Starting phenix.real_space_refine on Fri Jul 3 21:58:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cge_30355/07_2026/7cge_30355.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cge_30355/07_2026/7cge_30355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cge_30355/07_2026/7cge_30355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cge_30355/07_2026/7cge_30355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cge_30355/07_2026/7cge_30355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cge_30355/07_2026/7cge_30355.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cge_30355/07_2026/7cge_30355.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cge_30355/07_2026/7cge_30355.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 68 5.16 5 C 10624 2.51 5 N 2654 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16406 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "B" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1996 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 18, 'TRANS': 244} Chain: "C" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "D" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "E" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1996 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 18, 'TRANS': 244} Chain: "F" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "G" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "I" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "J" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "K" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "L" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 306 Unusual residues: {'PGW': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 204 Unusual residues: {'PGW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.71, per 1000 atoms: 0.23 Number of scatterers: 16406 At special positions: 0 Unit cell: (106.526, 114.135, 141.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 12 15.00 O 3048 8.00 N 2654 7.00 C 10624 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: 1.26 Conformation dependent library (CDL) restraints added in 721.4 milliseconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 18 sheets defined 41.9% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 5 through 32 removed outlier: 3.740A pdb=" N LEU A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.597A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 55 through 79 removed outlier: 3.657A pdb=" N SER A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 99 through 126 removed outlier: 3.526A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 134 removed outlier: 3.530A pdb=" N GLU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 143 through 175 removed outlier: 3.896A pdb=" N ARG A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 3.503A pdb=" N VAL A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.602A pdb=" N MET A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 223 removed outlier: 3.500A pdb=" N LEU A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 258 removed outlier: 3.828A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 55 removed outlier: 3.510A pdb=" N ILE B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.658A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 121 through 132 removed outlier: 3.739A pdb=" N VAL B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.587A pdb=" N LEU B 145 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 157 Processing helix chain 'B' and resid 176 through 193 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 237 through 246 removed outlier: 3.735A pdb=" N PHE B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 51 through 68 removed outlier: 3.526A pdb=" N GLN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 88 removed outlier: 3.586A pdb=" N LEU C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 32 removed outlier: 3.741A pdb=" N LEU D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.597A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 79 removed outlier: 3.657A pdb=" N SER D 62 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 86 through 97 Processing helix chain 'D' and resid 99 through 126 removed outlier: 3.525A pdb=" N ALA D 104 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 134 removed outlier: 3.530A pdb=" N GLU D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 143 through 175 removed outlier: 3.896A pdb=" N ARG D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Proline residue: D 156 - end of helix removed outlier: 3.503A pdb=" N VAL D 160 " --> pdb=" O PRO D 156 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.602A pdb=" N MET D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 223 removed outlier: 3.501A pdb=" N LEU D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 258 removed outlier: 3.828A pdb=" N SER D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 