) covalent geometry : angle 0.54925 / 0.26 (16720) hydrogen bonds : bond 0.02464 / 1.73 ( 399) hydrogen bonds : angle 3.46400 / 2.44 ( 1152) metal coordination : bond 0.00955 / 0.38 ( 4) metal coordination : angle 11.44267 / 6.78 ( 12) link_TRANS : bond 0.00017 / 0.01 ( 2) link_TRANS : angle 0.23173 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.424 Fit side-chains REVERT: B 872 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8338 (mm) REVERT: B 1013 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8798 (tp) REVERT: A 86 VAL cc_start: 0.8669 (p) cc_final: 0.8379 (m) REVERT: A 390 PRO cc_start: 0.7615 (Cg_exo) cc_final: 0.7110 (Cg_endo) REVERT: A 964 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.4893 (tp) outliers start: 37 outliers final: 34 residues processed: 146 average time/residue: 0.1310 time to fit residues: 26.7678 Evaluate side-chains 153 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 124 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.130152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113508 restraints weight = 18273.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112642 restraints weight = 22820.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.113750 restraints weight = 21245.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.113637 restraints weight = 15511.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.114017 restraints weight = 14891.771| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12199 Z= 0.094 Angle : 0.622 20.002 16738 Z= 0.258 Chirality : 0.039 0.158 2121 Planarity : 0.004 0.057 2115 Dihedral : 6.898 174.976 1832 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.68 % Rotamer: Outliers : 3.83 % Allowed : 16.85 % Favored : 79.31 % 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: -0.88 (0.21), residues: 1580 helix: 0.24 (0.19), residues: 811 sheet: -0.22 (0.43), residues: 136 loop : -1.70 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 998 TYR 0.017 0.001 TYR A 568 PHE 0.020 0.001 PHE B 254 TRP 0.012 0.001 TRP B 497 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.09 (12193) covalent geometry : angle 0.54170 / 0.26 (16720) hydrogen bonds : bond 0.02238 / 1.58 ( 399) hydrogen bonds : angle 3.36713 / 2.36 ( 1152) metal coordination : bond 0.00854 / 0.34 ( 4) metal coordination : angle 11.43309 / 6.67 ( 12) link_TRANS : bond 0.00024 / 0.01 ( 2) link_TRANS : angle 0.22539 / 0.09 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: B 194 ARG cc_start: 0.7598 (ttp80) cc_final: 0.7340 (ttp80) REVERT: B 755 TYR cc_start: 0.8348 (t80) cc_final: 0.8133 (t80) REVERT: B 872 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8341 (mm) REVERT: A 86 VAL cc_start: 0.8604 (p) cc_final: 0.8315 (m) REVERT: A 390 PRO cc_start: 0.7629 (Cg_exo) cc_final: 0.7158 (Cg_endo) REVERT: A 625 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: A 891 THR cc_start: 0.8350 (m) cc_final: 0.8086 (t) REVERT: A 964 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.4856 (tp) outliers start: 38 outliers final: 34 residues processed: 150 average time/residue: 0.1354 time to fit residues: 28.3781 Evaluate side-chains 155 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 342 TYR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 665 HIS Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 833 VAL Chi-restraints excluded: chain B residue 872 LEU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 250 LYS Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 689 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 116 optimal weight: 0.6980 chunk 72 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 36 optimal weight: 0.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114931 restraints weight = 18147.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.114238 restraints weight = 22987.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115069 restraints weight = 21456.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.115436 restraints weight = 15604.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115592 restraints weight = 16186.566| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12199 Z= 0.090 Angle : 0.612 19.364 16738 Z= 0.254 Chirality : 0.039 0.158 2121 Planarity : 0.004 0.061 2115 Dihedral : 6.779 172.285 1832 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.49 % Rotamer: Outliers : 4.04 % Allowed : 16.65 % Favored : 79.31 % 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: -0.64 (0.22), residues: 1580 helix: 0.45 (0.19), residues: 819 sheet: -0.22 (0.43), residues: 137 loop : -1.62 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 998 TYR 0.017 0.001 TYR A 568 PHE 0.020 0.001 PHE B 254 TRP 0.014 0.001 TRP B 497 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (12193) covalent geometry : angle 0.53693 / 0.25 (16720) hydrogen bonds : bond 0.02183 / 1.54 ( 399) hydrogen bonds : angle 3.29723 / 2.31 ( 1152) metal coordination : bond 0.00851 / 0.34 ( 4) metal coordination : angle 10.98627 / 6.53 ( 12) link_TRANS : bond 0.00025 / 0.01 ( 2) link_TRANS : angle 0.21046 / 0.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1967.85 seconds wall clock time: 34 minutes 38.71 seconds (2078.71 seconds total)