Starting phenix.real_space_refine on Thu Sep 26 05:11:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppj_20440/09_2024/6ppj_20440.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppj_20440/09_2024/6ppj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppj_20440/09_2024/6ppj_20440.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppj_20440/09_2024/6ppj_20440.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppj_20440/09_2024/6ppj_20440.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppj_20440/09_2024/6ppj_20440.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 1, 'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 5} 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: {'GLN:plan1': 1, 'GLU:plan': 4, 'UNK:plan-1': 11, 'ASP:plan': 5, 'ARG:plan': 3} 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: {'GLN:plan1': 2, 'ASN:plan1': 2, 'UNK:plan-1': 16, 'HIS:plan': 3, 'ARG:plan': 11, 'PHE:plan': 1, 'GLU:plan': 16, 'ASP:plan': 16} 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: {'GLN:plan1': 1, 'HIS:plan': 3, 'UNK:plan-1': 33, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 2} 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: {'GLN:plan1': 11, 'ASP:plan': 40, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 1, 'GLU:plan': 34, 'ARG:plan': 27} 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: 7.48, per 1000 atoms: 0.62 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: 2.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.37 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: 3.47 Time building geometry restraints manager: 3.25 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: 7133 35.78 - 71.56: 59 71.56 - 107.34: 6 107.34 - 143.12: 0 143.12 - 178.90: 2 Dihedral angle restraints: 7200 sinusoidal: 2208 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 7197 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.990 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.009 0.168 12193 Z= 0.581 Angle : 1.152 10.357 16720 Z= 0.667 Chirality : 0.065 0.490 2121 Planarity : 0.008 0.072 2115 Dihedral : 11.634 178.898 3922 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.81 (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 TRP 0.045 0.004 TRP A 616 HIS 0.014 0.002 HIS B 243 PHE 0.024 0.003 PHE A 477 TYR 0.030 0.003 TYR A 864 ARG 0.020 0.001 ARG B 597 *********************** 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 fitting. rotamer outliers: 18 poor density : 249 time to evaluate : 1.283 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: 0.3514 time to fit residues: 118.9217 Evaluate side-chains 155 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 133 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 143 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12193 Z= 0.182 Angle : 0.643 14.970 16720 Z= 0.320 Chirality : 0.041 0.138 2121 Planarity : 0.005 0.053 2115 Dihedral : 9.246 172.896 1874 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.43 % Allowed : 11.50 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.17), residues: 1580 helix: -3.51 (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 TRP 0.019 0.001 TRP B 497 HIS 0.008 0.001 HIS A 259 PHE 0.010 0.001 PHE A 618 TYR 0.018 0.002 TYR B 755 ARG 0.006 0.001 ARG B 614 *********************** 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 fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 1.285 Fit side-chains revert: symmetry clash REVERT: B 185 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 225 MET cc_start: 0.7835 (tmt) cc_final: 0.7457 (tmm) REVERT: B 290 THR cc_start: 0.8636 (m) cc_final: 0.8257 (p) REVERT: B 412 ASP cc_start: 0.7695 (m-30) cc_final: 0.7404 (m-30) REVERT: B 679 HIS cc_start: 0.6815 (p90) cc_final: 0.6540 (p-80) REVERT: A 126 ILE cc_start: 0.8828 (mm) cc_final: 0.8554 (mm) REVERT: A 568 TYR cc_start: 0.8479 (t80) cc_final: 0.8117 (t80) REVERT: A 606 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8265 (pp) REVERT: A 685 MET cc_start: 0.8508 (ttm) cc_final: 0.8118 (ttt) REVERT: A 964 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.5186 (tt) REVERT: A 1000 ARG cc_start: 0.7271 (tmm-80) cc_final: 0.6838 (tpp-160) outliers start: 34 outliers final: 17 residues processed: 180 average time/residue: 0.3035 time to fit residues: 73.4552 Evaluate side-chains 144 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 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 606 LEU 