55 removed outlier: 3.510A pdb=" N ILE E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.659A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 107 Processing helix chain 'E' and resid 121 through 132 removed outlier: 3.739A pdb=" N VAL E 132 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 145 removed outlier: 3.585A pdb=" N LEU E 145 " --> pdb=" O PRO E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 157 Processing helix chain 'E' and resid 176 through 193 Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 237 through 246 removed outlier: 3.735A pdb=" N PHE E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 51 through 68 removed outlier: 3.525A pdb=" N GLN F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 88 removed outlier: 3.586A pdb=" N LEU F 84 " --> pdb=" O LYS F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 27 Processing helix chain 'G' and resid 143 through 152 removed outlier: 3.826A pdb=" N ILE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 28 Processing helix chain 'H' and resid 144 through 151 Processing helix chain 'I' and resid 5 through 27 removed outlier: 3.568A pdb=" N TRP I 9 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU I 15 " --> pdb=" O GLY I 11 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA I 17 " --> pdb=" O PHE I 13 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS I 27 " --> pdb=" O PHE I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 152 removed outlier: 3.894A pdb=" N ILE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 27 Processing helix chain 'J' and resid 143 through 152 removed outlier: 4.005A pdb=" N ILE J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 28 Processing helix chain 'K' and resid 144 through 151 Processing helix chain 'L' and resid 5 through 26 removed outlier: 3.569A pdb=" N TRP L 9 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU L 15 " --> pdb=" O GLY L 11 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 152 removed outlier: 3.501A pdb=" N GLY L 148 " --> pdb=" O GLU L 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 32 removed outlier: 6.643A pdb=" N ILE B 23 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR B 17 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP B 25 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 15 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE B 27 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP B 13 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 9 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.609A pdb=" N HIS B 214 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 225 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 5 through 9 removed outlier: 8.753A pdb=" N ARG C 46 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 16 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N SER C 48 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N GLY C 18 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 50 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU C 20 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AA5, first strand: chain 'E' and resid 21 through 32 removed outlier: 6.642A pdb=" N ILE E 23 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR E 17 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP E 25 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER E 15 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ILE E 27 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP E 13 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 9 " --> pdb=" O VAL E 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 87 through 90 removed outlier: 3.610A pdb=" N HIS E 214 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 225 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 9 removed outlier: 8.753A pdb=" N ARG F 46 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU F 16 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N SER F 48 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N GLY F 18 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL F 50 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU F 20 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 41 through 42 Processing sheet with id=AA9, first strand: chain 'G' and resid 39 through 43 removed outlier: 8.417A pdb=" N VAL G 65 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL G 64 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE G 60 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY G 66 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 39 through 45 removed outlier: 3.773A pdb=" N LEU H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 63 through 66 removed outlier: 6.353A pdb=" N VAL H 58 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 73 through 74 removed outlier: 4.006A pdb=" N LEU I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N VAL I 65 