Starting phenix.real_space_refine on Sun Sep 29 14:03:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/09_2024/6ve3_21153.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/09_2024/6ve3_21153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/09_2024/6ve3_21153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/09_2024/6ve3_21153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/09_2024/6ve3_21153.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ve3_21153/09_2024/6ve3_21153.cif" } resolution = 4.3 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= 0.005 sd= 0.075 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: 3 Type Number sf(0) Gaussians C 13328 2.51 5 N 4578 2.21 5 O 4578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22484 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 1606 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 277} Link IDs: {'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 923 Unresolved non-hydrogen angles: 1181 Unresolved non-hydrogen dihedrals: 739 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 1, 'TYR:plan': 8, 'ASN:plan1': 19, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 9, 'GLU:plan': 20, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 460 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, N Time building chain proxies: 6.55, per 1000 atoms: 0.29 Number of scatterers: 22484 At special positions: 0 Unit cell: (143.55, 143.55, 129.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 4578 8.00 N 4578 7.00 C 13328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.42 Conformation dependent library (CDL) restraints added in 4.4 seconds 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8344 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 57 sheets defined 25.4% alpha, 65.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 12 through 27 Processing helix chain 'A' and resid 44 through 59 Processing helix chain 'A' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'B' and resid 12 through 27 Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'C' and resid 12 through 27 Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS C 107 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 removed outlier: 4.220A pdb=" N VAL C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG C 297 " --> pdb=" O PRO C 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 298 " --> pdb=" O TYR C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 325 Processing helix chain 'D' and resid 12 through 27 Processing helix chain 'D' and resid 44 through 59 Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS D 107 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG D 297 " --> pdb=" O PRO D 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 298 " --> pdb=" O TYR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'E' and resid 12 through 27 Processing helix chain 'E' and resid 44 through 59 Processing helix chain 'E' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS E 107 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 246 Processing helix chain 'E' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU E 292 " --> pdb=" O PHE E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG E 297 " --> pdb=" O PRO E 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU E 298 " --> pdb=" O TYR E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 325 Processing helix chain 'F' and resid 12 through 27 Processing helix chain 'F' and resid 44 through 59 Processing helix chain 'F' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS F 107 " --> pdb=" O ASN F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL F 136 " --> pdb=" O PRO F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'F' and resid 286 through 292 removed outlier: 3.688A pdb=" N LEU F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 299 removed outlier: 3.617A pdb=" N ARG F 297 " --> pdb=" O PRO F 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 298 " --> pdb=" O TYR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 325 Processing helix chain 'G' and resid 12 through 27 Processing helix chain 'G' and resid 44 through 59 Processing helix chain 'G' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 removed outlier: 4.217A pdb=" N VAL G 136 " --> pdb=" O PRO G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 246 Processing helix chain 'G' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU G 292 " --> pdb=" O PHE G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG G 297 " --> pdb=" O PRO G 293 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU G 298 " --> pdb=" O TYR G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 325 Processing helix chain 'H' and resid 12 through 27 Processing helix chain 'H' and resid 44 through 59 Processing helix chain 'H' and resid 103 through 115 removed outlier: 3.817A pdb=" N LYS H 107 " --> pdb=" O ASN