Starting phenix.real_space_refine on Sun Aug 4 17:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/08_2024/7c2k_30275.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/08_2024/7c2k_30275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/08_2024/7c2k_30275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/08_2024/7c2k_30275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/08_2024/7c2k_30275.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c2k_30275/08_2024/7c2k_30275.cif" } resolution = 2.93 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= 0.002 sd= 0.092 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 Zn 2 6.06 5 P 32 5.49 5 S 77 5.16 5 C 6667 2.51 5 N 1806 2.21 5 O 2108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ASP 29": "OD1" <-> "OD2" Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A ASP 291": "OD1" <-> "OD2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ASP 825": "OD1" <-> "OD2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 845": "OD1" <-> "OD2" Residue "A ASP 846": "OD1" <-> "OD2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 910": "OD1" <-> "OD2" Residue "A ARG 914": "NH1" <-> "NH2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "C ASP 44": "OD1" <-> "OD2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D ASP 161": "OD1" <-> "OD2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 190": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10692 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7464 Classifications: {'peptide': 927} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 905 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 111} Chain: "C" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 554 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 423 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 12} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "G" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "G" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {'F86': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p_pur': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2538 SG CYS A 310 75.724 40.795 50.289 1.00 27.08 S ATOM 3946 SG CYS A 487 88.847 46.521 69.558 1.00 31.06 S ATOM 5199 SG CYS A 645 90.765 48.370 66.495 1.00 36.06 S ATOM 5205 SG CYS A 646 88.957 44.100 65.770 1.00 34.53 S Time building chain proxies: 6.56, per 1000 atoms: 0.61 Number of scatterers: 10692 At special positions: 0 Unit cell: (104.14, 100.86, 132.84, 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) Zn 2 29.99 S 77 16.00 P 32 15.00 O 2108 8.00 N 1806 7.00 C 6667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.94 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 3 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 51.2% alpha, 15.1% beta 14 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.719A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 90 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.650A pdb=" N PHE A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 242 Processing helix chain 'A' and resid 242 through 248 removed outlier: 4.065A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 removed outlier: 4.460A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 256 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.234A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.570A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.503A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 480 removed outlier: 4.049A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.701A pdb=" N GLN A 492 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 493' Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.741A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.566A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 640 Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.512A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.598A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.618A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 846 through 851 Processing helix chain 'A' and resid 855 through 867 removed outlier: 3.628A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 874 through 903 removed outlier: 3.885A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP A 901 " --> pdb=" O GLY A 897 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 918 through 924 Processing helix chain 'B' and resid 77 through 97 removed outlier: 