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER I 59 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN I 115 " --> pdb=" O SER I 98 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER I 98 " --> pdb=" O ASN I 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 73 through 74 removed outlier: 4.006A pdb=" N LEU I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ILE I 134 " --> pdb=" O THR I 41 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR I 43 " --> pdb=" O ILE I 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 39 through 40 removed outlier: 3.904A pdb=" N THR J 83 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA J 69 " --> pdb=" O THR J 83 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N VAL J 65 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE J 60 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY J 66 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 73 through 74 removed outlier: 3.767A pdb=" N LEU J 79 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU J 42 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR J 43 " --> pdb=" O ILE J 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 73 through 74 removed outlier: 3.751A pdb=" N LEU K 79 " --> pdb=" O ASP K 74 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N ILE K 134 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N TYR K 43 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 63 through 66 removed outlier: 6.211A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 39 through 45 removed outlier: 6.793A pdb=" N ARG L 81 " --> pdb=" O ILE L 71 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE L 71 " --> pdb=" O ARG L 81 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N VAL L 65 " --> pdb=" O GLU L 87 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL L 58 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU L 114 " --> pdb=" O PRO L 57 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N SER L 59 " --> pdb=" O LEU L 114 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN L 115 " --> pdb=" O SER L 98 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER L 98 " --> pdb=" O ASN L 115 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2091 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: 2.69 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2643 1.31 - 1.43: 4026 1.43 - 1.56: 9824 1.56 - 1.68: 51 1.68 - 1.81: 124 Bond restraints: 16668 Sorted by residual: bond pdb=" C1 PGW A 301 " pdb=" O01 PGW A 301 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C1 PGW D 302 " pdb=" O01 PGW D 302 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C19 PGW A 301 " pdb=" O03 PGW A 301 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C19 PGW D 302 " pdb=" O03 PGW D 302 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" C1 PGW A 302 " pdb=" O01 PGW A 302 " ideal model delta sigma weight residual 1.332 1.418 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 16663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.86: 22382 6.86 - 13.73: 124 13.73 - 20.59: 0 20.59 - 27.46: 0 27.46 - 34.32: 12 Bond angle restraints: 22518 Sorted by residual: angle pdb=" C19 PGW D 304 " pdb=" C20 PGW D 304 " pdb=" C21 PGW D 304 " ideal model delta sigma weight residual 114.60 80.28 34.32 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C19 PGW A 303 " pdb=" C20 PGW A 303 " pdb=" C21 PGW A 303 " ideal model delta sigma weight residual 114.60 80.32 34.28 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C19 PGW A 304 " pdb=" C20 PGW A 304 " pdb=" C21 PGW A 304 " ideal model delta sigma weight residual 114.60 81.26 33.34 3.00e+00 1.11e-01 1.24e+02 angle pdb=" C19 PGW A 306 " pdb=" C20 PGW A 306 " pdb=" C21 PGW A 306 " ideal model delta sigma weight residual 114.60 81.29 33.31 3.00e+00 1.11e-01 1.23e+02 angle pdb=" C19 PGW J 201 " pdb=" C20 PGW J 201 " pdb=" C21 PGW J 201 " ideal model delta sigma weight residual 114.60 81.35 33.25 3.00e+00 1.11e-01 1.23e+02 ... (remaining 22513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.63: 9476 28.63 - 57.25: 446 57.25 - 85.88: 40 85.88 - 114.50: 26 114.50 - 143.13: 26 Dihedral angle restraints: 10014 sinusoidal: 4060 harmonic: 5954 Sorted by residual: dihedral pdb=" CA ASP J 136 " pdb=" C ASP J 136 " pdb=" N THR J 137 " pdb=" CA THR J 137 " ideal model delta harmonic sigma weight residual 180.00 150.20 29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA LYS J 129 " pdb=" C LYS J 129 " pdb=" N ASP J 130 " pdb=" CA ASP J 130 " ideal model delta harmonic sigma weight residual -180.00 -151.63 -28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA SER B 146 " pdb=" C SER B 146 " pdb=" N GLY B 147 " pdb=" CA GLY B 147 " ideal model delta harmonic sigma weight residual 180.00 -152.61 -27.39 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 10011 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2250 0.077 - 0.154: 379 0.154 - 0.230: 30 0.230 - 0.307: 