H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL H 136 " --> pdb=" O PRO H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 246 Processing helix chain 'H' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU H 292 " --> pdb=" O PHE H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG H 297 " --> pdb=" O PRO H 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 298 " --> pdb=" O TYR H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 325 Processing helix chain 'I' and resid 12 through 27 Processing helix chain 'I' and resid 44 through 59 Processing helix chain 'I' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS I 107 " --> pdb=" O ASN I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL I 136 " --> pdb=" O PRO I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 246 Processing helix chain 'I' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU I 292 " --> pdb=" O PHE I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 299 removed outlier: 3.617A pdb=" N ARG I 297 " --> pdb=" O PRO I 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU I 298 " --> pdb=" O TYR I 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 320 through 325 Processing helix chain 'J' and resid 12 through 27 Processing helix chain 'J' and resid 44 through 59 Processing helix chain 'J' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS J 107 " --> pdb=" O ASN J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL J 136 " --> pdb=" O PRO J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 246 Processing helix chain 'J' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU J 292 " --> pdb=" O PHE J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG J 297 " --> pdb=" O PRO J 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU J 298 " --> pdb=" O TYR J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 320 through 325 Processing helix chain 'K' and resid 12 through 27 Processing helix chain 'K' and resid 44 through 59 Processing helix chain 'K' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS K 107 " --> pdb=" O ASN K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL K 136 " --> pdb=" O PRO K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 246 Processing helix chain 'K' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU K 292 " --> pdb=" O PHE K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 299 removed outlier: 3.617A pdb=" N ARG K 297 " --> pdb=" O PRO K 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU K 298 " --> pdb=" O TYR K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 320 through 325 Processing helix chain 'L' and resid 12 through 27 Processing helix chain 'L' and resid 44 through 59 Processing helix chain 'L' and resid 103 through 115 removed outlier: 3.814A pdb=" N LYS L 107 " --> pdb=" O ASN L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 removed outlier: 4.218A pdb=" N VAL L 136 " --> pdb=" O PRO L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 246 Processing helix chain 'L' and resid 286 through 292 removed outlier: 3.688A pdb=" N LEU L 292 " --> pdb=" O PHE L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 299 removed outlier: 3.614A pdb=" N ARG L 297 " --> pdb=" O PRO L 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU L 298 " --> pdb=" O TYR L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 325 Processing helix chain 'M' and resid 12 through 27 Processing helix chain 'M' and resid 44 through 59 Processing helix chain 'M' and resid 103 through 115 removed outlier: 3.816A pdb=" N LYS M 107 " --> pdb=" O ASN M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 142 removed outlier: 4.220A pdb=" N VAL M 136 " --> pdb=" O PRO M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 241 through 246 Processing helix chain 'M' and resid 286 through 292 removed outlier: 3.687A pdb=" N LEU M 292 " --> pdb=" O PHE M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 292 through 299 removed outlier: 3.615A pdb=" N ARG M 297 " --> pdb=" O PRO M 293 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU M 298 " --> pdb=" O TYR M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 320 through 325 Processing helix chain 'N' and resid 12 through 27 Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 103 through 115 removed outlier: 3.815A pdb=" N LYS N 107 " --> pdb=" O ASN N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 142 removed outlier: 4.219A pdb=" N VAL N 136 " --> pdb=" O PRO N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 241 through 246 Processing helix chain 'N' and resid 286 through 292 removed outlier: 3.686A pdb=" N LEU N 292 " --> pdb=" O PHE N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 299 removed outlier: 3.616A pdb=" N ARG N 297 " --> pdb=" O PRO N 293 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU N 298 " --> pdb=" O TYR N 294 " (cutoff:3.500A) Processing helix chain 'N' and resid 320 through 325 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 