3.981A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.566A pdb=" N TYR B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.537A pdb=" N ILE B 172 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 20 Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.553A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 Processing helix chain 'D' and resid 54 through 83 removed outlier: 3.658A pdb=" N GLN D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.771A pdb=" N ASN D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 20 removed outlier: 4.039A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.650A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.251A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.650A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 672 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.650A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 672 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 821 Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.605A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 143 " --> pdb=" O THR D 146 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1689 1.27 - 1.40: 2878 1.40 - 1.54: 6175 1.54 - 1.67: 125 1.67 - 1.81: 118 Bond restraints: 10985 Sorted by residual: bond pdb=" C1 F86 G 4 " pdb=" C5 F86 G 4 " ideal model delta sigma weight residual 1.507 1.381 0.126 1.00e-02 1.00e+04 1.59e+02 bond pdb=" C4 F86 G 4 " pdb=" O1 F86 G 4 " ideal model delta sigma weight residual 1.435 1.284 0.151 1.20e-02 6.94e+03 1.57e+02 bond pdb=" C11 F86 G 4 " pdb=" N5 F86 G 4 " ideal model delta sigma weight residual 1.337 1.451 -0.114 1.00e-02 1.00e+04 1.30e+02 bond pdb=" C3 F86 G 4 " pdb=" C4 F86 G 4 " ideal model delta sigma weight residual 1.526 1.670 -0.144 1.40e-02 5.10e+03 1.05e+02 bond pdb=" O7 F86 G 4 " pdb=" P1 F86 G 4 " ideal model delta sigma weight residual 1.491 1.649 -0.158 1.70e-02 3.46e+03 8.66e+01 ... (remaining 10980 not shown) Histogram of bond angle deviations from ideal: 82.08 - 101.65: 69 101.65 - 121.21: 12237 121.21 - 140.78: 2742 140.78 - 160.35: 0 160.35 - 179.91: 1 Bond angle restraints: 15049 Sorted by residual: angle pdb=" O2' C F -2 " pdb=" C2' C F -2 " pdb=" C1' C F -2 " ideal model delta sigma weight residual 108.40 82.08 26.32 1.50e+00 4.44e-01 3.08e+02 angle pdb=" C12 F86 G 4 " pdb=" N2 F86 G 4 " pdb=" N1 F86 G 4 " ideal model delta sigma weight residual 111.53 121.71 -10.18 1.00e+00 1.00e+00 1.04e+02 angle pdb=" N2 F86 G 4 " pdb=" C12 F86 G 4 " pdb=" N4 F86 G 4 " ideal model delta sigma weight residual 128.74 120.63 8.11 1.17e+00 7.33e-01 4.82e+01 angle pdb=" C3' C F -2 " pdb=" C2' C F -2 " pdb=" O2' C F -2 " ideal model delta sigma weight residual 110.70 119.92 -9.22 1.50e+00 4.44e-01 3.78e+01 angle pdb=" C9 F86 G 4 " pdb=" N1 F86 G 4 " pdb=" N2 F86 G 4 " ideal model delta sigma weight residual 124.86 119.91 4.95 1.00e+00 1.00e+00 2.45e+01 ... (remaining 15044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5876 17.75 - 35.50: 558 35.50 - 53.26: 102 53.26 - 71.01: 51 71.01 - 88.76: 16 Dihedral angle restraints: 6603 sinusoidal: 2875 harmonic: 3728 Sorted by residual: dihedral pdb=" CA TRP D 182 " pdb=" C TRP D 182 " pdb=" N PRO D 183 " pdb=" CA PRO D 183 " ideal model delta harmonic sigma weight residual 180.00 143.54 36.46 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA TYR A 606 " pdb=" C TYR A 606 " pdb=" N SER A 607 " pdb=" CA SER A 607 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASP A 109 " pdb=" C ASP A 109 " pdb=" N MET A 110 " pdb=" CA MET A 110 " ideal model delta harmonic sigma weight residual 180.00 154.11 25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 6600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1468 0.060 - 0.120: 229 0.120 - 0.180: 18 0.180 - 0.239: 3 0.239 - 0.299: 2 Chirality restraints: 1720 Sorted by residual: chirality pdb=" P C F -3 " pdb=" OP1 C F -3 " pdb=" OP2 C F -3 " pdb=" O5' C F -3 " both_signs ideal model delta sigma weight residual True 2.41 -2.11 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB THR A 120 " pdb=" CA THR A 120 " pdb=" OG1 THR A 120 " pdb=" CG2 THR A 120 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3 F86 G 4 " pdb=" C2 F86 G 4 " pdb=" C4 F86 G 4 " pdb=" O3 F86 G 4 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 1717 not shown) Planarity restraints: 1807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 182 " 0.055 5.00e-02 4.00e+02 8.31e-02 1.10e+01 pdb=" N PRO D 183 