5 0.307 - 0.384: 4 Chirality restraints: 2668 Sorted by residual: chirality pdb=" CB ILE E 223 " pdb=" CA ILE E 223 " pdb=" CG1 ILE E 223 " pdb=" CG2 ILE E 223 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CB ILE B 223 " pdb=" CA ILE B 223 " pdb=" CG1 ILE B 223 " pdb=" CG2 ILE B 223 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB THR E 114 " pdb=" CA THR E 114 " pdb=" OG1 THR E 114 " pdb=" CG2 THR E 114 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 2665 not shown) Planarity restraints: 2796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 120 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO I 121 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO I 121 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 121 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 155 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO D 156 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 155 " -0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO A 156 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.038 5.00e-02 4.00e+02 ... (remaining 2793 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1752 2.74 - 3.28: 14582 3.28 - 3.82: 24937 3.82 - 4.36: 30657 4.36 - 4.90: 53591 Nonbonded interactions: 125519 Sorted by model distance: nonbonded pdb=" O LEU E 110 " pdb=" OG1 THR E 114 " model vdw 2.198 3.040 nonbonded pdb=" O LEU B 110 " pdb=" OG1 THR B 114 " model vdw 2.199 3.040 nonbonded pdb=" CE1 PHE G 46 " pdb=" CG2 THR G 137 " model vdw 2.225 3.760 nonbonded pdb=" CD1 PHE G 46 " pdb=" CG2 THR G 137 " model vdw 2.234 3.760 nonbonded pdb=" O PRO J 94 " pdb=" OG SER J 97 " model vdw 2.284 3.040 ... (remaining 125514 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' and resid 3 through 304) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'G' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'H' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'I' selection = (chain 'J' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'K' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'L' } 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: 2.530 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: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.040 Find NCS groups from input model: 0.350 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:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 : 0.011 0.090 16668 Z= 0.474 Angle : 1.494 34.319 22518 Z= 0.674 Chirality : 0.059 0.384 2668 Planarity : 0.007 0.075 2796 Dihedral : 18.718 143.126 6190 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.19 % Favored : 88.23 % Rotamer: Outliers : 0.95 % Allowed : 6.06 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.74 (0.13), residues: 2056 helix: -4.53 (0.06), residues: 878 sheet: -2.34 (0.29), residues: 290 loop : -3.39 (0.16), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 111 TYR 0.035 0.003 TYR B 261 PHE 0.028 0.003 PHE G 118 TRP 0.011 0.002 TRP K 9 HIS 0.009 0.002 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.01061 / 0.47 (16668) covalent geometry : angle 1.49417 / 0.67 (22518) hydrogen bonds : bond 0.30308 / 19.68 ( 714) hydrogen bonds : angle 10.17861 / 7.05 ( 2091) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 332 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7862 (mtm-85) REVERT: A 134 MET cc_start: 0.9257 (mmt) cc_final: 0.9048 (mmm) REVERT: A 197 MET cc_start: 0.8645 (mmm) cc_final: 0.8414 (tpt) REVERT: B 13 ASP cc_start: 0.7032 (t70) cc_final: 0.6504 (t0) REVERT: B 130 GLU cc_start: 0.8159 (tp30) cc_final: 0.7923 (tp30) REVERT: C 21 ASP cc_start: 0.8047 (t70) cc_final: 0.7569 (t70) REVERT: C 22 GLN cc_start: 0.8718 (pp30) cc_final: 0.8405 (pp30) REVERT: C 23 ASP cc_start: 0.8515 (p0) cc_final: 0.8052 (p0) REVERT: D 18 ARG cc_start: 0.8115 (ptm160) cc_final: 0.7862 (mtm-85) REVERT: D 39 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8789 (tppt) REVERT: D 134 MET cc_start: 0.9271 (mmt) cc_final: 0.9034 (mmm) REVERT: D 197 MET cc_start: 0.8660 (mmm) cc_final: 0.8430 (tpt) REVERT: E 13 ASP cc_start: 0.7137 (t70) cc_final: 0.6517 (t0) REVERT: E 40 MET cc_start: 0.8519 (mtm) cc_final: 0.8314 (mtm) REVERT: E 130 GLU cc_start: 0.8272 (tp30) cc_final: 0.8030 (tp30) REVERT: E 180 MET cc_start: 0.8935 (mtt) cc_final: 0.8722 (mtm) REVERT: F 14 LEU cc_start: 0.8457 (tp) cc_final: 0.8255 (tm) REVERT: F 21 ASP cc_start: 0.8002 (t70) cc_final: 0.7559 (t70) REVERT: F 22 GLN cc_start: 0.8728 (pp30) cc_final: 0.8421 (pp30) REVERT: F 23 ASP cc_start: 0.8647 (p0) cc_final: 0.8156 (p0) REVERT: G 5 LYS cc_start: 0.8496 (tppt) cc_final: 0.8278 (tmmm) REVERT: G 88 GLN cc_start: 0.7923 (tp40) cc_final: 0.7174 (pm20) REVERT: G 92 HIS cc_start: 0.7626 (t70) cc_final: 0.7313 (t-170) REVERT: I 85 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7730 (mm-30) REVERT: J 5 LYS cc_start: 0.8506 (tppt) cc_final: 0.8273 (tmmm) REVERT: J 67 ARG cc_start: 0.6422 (mmt180) cc_final: 