152 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP A 302 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL A 84 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG A 300 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 272 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU A 315 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL A 270 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 271 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 152 Processing sheet with id=AA5, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP B 302 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL B 84 " --> pdb=" O ARG B 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 300 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 272 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU B 315 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL B 270 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE B 271 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 148 through 152 Processing sheet with id=AA7, first strand: chain 'C' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP C 302 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL C 84 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG C 300 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY C 272 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU C 315 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL C 270 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE C 271 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU D 166 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 152 Processing sheet with id=AA9, first strand: chain 'D' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP D 302 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL D 84 " --> pdb=" O ARG D 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG D 300 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY D 272 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU D 315 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL D 270 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE D 271 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU E 166 " --> pdb=" O LYS D 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 148 through 152 Processing sheet with id=AB2, first strand: chain 'E' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP E 302 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL E 84 " --> pdb=" O ARG E 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG E 300 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY E 272 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU E 315 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL E 270 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE E 271 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 166 " --> pdb=" O LYS E 285 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 148 through 152 Processing sheet with id=AB4, first strand: chain 'F' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP F 302 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL F 84 " --> pdb=" O ARG F 300 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG F 300 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY F 272 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU F 315 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL F 270 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE F 271 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 148 through 152 Processing sheet with id=AB6, first strand: chain 'G' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP G 302 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL G 84 " --> pdb=" O ARG G 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG G 300 " --> pdb=" O VAL G 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY G 272 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU G 315 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL G 270 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE G 271 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU H 166 " --> pdb=" O LYS G 285 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 148 through 152 Processing sheet with id=AB8, first strand: chain 'H' and resid 93 through 95 removed outlier: 3.581A pdb=" N ASP H 302 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL H 84 " --> pdb=" O ARG H 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG H 300 " --> pdb=" O VAL H 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY H 272 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU H 315 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL H 270 " --> pdb=" O LEU H 315 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE H 271 " --> pdb=" O VAL I 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 148 through 152 Processing sheet with id=AC1, first strand: chain 'I' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP I 302 " --> pdb=" O LEU I 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL I 84 " --> pdb=" O ARG I 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG I 300 " --> pdb=" O VAL I 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY I 272 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU I 315 " --> pdb=" O VAL I 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL I 270 " --> pdb=" O LEU I 315 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE I 271 " --> pdb=" O VAL J 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 148 through 152 Processing sheet with id=AC3, first strand: chain 'J' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP J 302 " --> pdb=" O LEU J 82 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL J 84 " --> pdb=" O ARG J 300 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG J 300 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY J 272 " --> pdb=" O VAL J 313 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU J 315 " --> pdb=" O VAL J 270 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL J 270 " --> pdb=" O LEU J 315 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE J 271 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU K 166 " --> pdb=" O LYS J 285 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 148 through 152 Processing sheet with id=AC5, first strand: chain 'K' and resid 93 through 95 removed outlier: 3.583A pdb=" N ASP K 302 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL K 84 " --> pdb=" O ARG K 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG K 300 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY K 272 " --> pdb=" O VAL K 313 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU K 315 " --> pdb=" O VAL K 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL K 270 " --> pdb=" O LEU K 315 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE K 271 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU L 166 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 148 through 152 Processing sheet with id=AC7, first strand: chain 'L' and resid 93 through 95 removed outlier: 3.582A pdb=" N ASP L 302 " --> pdb=" O LEU L 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL L 84 " --> pdb=" O ARG L 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG L 300 " --> pdb=" O VAL L 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY L 272 " --> pdb=" O VAL L 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU L 315 " --> pdb=" O VAL L 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL L 270 " --> pdb=" O LEU L 315 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE L 271 " --> pdb=" O VAL M 180 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU M 166 " --> pdb=" O LYS L 285 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 148 through 152 Processing sheet with id=AC9, first strand: chain 'M' and resid 93 through 95 removed outlier: 3.584A pdb=" N ASP M 302 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N VAL M 84 " --> pdb=" O ARG M 300 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG M 300 " --> pdb=" O VAL M 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY M 272 " --> pdb=" O VAL M 313 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU M 315 " --> pdb=" O VAL M 270 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL M 270 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE M 271 " --> pdb=" O VAL N 180 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 148 through 152 Processing sheet with id=AD2, first strand: chain 'N' and resid 93 through 95 removed outlier: 3.581A pdb=" N ASP N 302 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL N 84 " --> pdb=" O ARG N 300 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG N 300 " --> pdb=" O VAL N 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY N 272 " --> pdb=" O VAL N 313 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU N 315 " --> pdb=" O VAL N 270 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL N 270 " --> pdb=" O LEU N 315 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE N 271 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 166 " --> pdb=" O LYS N 285 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 117 through 119 Processing sheet with id=AD4, first strand: chain 'A' and resid 187 through 201 removed outlier: 3.869A pdb=" N ARG A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 228 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG D 228 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG E 228 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG F 228 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG G 228 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG H 228 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG I 228 " --> pdb=" O THR I 224 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG J 228 " --> pdb=" O THR J 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG K 