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C F -2 " 0.040 2.00e-02 2.50e+03 2.09e-02 9.78e+00 pdb=" N1 C F -2 " -0.042 2.00e-02 2.50e+03 pdb=" C2 C F -2 " -0.014 2.00e-02 2.50e+03 pdb=" O2 C F -2 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C F -2 " 0.011 2.00e-02 2.50e+03 pdb=" C4 C F -2 " 0.010 2.00e-02 2.50e+03 pdb=" N4 C F -2 " 0.005 2.00e-02 2.50e+03 pdb=" C5 C F -2 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C F -2 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C F -3 " 0.015 2.00e-02 2.50e+03 1.69e-02 6.39e+00 pdb=" N1 C F -3 " -0.022 2.00e-02 2.50e+03 pdb=" C2 C F -3 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C F -3 " -0.009 2.00e-02 2.50e+03 pdb=" N3 C F -3 " 0.022 2.00e-02 2.50e+03 pdb=" C4 C F -3 " -0.033 2.00e-02 2.50e+03 pdb=" N4 C F -3 " 0.013 2.00e-02 2.50e+03 pdb=" C5 C F -3 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C F -3 " 0.006 2.00e-02 2.50e+03 ... (remaining 1804 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2573 2.78 - 3.31: 9523 3.31 - 3.84: 17807 3.84 - 4.37: 22073 4.37 - 4.90: 36991 Nonbonded interactions: 88967 Sorted by model distance: nonbonded pdb=" OD2 ASP A 170 " pdb=" NH2 ARG A 173 " model vdw 2.256 3.120 nonbonded pdb=" O SER C 54 " pdb=" OG SER C 57 " model vdw 2.291 3.040 nonbonded pdb=" NH2 ARG A 279 " pdb=" OG SER A 318 " model vdw 2.302 3.120 nonbonded pdb=" O SER D 151 " pdb=" OG SER D 151 " model vdw 2.305 3.040 nonbonded pdb=" O GLU A 144 " pdb=" OG1 THR A 148 " model vdw 2.312 3.040 ... (remaining 88962 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 individual isotropic 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: 2.090 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 35.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 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 : 0.007 0.250 10985 Z= 0.415 Angle : 0.675 26.321 15049 Z= 0.408 Chirality : 0.044 0.299 1720 Planarity : 0.004 0.083 1807 Dihedral : 15.538 88.760 4191 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -2.91 (0.20), residues: 1246 helix: -1.20 (0.19), residues: 588 sheet: -2.00 (0.39), residues: 129 loop : -2.70 (0.22), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.017 0.001 PHE A 741 TYR 0.013 0.001 TYR A 788 ARG 0.002 0.000 ARG A 640 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.173 Fit side-chains REVERT: A 794 MET cc_start: 0.9111 (ttp) cc_final: 0.8884 (ttp) outliers start: 0 outliers final: 1 residues processed: 146 average time/residue: 1.3373 time to fit residues: 209.4250 Evaluate side-chains 120 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 9 ASN A 75 HIS A 81 GLN A 99 HIS A 138 ASN A 168 ASN A 312 ASN A 356 ASN ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 534 ASN A 613 HIS A 725 HIS B 140 ASN B 158 GLN B 192 ASN C 31 GLN C 69 ASN D 105 ASN D 108 ASN D 109 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10985 Z= 0.205 Angle : 0.545 7.589 15049 Z= 0.285 Chirality : 0.041 0.159 1720 Planarity : 0.004 0.074 1807 Dihedral : 13.004 82.802 1858 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.90 % Allowed : 10.40 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.55 (0.22), residues: 1246 helix: 0.03 (0.21), residues: 593 sheet: -1.21 (0.41), residues: 131 loop : -2.21 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 182 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.003 0.000 ARG A 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.158 Fit side-chains REVERT: A 756 MET cc_start: 0.8984 (ttp) cc_final: 0.8773 (ttm) REVERT: A 794 MET cc_start: 0.9057 (ttp) cc_final: 0.8760 (ttp) REVERT: B 168 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7943 (mm-40) outliers start: 21 outliers final: 9 residues processed: 147 average time/residue: 1.1715 time to fit residues: 186.5620 Evaluate side-chains 125 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain D residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 497 ASN A 734 ASN C 36 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10985 Z= 0.295 Angle : 0.566 8.328 15049 Z= 0.298 Chirality : 0.042 0.167 1720 Planarity : 0.004 0.072 1807 Dihedral : 12.973 77.498 1858 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.44 % Allowed : 12.57 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.15 (0.23), residues: 1246 helix: 0.38 (0.22), residues: 593 sheet: -0.93 (0.43), residues: 131 loop : -2.07 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.007 0.001 HIS A 