0.5813 (mmm-85) REVERT: J 89 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7860 (mpp-170) REVERT: J 92 HIS cc_start: 0.7846 (t70) cc_final: 0.7394 (t70) REVERT: L 85 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7787 (mm-30) outliers start: 16 outliers final: 3 residues processed: 342 average time/residue: 0.7566 time to fit residues: 281.5613 Evaluate side-chains 272 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 269 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 83 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 0.0170 chunk 194 optimal weight: 0.0970 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN A 50 ASN A 190 GLN B 7 ASN B 57 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 175 GLN B 226 HIS C 89 ASN D 29 ASN D 50 ASN D 190 GLN E 7 ASN E 57 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN E 175 GLN E 226 HIS F 89 ASN G 88 GLN G 110 GLN J 110 GLN L 110 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.140266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100795 restraints weight = 22092.493| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.93 r_work: 0.3042 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16668 Z= 0.131 Angle : 0.701 8.420 22518 Z= 0.358 Chirality : 0.042 0.201 2668 Planarity : 0.006 0.057 2796 Dihedral : 18.328 135.214 2640 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.24 % Favored : 90.52 % Rotamer: Outliers : 2.08 % Allowed : 15.26 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.16), residues: 2056 helix: -1.23 (0.15), residues: 856 sheet: -1.77 (0.33), residues: 248 loop : -2.94 (0.17), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 97 TYR 0.015 0.001 TYR E 261 PHE 0.015 0.001 PHE G 118 TRP 0.010 0.001 TRP G 9 HIS 0.003 0.001 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16668) covalent geometry : angle 0.70127 / 0.36 (22518) hydrogen bonds : bond 0.05039 / 3.26 ( 714) hydrogen bonds : angle 5.15751 / 3.55 ( 2091) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 311 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 PHE cc_start: 0.9135 (m-80) cc_final: 0.8896 (m-80) REVERT: A 38 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8599 (ttm170) REVERT: A 197 MET cc_start: 0.9099 (mmm) cc_final: 0.8861 (tpt) REVERT: B 139 LYS cc_start: 0.9089 (mtpp) cc_final: 0.8882 (mmmt) REVERT: C 22 GLN cc_start: 0.8813 (pp30) cc_final: 0.8605 (pp30) REVERT: C 31 MET cc_start: 0.7305 (mmm) cc_final: 0.7105 (mmm) REVERT: C 75 GLN cc_start: 0.7278 (pt0) cc_final: 0.6588 (mt0) REVERT: D 20 PHE cc_start: 0.9126 (m-80) cc_final: 0.8896 (m-80) REVERT: D 39 LYS cc_start: 0.9013 (mtpp) cc_final: 0.8786 (tppt) REVERT: D 197 MET cc_start: 0.9128 (mmm) cc_final: 0.8847 (tpt) REVERT: E 222 LYS cc_start: 0.8751 (mmtp) cc_final: 0.8509 (mmmm) REVERT: F 21 ASP cc_start: 0.8506 (t70) cc_final: 0.7795 (t70) REVERT: F 22 GLN cc_start: 0.8781 (pp30) cc_final: 0.8234 (pp30) REVERT: F 23 ASP cc_start: 0.8570 (p0) cc_final: 0.8011 (p0) REVERT: F 31 MET cc_start: 0.7525 (mmm) cc_final: 0.7303 (mmm) REVERT: F 49 ARG cc_start: 0.8413 (pmt170) cc_final: 0.8142 (pmt170) REVERT: G 89 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7693 (mmp80) REVERT: G 92 HIS cc_start: 0.7900 (t70) cc_final: 0.7467 (t70) REVERT: G 93 ILE cc_start: 0.7353 (OUTLIER) cc_final: 0.6962 (mp) REVERT: H 27 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8228 (tttm) REVERT: H 144 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7257 (mp0) REVERT: I 73 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7728 (tp) REVERT: I 85 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8120 (mm-30) REVERT: J 55 ARG cc_start: 0.7841 (mtp-110) cc_final: 0.7508 (mtm180) REVERT: J 83 THR cc_start: 0.6308 (OUTLIER) cc_final: 0.6016 (t) REVERT: J 89 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7580 (mmp80) REVERT: J 92 HIS cc_start: 0.8005 (t70) cc_final: 0.7490 (t70) REVERT: K 27 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8196 (tttm) REVERT: L 76 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6398 (tptp) REVERT: L 85 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8103 (mm-30) outliers start: 35 outliers final: 7 residues processed: 330 average time/residue: 0.7218 time to fit residues: 259.6005 Evaluate side-chains 281 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 269 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain L residue 76 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 119 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 GLN B 175 GLN E 57 GLN E 175 GLN H 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.141368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102258 restraints weight = 22408.238| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.90 r_work: 0.3040 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16668 Z= 0.122 Angle : 0.644 7.920 22518 Z= 0.325 Chirality : 0.042 0.185 