228 " --> pdb=" O THR K 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG L 228 " --> pdb=" O THR L 224 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG M 228 " --> pdb=" O THR M 224 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG N 228 " --> pdb=" O THR N 224 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 2 through 7 Processing sheet with id=AD6, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AD7, first strand: chain 'C' and resid 2 through 7 Processing sheet with id=AD8, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AD9, first strand: chain 'D' and resid 2 through 7 Processing sheet with id=AE1, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AE2, first strand: chain 'E' and resid 2 through 7 Processing sheet with id=AE3, first strand: chain 'E' and resid 117 through 119 Processing sheet with id=AE4, first strand: chain 'F' and resid 2 through 7 Processing sheet with id=AE5, first strand: chain 'F' and resid 117 through 119 Processing sheet with id=AE6, first strand: chain 'G' and resid 2 through 7 Processing sheet with id=AE7, first strand: chain 'G' and resid 117 through 119 Processing sheet with id=AE8, first strand: chain 'H' and resid 2 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 117 through 119 Processing sheet with id=AF1, first strand: chain 'I' and resid 2 through 7 Processing sheet with id=AF2, first strand: chain 'I' and resid 117 through 119 Processing sheet with id=AF3, first strand: chain 'J' and resid 2 through 7 Processing sheet with id=AF4, first strand: chain 'J' and resid 117 through 119 Processing sheet with id=AF5, first strand: chain 'K' and resid 2 through 7 Processing sheet with id=AF6, first strand: chain 'K' and resid 117 through 119 Processing sheet with id=AF7, first strand: chain 'L' and resid 2 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 117 through 119 Processing sheet with id=AF9, first strand: chain 'M' and resid 2 through 7 Processing sheet with id=AG1, first strand: chain 'M' and resid 117 through 119 Processing sheet with id=AG2, first strand: chain 'N' and resid 2 through 7 Processing sheet with id=AG3, first strand: chain 'N' and resid 117 through 119 2750 hydrogen bonds defined for protein. 7620 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: 10.90 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 4578 1.29 - 1.35: 4550 1.35 - 1.42: 0 1.42 - 1.49: 4578 1.49 - 1.56: 8750 Bond restraints: 22456 Sorted by residual: bond pdb=" CA SER J 203 " pdb=" CB SER J 203 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.33e-02 5.65e+03 3.68e+00 bond pdb=" CA SER G 203 " pdb=" CB SER G 203 " ideal model delta sigma weight residual 1.524 1.498 0.025 1.33e-02 5.65e+03 3.57e+00 bond pdb=" CA SER C 203 " pdb=" CB SER C 203 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.33e-02 5.65e+03 3.56e+00 bond pdb=" CA SER K 203 " pdb=" CB SER K 203 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.33e-02 5.65e+03 3.52e+00 bond pdb=" C SER G 209 " pdb=" N PHE G 210 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.30e-02 5.92e+03 3.42e+00 ... (remaining 22451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 28881 1.97 - 3.94: 1810 3.94 - 5.92: 355 5.92 - 7.89: 76 7.89 - 9.86: 28 Bond angle restraints: 31150 Sorted by residual: angle pdb=" N SER D 203 " pdb=" CA SER D 203 " pdb=" C SER D 203 " ideal model delta sigma weight residual 108.56 118.41 -9.85 1.74e+00 3.30e-01 3.21e+01 angle pdb=" N SER F 203 " pdb=" CA SER F 203 " pdb=" C SER F 203 " ideal model delta sigma weight residual 108.56 118.40 -9.84 1.74e+00 3.30e-01 3.20e+01 angle pdb=" N SER L 203 " pdb=" CA SER L 203 " pdb=" C SER L 203 " ideal model delta sigma weight residual 108.56 118.39 -9.83 1.74e+00 3.30e-01 3.19e+01 angle pdb=" N SER H 203 " pdb=" CA SER H 203 " pdb=" C SER H 203 " ideal model delta sigma weight residual 108.56 118.39 -9.83 1.74e+00 3.30e-01 3.19e+01 angle pdb=" N SER A 203 " pdb=" CA SER A 203 " pdb=" C SER A 203 " ideal model delta sigma weight residual 108.56 118.35 -9.79 1.74e+00 3.30e-01 3.17e+01 ... (remaining 31145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.74: 9907 3.74 - 7.48: 2160 7.48 - 11.22: 589 11.22 - 14.96: 210 14.96 - 18.70: 28 Dihedral angle restraints: 12894 sinusoidal: 0 harmonic: 12894 Sorted by residual: dihedral pdb=" C SER D 203 " pdb=" N SER D 203 " pdb=" CA SER D 203 " pdb=" CB SER D 203 " ideal model delta harmonic sigma weight residual -122.60 -133.37 10.77 0 2.50e+00 1.60e-01 1.85e+01 dihedral pdb=" C SER H 203 " pdb=" N SER H 203 " pdb=" CA SER H 203 " pdb=" CB SER H 203 " ideal model delta harmonic sigma weight residual -122.60 -133.34 10.74 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C SER J 203 " pdb=" N SER J 203 " pdb=" CA SER J 203 " pdb=" CB SER J 203 " ideal model delta harmonic sigma weight residual -122.60 -133.27 10.67 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 12891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 