309 PHE 0.017 0.002 PHE A 694 TYR 0.014 0.001 TYR A 788 ARG 0.003 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 123 time to evaluate : 1.234 Fit side-chains REVERT: A 138 ASN cc_start: 0.7476 (t0) cc_final: 0.7188 (t0) REVERT: A 794 MET cc_start: 0.9120 (ttp) cc_final: 0.8820 (ttp) REVERT: D 129 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7655 (mtp) outliers start: 27 outliers final: 16 residues processed: 135 average time/residue: 1.2923 time to fit residues: 188.3352 Evaluate side-chains 135 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 167 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 705 ASN A 734 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10985 Z= 0.156 Angle : 0.495 7.387 15049 Z= 0.261 Chirality : 0.039 0.149 1720 Planarity : 0.003 0.064 1807 Dihedral : 12.899 74.472 1856 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.99 % Allowed : 14.01 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.70 (0.24), residues: 1246 helix: 0.73 (0.22), residues: 598 sheet: -0.67 (0.44), residues: 131 loop : -1.87 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 182 HIS 0.006 0.001 HIS A 309 PHE 0.013 0.001 PHE A 753 TYR 0.013 0.001 TYR A 788 ARG 0.004 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.267 Fit side-chains REVERT: A 138 ASN cc_start: 0.7377 (t0) cc_final: 0.7110 (t0) REVERT: A 543 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7620 (m110) REVERT: A 794 MET cc_start: 0.9057 (ttp) cc_final: 0.8781 (ttp) REVERT: A 902 MET cc_start: 0.6986 (ptp) cc_final: 0.6701 (ptm) REVERT: B 127 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8719 (ttpt) outliers start: 22 outliers final: 14 residues processed: 150 average time/residue: 1.1756 time to fit residues: 191.1711 Evaluate side-chains 141 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 136 ASN Chi-restraints excluded: chain D residue 167 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 90 optimal weight: 0.0470 chunk 50 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 568 ASN A 790 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10985 Z= 0.192 Angle : 0.516 8.781 15049 Z= 0.270 Chirality : 0.040 0.156 1720 Planarity : 0.003 0.062 1807 Dihedral : 12.833 73.158 1856 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.53 % Allowed : 14.65 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.51 (0.24), residues: 1246 helix: 0.85 (0.22), residues: 598 sheet: -0.53 (0.44), residues: 132 loop : -1.72 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 182 HIS 0.006 0.001 HIS A 309 PHE 0.015 0.001 PHE A 753 TYR 0.014 0.001 TYR A 788 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.184 Fit side-chains REVERT: A 138 ASN cc_start: 0.7440 (t0) cc_final: 0.7164 (t0) REVERT: A 543 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7641 (m110) REVERT: A 794 MET cc_start: 0.9086 (ttp) cc_final: 0.8799 (ttp) REVERT: A 902 MET cc_start: 0.6935 (ptp) cc_final: 0.6632 (ptm) REVERT: B 168 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7949 (mm-40) REVERT: D 127 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7173 (tttt) REVERT: D 129 MET cc_start: 0.7922 (mtp) cc_final: 0.7534 (mtt) outliers start: 28 outliers final: 15 residues processed: 141 average time/residue: 1.1693 time to fit residues: 178.6697 Evaluate side-chains 140 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 127 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 56 optimal weight: 0.0070 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 overall best weight: 1.2204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 790 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10985 Z= 0.226 Angle : 0.530 8.003 15049 Z= 0.277 Chirality : 0.041 0.158 1720 Planarity : 0.004 0.060 1807 Dihedral : 12.785 73.195 1856 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.53 % Allowed : 15.55 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.43 (0.24), residues: 1246 helix: 0.90 (0.22), residues: 597 sheet: -0.41 (0.44), residues: 132 loop : -1.68 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 290 HIS 0.007 0.001 HIS A 309 PHE 0.021 0.001 PHE A 340 TYR 0.015 0.001 TYR A 788 ARG 0.002 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 1.205 Fit side-chains REVERT: A 138 ASN cc_start: 0.7505 (t0) cc_final: 0.7221 (t0) REVERT: A 543 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7625 (m110) REVERT: A 734 ASN cc_start: 0.8078 (t0) cc_final: 0.7875 (t0) REVERT: A 