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 79 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 155 optimal weight: 0.0470 chunk 128 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS A 419 GLN A 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12193 Z= 0.194 Angle : 0.578 13.913 16720 Z= 0.285 Chirality : 0.041 0.133 2121 Planarity : 0.004 0.042 2115 Dihedral : 7.892 179.544 1864 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.64 % Allowed : 11.20 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.19), residues: 1580 helix: -2.45 (0.16), residues: 813 sheet: -0.80 (0.47), residues: 129 loop : -2.47 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 497 HIS 0.005 0.001 HIS A 775 PHE 0.014 0.001 PHE A 618 TYR 0.017 0.001 TYR A 864 ARG 0.007 0.001 ARG B 588 *********************** 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 180 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 134 time to evaluate : 1.376 Fit side-chains REVERT: B 128 ARG cc_start: 0.7792 (ttm-80) cc_final: 0.7590 (ttm110) REVERT: B 225 MET cc_start: 0.7893 (tmt) cc_final: 0.7416 (tmm) REVERT: B 290 THR cc_start: 0.8563 (m) cc_final: 0.8251 (p) REVERT: B 412 ASP cc_start: 0.7629 (m-30) cc_final: 0.7385 (m-30) REVERT: B 872 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8339 (mm) REVERT: A 126 ILE cc_start: 0.8761 (mm) cc_final: 0.8500 (mm) REVERT: A 568 TYR cc_start: 0.8533 (t80) cc_final: 0.8104 (t80) REVERT: A 685 MET cc_start: 0.8494 (ttm) cc_final: 0.8196 (ttm) REVERT: A 964 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5038 (tp) outliers start: 46 outliers final: 23 residues processed: 167 average time/residue: 0.2621 time to fit residues: 61.4620 Evaluate side-chains 142 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL 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 319 ILE Chi-restraints excluded: chain B residue 342 TYR 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 A residue 28 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 964 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 96 optimal weight: 0.3980 chunk 144 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 136 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12193 Z= 0.224 Angle : 0.582 12.838 16720 Z= 0.286 Chirality : 0.042 0.163 2121 Planarity : 0.004 0.038 2115 Dihedral : 7.661 176.714 1864 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.94 % Allowed : 12.21 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.19), residues: 1580 helix: -1.88 (0.17), residues: 819 sheet: -0.76 (0.46), residues: 129 loop : -2.31 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 497 HIS 0.006 0.001 HIS A 775 PHE 0.012 0.001 PHE B 941 TYR 0.016 0.002 TYR A 864 ARG 0.006 0.001 ARG A 127 *********************** 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 fitting. rotamer outliers: 49 poor density : 124 time to evaluate : 1.253 Fit side-chains REVERT: B 225 MET cc_start: 0.7894 (tmt) cc_final: 0.7443 (tmm) REVERT: B 290 THR cc_start: 0.8619 (m) cc_final: 0.8320 (p) REVERT: B 412 ASP cc_start: 0.7610 (m-30) cc_final: 0.7395 (m-30) REVERT: B 842 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7705 (mtm-85) REVERT: B 872 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8343 (mm) REVERT: A 86 VAL cc_start: 0.8796 (p) cc_final: 0.8549 (m) REVERT: A 126 ILE cc_start: 0.8759 (mm) cc_final: 0.8486 (mm) REVERT: A 568 TYR cc_start: 0.8564 (t80) cc_final: 0.8323 (t80) REVERT: A 685 MET cc_start: 0.8508 (ttm) cc_final: 0.8207 (ttm) REVERT: A 964 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.4987 (tp) outliers start: 49 outliers final: 32 residues processed: 162 average time/residue: 0.2685 time to fit residues: 60.8626 Evaluate side-chains 152 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 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 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 A residue 28 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 203 ILE 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 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 837 SER 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 127 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 105 optimal weight: 0.0070 chunk 0 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12193 Z= 0.148 Angle : 0.531 10.441 16720 Z= 0.259 Chirality : 0.040 0.170 2121 Planarity : 0.004 0.034 2115 Dihedral : 7.101 171.890 1864 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.05 % Allowed : 13.42 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.20), residues: 1580 helix: -1.31 (0.18), residues: 817 sheet: -0.67 (0.45), residues: 129 loop : -2.10 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 497 HIS 0.004 0.001 HIS B 243 PHE 0.011 0.001 PHE B 941 TYR 0.015 0.001 TYR B 755 ARG 0.009 0.001 ARG B 998 *********************** 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 179 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 129 time to evaluate : 1.633 Fit side-chains REVERT: B 225 MET cc_start: 0.7888 (tmt) cc_final: 0.7484 (tmm) REVERT: B 290 THR cc_start: 0.8559 (m) cc_final: 0.8281 (p) REVERT: B 412 ASP cc_start: 0.7434 (m-30) cc_final: 0.7232 (m-30) REVERT: B 842 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7693 (mtm-85) REVERT: B 872 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8350 (mm) REVERT: A 86 VAL cc_start: 0.8744 (p) cc_final: 0.8501 (m) REVERT: A 126 ILE cc_start: 0.8716 (mm) cc_final: 0.8510 (mm) REVERT: A 568 TYR cc_start: 0.8557 (t80) cc_final: 0.8313 (t80) REVERT: A 685 MET cc_start: 0.8473 (ttm) cc_final: 0.8173 (ttm) REVERT: A 964 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.4969 (tp) outliers start: 50 outliers final: 33 residues processed: 169 average time/residue: 0.2804 time to fit residues: 66.1485 Evaluate side-chains 153 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 1.336 ------------------------------------------------------------------------------- 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 172 VAL 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 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 1034 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 244 THR 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 377 ILE 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 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 Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 4.9990 chunk 137 optimal weight: 0.1980 chunk 30 optimal weight: 0.0970 chunk 89 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 12 optimal weight: 0.0050 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 0.0870 overall best weight: 0.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12193 Z= 0.118 Angle : 0.503 8.294 16720 Z= 0.244 Chirality : 0.038 0.166 2121 Planarity : 0.004 0.033 2115 Dihedral : 6.484 161.778 1864 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.83 % Allowed : 14.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.21), residues: 1580 helix: -0.59 (0.19), residues: 803 sheet: -0.57 (0.42), residues: 139 loop : -1.82 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 497 HIS 0.002 0.000 HIS A 372 PHE 0.026 0.001 PHE B 254 TYR 0.015 0.001 TYR B 755 ARG 0.010 0.000 ARG B 998 *********************** 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 173 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: B 290 THR cc_start: 0.8496 (m) cc_final: 0.8258 (p) REVERT: B 842 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7708 (mtm-85) REVERT: B 872 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8321 (mm) REVERT: A 86 VAL cc_start: 0.8674 (p) cc_final: 0.8422 (m) REVERT: A 126 ILE cc_start: 0.8654 (mm) cc_final: 0.8453 (mm) REVERT: A 568 TYR cc_start: 0.8484 (t80) cc_final: 0.8219 (t80) REVERT: A 685 MET cc_start: 0.8443 (ttm) cc_final: 0.8172 (ttm) outliers start: 38 outliers final: 25 residues processed: 163 average time/residue: 0.2572 time to fit residues: 59.0893 Evaluate side-chains 149 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 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 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 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 886 THR 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 147 optimal weight: 0.0670 chunk 17 optimal weight: 0.0870 chunk 87 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12193 Z= 0.244 Angle : 0.580 9.345 16720 Z= 0.281 Chirality : 0.042 0.156 2121 Planarity : 0.004 0.049 2115 Dihedral : 6.735 165.897 1862 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.84 % Allowed : 15.24 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1580 helix: -0.41 (0.19), residues: 794 sheet: -0.56 (0.44), residues: 129 loop : -1.81 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 497 HIS 0.005 0.001 HIS A 775 PHE 0.020 0.002 PHE B 254 TYR 0.015 0.001 TYR B 755 ARG 0.011 0.001 ARG B 998 *********************** 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 