3696 0.106 - 0.212: 448 0.212 - 0.318: 14 0.318 - 0.424: 0 0.424 - 0.530: 14 Chirality restraints: 4172 Sorted by residual: chirality pdb=" CA SER D 203 " pdb=" N SER D 203 " pdb=" C SER D 203 " pdb=" CB SER D 203 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" CA SER H 203 " pdb=" N SER H 203 " pdb=" C SER H 203 " pdb=" CB SER H 203 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CA SER F 203 " pdb=" N SER F 203 " pdb=" C SER F 203 " pdb=" CB SER F 203 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.90e+00 ... (remaining 4169 not shown) Planarity restraints: 4550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 201 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C SER A 201 " -0.077 2.00e-02 2.50e+03 pdb=" O SER A 201 " 0.029 2.00e-02 2.50e+03 pdb=" N SER A 202 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 201 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C SER C 201 " -0.077 2.00e-02 2.50e+03 pdb=" O SER C 201 " 0.029 2.00e-02 2.50e+03 pdb=" N SER C 202 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 135 " -0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C PHE L 135 " 0.077 2.00e-02 2.50e+03 pdb=" O PHE L 135 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL L 136 " -0.026 2.00e-02 2.50e+03 ... (remaining 4547 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3707 2.77 - 3.30: 20769 3.30 - 3.83: 34554 3.83 - 4.37: 36610 4.37 - 4.90: 61221 Nonbonded interactions: 156861 Sorted by model distance: nonbonded pdb=" O SER E 203 " pdb=" N GLY F 204 " model vdw 2.233 3.120 nonbonded pdb=" O SER L 203 " pdb=" N GLY M 204 " model vdw 2.234 3.120 nonbonded pdb=" N GLY A 204 " pdb=" O SER N 203 " model vdw 2.239 3.120 nonbonded pdb=" O SER G 203 " pdb=" N GLY H 204 " model vdw 2.242 3.120 nonbonded pdb=" O SER I 203 " pdb=" N GLY J 204 " model vdw 2.264 3.120 ... (remaining 156856 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.380 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: 0.040 Extract box with map and model: 0.860 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 50.870 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.080 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 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 : 0.005 0.036 22456 Z= 0.380 Angle : 1.167 9.861 31150 Z= 0.742 Chirality : 0.071 0.530 4172 Planarity : 0.007 0.045 4550 Dihedral : 5.955 18.704 4550 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.41 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 4522 helix: 0.88 (0.17), residues: 854 sheet: 1.02 (0.11), residues: 1946 loop : -2.32 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.535 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2002 time to fit residues: 29.7667 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 378 optimal weight: 30.0000 chunk 339 optimal weight: 6.9990 chunk 188 optimal weight: 50.0000 chunk 115 optimal weight: 5.9990 chunk 229 optimal weight: 20.0000 chunk 181 optimal weight: 30.0000 chunk 351 optimal weight: 5.9990 chunk 135 optimal weight: 50.0000 chunk 213 optimal weight: 40.0000 chunk 261 optimal weight: 6.9990 chunk 406 optimal weight: 20.0000 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 22456 Z= 0.353 Angle : 0.786 7.036 31150 Z= 0.486 Chirality : 0.055 0.148 4172 Planarity : 0.005 0.027 4550 Dihedral : 7.726 32.283 4550 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.08 (0.12), residues: 4522 helix: 1.01 (0.18), residues: 826 sheet: 1.08 (0.10), residues: 2184 loop : -2.15 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.486 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1944 time to fit residues: 29.1391 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 226 optimal weight: 20.0000 chunk 126 optimal weight: 6.9990 chunk 338 optimal weight: 20.0000 chunk 277 optimal weight: 40.0000 chunk 112 optimal weight: 7.9990 chunk 407 optimal weight: 50.0000 chunk 440 optimal weight: 10.0000 chunk 362 optimal weight: 40.0000 chunk 404 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 326 optimal weight: 20.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.7205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22456 Z= 0.308 Angle : 0.691 6.664 31150 Z= 0.434 Chirality : 0.053 0.137 4172 Planarity : 0.004 0.023 4550 Dihedral : 7.401 26.863 4550 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -0.29 (0.12), residues: 4522 helix: 1.42 (0.19), residues: 742 sheet: 0.71 (0.10), residues: 2212 loop : -2.41 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.522 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2022 time to fit residues: 30.1563 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 402 optimal weight: 30.0000 chunk 306 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 194 optimal weight: 8.9990 chunk 273 optimal weight: 50.0000 chunk 409 optimal weight: 30.0000 chunk 433 optimal weight: 50.0000 chunk 213 optimal weight: 30.0000 chunk 387 optimal weight: 30.0000 chunk 116 optimal weight: 7.9990 overall best weight: 12.