794 MET cc_start: 0.9112 (ttp) cc_final: 0.8802 (ttp) REVERT: A 902 MET cc_start: 0.6945 (ptp) cc_final: 0.6619 (ptm) REVERT: C 18 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8470 (tp40) REVERT: D 127 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7190 (tttt) REVERT: D 129 MET cc_start: 0.7925 (mtp) cc_final: 0.7546 (mtt) outliers start: 28 outliers final: 17 residues processed: 142 average time/residue: 1.1449 time to fit residues: 176.7799 Evaluate side-chains 141 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 136 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.4980 chunk 121 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 568 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10985 Z= 0.151 Angle : 0.495 7.548 15049 Z= 0.258 Chirality : 0.039 0.155 1720 Planarity : 0.003 0.056 1807 Dihedral : 12.695 73.083 1856 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.62 % Allowed : 15.28 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.15 (0.24), residues: 1246 helix: 1.11 (0.22), residues: 594 sheet: -0.26 (0.44), residues: 132 loop : -1.49 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 182 HIS 0.006 0.001 HIS A 309 PHE 0.017 0.001 PHE A 340 TYR 0.014 0.001 TYR A 788 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.299 Fit side-chains REVERT: A 18 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7345 (mtm-85) REVERT: A 138 ASN cc_start: 0.7268 (t0) cc_final: 0.7012 (t0) REVERT: A 543 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7699 (m110) REVERT: A 794 MET cc_start: 0.9062 (ttp) cc_final: 0.8762 (ttp) REVERT: A 902 MET cc_start: 0.6915 (ptp) cc_final: 0.6641 (ptm) REVERT: B 168 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7967 (mm-40) REVERT: D 127 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7192 (tttt) REVERT: D 129 MET cc_start: 0.7907 (mtp) cc_final: 0.7503 (mtt) outliers start: 29 outliers final: 17 residues processed: 140 average time/residue: 1.2306 time to fit residues: 186.3621 Evaluate side-chains 139 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 CYS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 136 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.2227 > 50: distance: 20 - 46: 20.634 distance: 24 - 54: 5.415 distance: 28 - 62: 3.306 distance: 38 - 46: 19.303 distance: 39 - 70: 5.065 distance: 46 - 47: 15.803 distance: 47 - 48: 17.014 distance: 47 - 50: 14.850 distance: 48 - 49: 11.235 distance: 48 - 54: 9.761 distance: 49 - 79: 13.965 distance: 50 - 51: 12.796 distance: 51 - 52: 5.707 distance: 51 - 53: 12.594 distance: 54 - 55: 8.326 distance: 55 - 56: 6.238 distance: 56 - 57: 9.419 distance: 56 - 62: 5.711 distance: 57 - 86: 7.895 distance: 58 - 59: 10.148 distance: 59 - 60: 4.253 distance: 60 - 61: 5.308 distance: 63 - 64: 6.489 distance: 64 - 65: 9.948 distance: 64 - 70: 4.348 distance: 65 - 93: 22.464 distance: 66 - 67: 4.884 distance: 67 - 68: 6.280 distance: 67 - 69: 3.567 distance: 70 - 71: 7.979 distance: 71 - 72: 12.064 distance: 71 - 74: 15.031 distance: 72 - 73: 7.500 distance: 72 - 79: 7.324 distance: 74 - 75: 16.790 distance: 75 - 76: 6.008 distance: 76 - 77: 11.359 distance: 77 - 78: 5.168 distance: 79 - 80: 12.067 distance: 80 - 81: 14.164 distance: 80 - 83: 16.623 distance: 81 - 82: 12.351 distance: 81 - 86: 23.757 distance: 83 - 84: 14.646 distance: 83 - 85: 23.936 distance: 86 - 87: 14.601 distance: 87 - 88: 13.318 distance: 87 - 90: 9.663 distance: 88 - 89: 21.559 distance: 88 - 93: 16.176 distance: 90 - 91: 27.696 distance: 90 - 92: 16.855 distance: 93 - 94: 29.112 distance: 94 - 95: 39.702 distance: 94 - 97: 10.256 distance: 95 - 96: 48.577 distance: 95 - 105: 32.975 distance: 97 - 98: 15.927 distance: 98 - 99: 13.889 distance: 98 - 100: 11.554 distance: 99 - 101: 21.098 distance: 100 - 102: 21.171 distance: 101 - 103: 13.409 distance: 102 - 103: 10.299 distance: 103 - 104: 4.032 distance: 105 - 106: 23.854 distance: 106 - 107: 27.564 distance: 106 - 109: 39.764 distance: 107 - 108: 16.846 distance: 107 - 111: 21.077 distance: 109 - 110: 40.861 distance: 111 - 112: 23.311 distance: 112 - 113: 28.870 distance: 112 - 115: 27.258 distance: 113 - 114: 12.182 distance: 113 - 119: 21.498 distance: 115 - 116: 12.205 distance: 116 - 117: 23.238 distance: 116 - 118: 12.753 distance: 119 - 120: 10.130 distance: 120 - 121: 9.747 distance: 120 - 123: 19.167 distance: 121 - 122: 11.413 distance: 121 - 126: 6.984 distance: 123 - 124: 6.351 distance: 123 - 125: 13.176