fitting. rotamer outliers: 48 poor density : 123 time to evaluate : 1.334 Fit side-chains REVERT: B 290 THR cc_start: 0.8619 (m) cc_final: 0.8353 (p) REVERT: B 412 ASP cc_start: 0.7501 (m-30) cc_final: 0.7244 (m-30) REVERT: B 842 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7697 (mtm-85) REVERT: B 872 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8340 (mm) REVERT: A 86 VAL cc_start: 0.8691 (p) cc_final: 0.8448 (m) REVERT: A 126 ILE cc_start: 0.8755 (mm) cc_final: 0.8552 (mm) REVERT: A 568 TYR cc_start: 0.8481 (t80) cc_final: 0.8279 (t80) REVERT: A 685 MET cc_start: 0.8465 (ttm) cc_final: 0.8180 (ttm) REVERT: A 964 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5016 (tp) outliers start: 48 outliers final: 42 residues processed: 161 average time/residue: 0.2677 time to fit residues: 60.5642 Evaluate side-chains 160 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 116 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 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 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 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 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU 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 363 MET Chi-restraints excluded: chain A residue 377 ILE 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 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 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 94 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 103 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 119 optimal weight: 0.0010 chunk 138 optimal weight: 2.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12193 Z= 0.138 Angle : 0.524 9.364 16720 Z= 0.253 Chirality : 0.039 0.165 2121 Planarity : 0.004 0.049 2115 Dihedral : 6.391 160.262 1862 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.63 % Allowed : 16.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1580 helix: -0.08 (0.19), residues: 797 sheet: -0.36 (0.44), residues: 129 loop : -1.72 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 497 HIS 0.004 0.001 HIS B 243 PHE 0.024 0.001 PHE B 254 TYR 0.016 0.001 TYR B 755 ARG 0.013 0.000 ARG B 998 *********************** 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 158 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 122 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: B 290 THR cc_start: 0.8588 (m) cc_final: 0.8331 (p) REVERT: B 842 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7670 (mtm-85) REVERT: B 872 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8320 (mm) REVERT: A 86 VAL cc_start: 0.8663 (p) cc_final: 0.8406 (m) REVERT: A 390 PRO cc_start: 0.7371 (Cg_exo) cc_final: 0.6819 (Cg_endo) REVERT: A 568 TYR cc_start: 0.8451 (t80) cc_final: 0.8211 (t80) REVERT: A 685 MET cc_start: 0.8437 (ttm) cc_final: 0.8154 (ttm) REVERT: A 891 THR cc_start: 0.8319 (m) cc_final: 0.8011 (t) REVERT: A 964 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.4961 (tp) outliers start: 36 outliers final: 31 residues processed: 149 average time/residue: 0.2663 time to fit residues: 56.1105 Evaluate side-chains 153 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 120 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 172 VAL 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 342 TYR 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 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 58 LEU 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 363 MET Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 786 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12193 Z= 0.228 Angle : 0.571 9.664 16720 Z= 0.276 Chirality : 0.042 0.156 2121 Planarity : 0.004 0.059 2115 Dihedral : 6.500 158.784 1862 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 4.54 % Allowed : 15.54 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1580 helix: -0.07 (0.19), residues: 806 sheet: -0.48 (0.44), residues: 130 loop : -1.71 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 497 HIS 0.005 0.001 HIS A 775 PHE 0.024 0.002 PHE B 254 TYR 0.016 0.001 TYR B 755 ARG 0.012 0.001 ARG B 998 *********************** 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 166 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 121 time to evaluate : 1.301 Fit side-chains REVERT: B 290 THR cc_start: 0.8613 (m) cc_final: 0.8404 (p) REVERT: B 842 ARG cc_start: 0.7914 (mtm-85) cc_final: 0.7677 (mtm-85) REVERT: B 872 