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.8475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22456 Z= 0.403 Angle : 0.780 7.768 31150 Z= 0.493 Chirality : 0.053 0.148 4172 Planarity : 0.005 0.022 4550 Dihedral : 8.351 29.604 4550 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.29 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.41 (0.12), residues: 4522 helix: -0.58 (0.17), residues: 924 sheet: 0.76 (0.12), residues: 1890 loop : -3.24 (0.12), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.294 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1945 time to fit residues: 28.9247 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 360 optimal weight: 30.0000 chunk 245 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 322 optimal weight: 5.9990 chunk 178 optimal weight: 30.0000 chunk 369 optimal weight: 50.0000 chunk 299 optimal weight: 0.0870 chunk 0 optimal weight: 30.0000 chunk 221 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 109 optimal weight: 30.0000 overall best weight: 8.2168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.8621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22456 Z= 0.281 Angle : 0.646 7.497 31150 Z= 0.402 Chirality : 0.053 0.138 4172 Planarity : 0.004 0.019 4550 Dihedral : 7.416 28.201 4550 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -1.48 (0.12), residues: 4522 helix: 0.13 (0.18), residues: 924 sheet: 0.41 (0.12), residues: 1904 loop : -3.40 (0.12), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.491 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1979 time to fit residues: 29.4901 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 448 random chunks: chunk 145 optimal weight: 30.0000 chunk 389 optimal weight: 6.9990 chunk 85 optimal weight: 40.0000 chunk 254 optimal weight: 9.9990 chunk 106 optimal weight: 30.0000 chunk 433 optimal weight: 50.0000 chunk 359 optimal weight: 50.0000 chunk 200 optimal weight: 50.0000 chunk 36 optimal weight: 40.0000 chunk 143 optimal weight: 6.9990 chunk 227 optimal weight: 30.0000 overall best weight: 16.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.9722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 22456 Z= 0.488 Angle : 0.901 10.039 31150 Z= 0.568 Chirality : 0.054 0.184 4172 Planarity : 0.005 0.021 4550 Dihedral : 9.221 36.342 4550 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.88 % Allowed : 12.36 % Favored : 86.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.44 % 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: -2.18 (0.12), residues: 4522 helix: -1.07 (0.17), residues: 812 sheet: -0.12 (0.12), residues: 1960 loop : -3.23 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 86 PHE 0.000 0.000 PHE A 20 TYR 0.000 0.000 TYR A 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9044 Ramachandran restraints generated. 4522 Oldfield, 0 Emsley, 4522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.530 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2026 time to fit residues: 30.0162 Evaluate side-chains 70 residues out of total 3878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 64.445 > 50: distance: 9 - 115: 9.392 distance: 12 - 112: 13.820 distance: 19 - 105: 7.287 distance: 22 - 102: 5.963 distance: 29 - 95: 29.975 distance: 32 - 92: 27.129 distance: 38 - 85: 27.143 distance: 41 - 82: 23.594 distance: 48 - 75: 30.444 distance: 51 - 72: 26.265 distance: 64 - 67: 7.949 distance: 67 - 68: 25.372 distance: 69 - 70: 41.472 distance: 72 - 73: 37.536 distance: 73 - 74: 8.814 distance: 73 - 76: 27.911 distance: 74 - 75: 11.346 distance: 74 - 77: 9.992 distance: 77 - 78: 42.561 distance: 78 - 79: 40.775 distance: 78 - 81: 39.658 distance: 79 - 82: 29.117 distance: 82 - 83: 38.830 distance: 83 - 84: 22.742 distance: 83 - 86: 11.132 distance: 84 - 85: 5.592 distance: 84 - 87: 3.948 distance: 87 - 88: 12.218 distance: 87 - 153: 30.187 distance: 88 - 89: 4.860 distance: 88 - 91: 11.532 distance: 89 - 90: 6.623 distance: 89 - 92: 6.739 distance: 90 - 150: 27.797 distance: 92 - 93: 6.984 distance: 93 - 94: 8.250 distance: 93 - 96: 15.085 distance: 94 - 95: 13.975 distance: 94 - 97: 6.447 distance: 97 - 98: 13.870 distance: 97 - 143: 27.142 distance: 98 - 99: 6.144 distance: 98 - 101: 17.797 distance: 99 - 100: 6.110 distance: 99 - 102: 6.654 distance: 100 - 140: 17.502 distance: 102 - 103: 3.134 distance: 103 - 104: 8.737 distance: 103 - 106: 8.340 distance: 104 - 105: 5.048 distance: 104 - 107: 6.751 distance: 107 - 108: 8.831 distance: 107 - 133: 6.842 distance: 108 - 109: 20.122 distance: 108 - 111: 5.809 distance: 109 - 110: 13.729 distance: 109 - 112: 16.069 distance: 110 - 130: 25.152 distance: 112 - 113: 13.036 distance: 113 - 114: 13.323 distance: 113 - 116: 17.379 distance: 114 - 115: 16.131 distance: 114 - 117: 9.304 distance: 117 - 124: 3.003