2668 Planarity : 0.005 0.058 2796 Dihedral : 16.591 140.422 2639 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.39 % Favored : 90.47 % Rotamer: Outliers : 3.50 % Allowed : 16.75 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.18), residues: 2056 helix: 0.53 (0.18), residues: 856 sheet: -1.59 (0.33), residues: 248 loop : -2.71 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 67 TYR 0.018 0.001 TYR E 261 PHE 0.011 0.001 PHE G 13 TRP 0.006 0.001 TRP D 186 HIS 0.003 0.001 HIS H 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (16668) covalent geometry : angle 0.64399 / 0.33 (22518) hydrogen bonds : bond 0.04392 / 2.86 ( 714) hydrogen bonds : angle 4.50020 / 3.10 ( 2091) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9087 (mmm) cc_final: 0.8831 (tpt) REVERT: B 175 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8877 (mm110) REVERT: C 14 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8356 (tm) REVERT: C 31 MET cc_start: 0.7423 (mmm) cc_final: 0.7103 (mmm) REVERT: C 49 ARG cc_start: 0.8571 (pmt170) cc_final: 0.8120 (pmt170) REVERT: C 75 GLN cc_start: 0.7309 (pt0) cc_final: 0.6776 (mt0) REVERT: D 197 MET cc_start: 0.9115 (mmm) cc_final: 0.8859 (tpt) REVERT: E 58 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.6936 (pt) REVERT: E 98 THR cc_start: 0.8842 (m) cc_final: 0.8376 (p) REVERT: F 21 ASP cc_start: 0.8498 (t70) cc_final: 0.7803 (t70) REVERT: F 22 GLN cc_start: 0.8759 (pp30) cc_final: 0.8456 (pp30) REVERT: F 23 ASP cc_start: 0.8528 (p0) cc_final: 0.7938 (p0) REVERT: F 31 MET cc_start: 0.7389 (mmm) cc_final: 0.7088 (mmm) REVERT: G 88 GLN cc_start: 0.7641 (tp-100) cc_final: 0.6855 (pm20) REVERT: G 92 HIS cc_start: 0.7870 (t70) cc_final: 0.7385 (t70) REVERT: G 93 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7044 (mp) REVERT: G 139 SER cc_start: 0.7962 (p) cc_final: 0.7500 (m) REVERT: H 27 LYS cc_start: 0.8650 (ttmm) cc_final: 0.8206 (tttm) REVERT: H 144 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7330 (mp0) REVERT: I 109 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7686 (tp30) REVERT: J 83 THR cc_start: 0.6182 (OUTLIER) cc_final: 0.5940 (t) REVERT: J 89 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7543 (mmp80) REVERT: J 92 HIS cc_start: 0.8047 (t70) cc_final: 0.7552 (t70) REVERT: K 27 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8254 (tttm) REVERT: L 76 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6411 (tptp) outliers start: 59 outliers final: 16 residues processed: 311 average time/residue: 0.6965 time to fit residues: 235.7598 Evaluate side-chains 284 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 262 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 14 LEU Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain L residue 76 LYS Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 141 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.9508 > 50: distance: 94 - 100: 11.823 distance: 100 - 101: 19.438 distance: 101 - 102: 11.382 distance: 101 - 104: 19.487 distance: 102 - 103: 22.586 distance: 104 - 105: 21.098 distance: 105 - 106: 26.874 distance: 105 - 107: 14.834 distance: 108 - 109: 27.684 distance: 109 - 110: 18.256 distance: 109 - 112: 26.480 distance: 110 - 111: 33.038 distance: 110 - 117: 31.324 distance: 112 - 113: 35.063 distance: 113 - 114: 27.192 distance: 114 - 115: 15.563 distance: 115 - 116: 34.616 distance: 117 - 118: 17.891 distance: 118 - 119: 30.487 distance: 118 - 121: 15.979 distance: 119 - 120: 16.581 distance: 119 - 125: 33.114 distance: 121 - 122: 13.457 distance: 122 - 123: 35.236 distance: 122 - 124: 28.280 distance: 125 - 126: 9.690 distance: 126 - 127: 41.183 distance: 127 - 128: 13.070 distance: 127 - 129: 30.289 distance: 129 - 130: 14.160 distance: 130 - 131: 10.687 distance: 130 - 133: 6.917 distance: 131 - 132: 7.872 distance: 131 - 137: 15.460 distance: 133 - 134: 12.780 distance: 134 - 135: 17.134 distance: 134 - 136: 10.156 distance: 137 - 138: 14.372 distance: 138 - 139: 3.872 distance: 138 - 141: 9.283 distance: 139 - 140: 12.356 distance: 139 - 144: 9.056 distance: 141 - 142: 18.166 distance: 141 - 143: 13.522 distance: 144 - 145: 9.920 distance: 145 - 146: 10.692 distance: 145 - 148: 13.070 distance: 146 - 147: 8.551 distance: 146 - 152: 12.150 distance: 148 - 149: 5.639 distance: 148 - 150: 11.905 distance: 149 - 151: 12.256 distance: 152 - 153: 16.863 distance: 153 - 154: 17.079 distance: 153 - 156: 15.351 distance: 154 - 161: 7.810 distance: 156 - 157: 16.564 distance: 157 - 158: 8.212 distance: 158 - 159: 7.188 distance: 158 - 160: 6.910 distance: 161 - 162: 18.477 distance: 162 - 163: 17.930 distance: 162 - 165: 5.930 distance: 163 - 169: 18.886 distance: 165 - 166: 16.524 distance: 166 - 167: 10.724 distance: 169 - 170: 7.885 distance: 170 - 171: 7.246 distance: 170 - 173: 11.591 distance: 171 - 172: 4.980 distance: 171 - 176: 10.281 distance: 173 - 174: 17.491 distance: 173 - 175: 20.902