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8331 (mm) REVERT: A 86 VAL cc_start: 0.8676 (p) cc_final: 0.8423 (m) REVERT: A 390 PRO cc_start: 0.7566 (Cg_exo) cc_final: 0.7054 (Cg_endo) REVERT: A 568 TYR cc_start: 0.8495 (t80) cc_final: 0.8272 (t80) REVERT: A 685 MET cc_start: 0.8462 (ttm) cc_final: 0.8174 (ttm) REVERT: A 891 THR cc_start: 0.8410 (m) cc_final: 0.8074 (t) REVERT: A 964 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.4969 (tp) outliers start: 45 outliers final: 37 residues processed: 157 average time/residue: 0.2563 time to fit residues: 56.9980 Evaluate side-chains 160 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 VAL 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 296 ILE 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 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 58 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 363 MET Chi-restraints excluded: chain A residue 377 ILE 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 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 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 91 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 76 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12193 Z= 0.183 Angle : 0.554 10.342 16720 Z= 0.266 Chirality : 0.040 0.162 2121 Planarity : 0.004 0.062 2115 Dihedral : 6.374 155.234 1862 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.57 % Favored : 94.37 % Rotamer: Outliers : 4.14 % Allowed : 16.25 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1580 helix: 0.12 (0.19), residues: 801 sheet: -0.42 (0.44), residues: 130 loop : -1.68 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 497 HIS 0.004 0.001 HIS B 243 PHE 0.025 0.001 PHE B 254 TYR 0.017 0.001 TYR B 755 ARG 0.014 0.000 ARG B 998 ********************** 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 162 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 121 time to evaluate : 1.173 Fit side-chains REVERT: B 194 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7424 (ttp80) REVERT: B 290 THR cc_start: 0.8610 (m) cc_final: 0.8387 (p) REVERT: B 842 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7680 (mtm-85) REVERT: B 872 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8327 (mm) REVERT: A 86 VAL cc_start: 0.8673 (p) cc_final: 0.8420 (m) REVERT: A 390 PRO cc_start: 0.7566 (Cg_exo) cc_final: 0.7082 (Cg_endo) REVERT: A 685 MET cc_start: 0.8454 (ttm) cc_final: 0.8172 (ttm) REVERT: A 891 THR cc_start: 0.8433 (m) cc_final: 0.8149 (t) REVERT: A 964 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.4939 (tp) outliers start: 41 outliers final: 38 residues processed: 152 average time/residue: 0.2721 time to fit residues: 57.6682 Evaluate side-chains 159 residues out of total 1300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 119 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 172 VAL 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 296 ILE 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 1034 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 58 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 363 MET Chi-restraints excluded: chain A residue 377 ILE 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 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 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 38 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 128 optimal weight: 0.0870 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.131936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.115166 restraints weight = 18118.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.114690 restraints weight = 21778.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.115699 restraints weight = 19512.575| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12193 Z= 0.127 Angle : 0.518 10.804 16720 Z= 0.247 Chirality : 0.039 0.168 2121 Planarity : 0.004 0.055 2115 Dihedral : 5.891 143.915 1862 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.25 % Favored : 94.68 % Rotamer: Outliers : 3.43 % Allowed : 16.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.22), residues: 1580 helix: 0.52 (0.19), residues: 801 sheet: -0.22 (0.43), residues: 137 loop : -1.57 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 497 HIS 0.003 0.000 HIS B 243 PHE 0.025 0.001 PHE B 254 TYR 0.016 0.001 TYR B 755 ARG 0.013 0.000 ARG B 998 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2338.24 seconds wall clock time: 44 minutes 23.45 seconds (2663.45 seconds total)