Starting phenix.real_space_refine on Sat Jan 18 02:12:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7khf_22879/01_2025/7khf_22879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7khf_22879/01_2025/7khf_22879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7khf_22879/01_2025/7khf_22879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7khf_22879/01_2025/7khf_22879.map" model { file = "/net/cci-nas-00/data/ceres_data/7khf_22879/01_2025/7khf_22879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7khf_22879/01_2025/7khf_22879.cif" } resolution = 3.54 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= -0.003 sd= 0.081 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: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 7283 2.51 5 N 1924 2.21 5 O 2314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11559 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3250 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 396} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1607 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "A" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3253 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 396} Chain: "B" Number of atoms: 1607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1607 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 198} Chain: "D" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "C" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.48, per 1000 atoms: 0.65 Number of scatterers: 11559 At special positions: 0 Unit cell: (106.134, 137.541, 132.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 2314 8.00 N 1924 7.00 C 7283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 251 " - pdb=" SG CYS H 302 " distance=2.03 Simple disulfide: pdb=" SG CYS H 339 " - pdb=" SG CYS B 213 " distance=2.71 Simple disulfide: pdb=" SG CYS H 352 " - pdb=" SG CYS H 408 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 302 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 242 " - pdb=" SG CYS D 264 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 264 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 501 " - " ASN A 207 " " NAG E 1 " - " ASN H 186 " " NAG F 1 " - " ASN H 246 " " NAG G 1 " - " ASN A 186 " " NAG H 501 " - " ASN H 207 " " NAG I 1 " - " ASN A 246 " Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.9 seconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2788 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 31 sheets defined 15.0% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'H' and resid 63 through 69 removed outlier: 3.814A pdb=" N LYS H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER H 67 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU H 69 " --> pdb=" O LYS H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 197 removed outlier: 3.749A pdb=" N TYR H 196 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY H 197 " --> pdb=" O ARG H 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 193 through 197' Processing helix chain 'H' and resid 413 through 416 Processing helix chain 'L' and resid 25 through 29 removed outlier: 3.632A pdb=" N ALA L 28 " --> pdb=" O ASP L 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG L 29 " --> pdb=" O SER L 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 25 through 29' Processing helix chain 'L' and resid 123 through 129 removed outlier: 4.050A pdb=" N LEU L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN L 128 " --> pdb=" O SER L 124 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA L 129 " --> pdb=" O GLU L 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 129' Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.562A pdb=" N LYS L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 193 through 197 removed outlier: 4.044A pdb=" N GLY A 197 " --> pdb=" O ARG A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 removed outlier: 4.035A pdb=" N GLY A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.596A pdb=" N HIS B 190 " --> pdb=" O GLN B 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 205 removed outlier: 3.819A pdb=" N ALA D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.801A pdb=" N GLU D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 237 Processing helix chain 'D' and resid 238 through 242 Processing helix chain 'D' and resid 261 through 272 Processing helix chain 'D' and resid 282 through 303 Processing helix chain 'C' and resid 187 through 205 removed outlier: 4.052A pdb=" N ALA C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.637A pdb=" N GLU C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 217 removed outlier: 4.018A pdb=" N SER C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 212 through 217' Processing helix chain 'C' and resid 225 through 237 removed outlier: 4.256A pdb=" N ILE C 229 " --> pdb=" O ASP C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 242 Processing helix chain 'C' and resid 261 through 272 removed outlier: 3.551A pdb=" N SER C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 303 removed outlier: 3.622A pdb=" N GLY C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.708A pdb=" N ARG H 79 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 59 through 61 removed outlier: 5.201A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY H 35 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASN H 109 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 132 through 136 removed outlier: 4.049A pdb=" N GLN H 136 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR H 148 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 183 " --> pdb=" O SER H 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 140 through 141 removed outlier: 6.805A pdb=" N VAL H 141 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU H 313 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE H 223 " --> pdb=" O LEU H 313 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 140 through 141 removed outlier: 6.805A pdb=" N VAL H 141 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY H 198 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL H 161 " --> pdb=" O TYR H 203 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN H 172 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 175 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN C 276 " --> pdb=" O GLY H 175 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 231 through 235 removed outlier: 6.107A pdb=" N VAL H 247 " --> pdb=" O MET H 289 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 240 through 241 removed outlier: 3.752A pdb=" N TYR H 300 " --> pdb=" O LEU H 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 333 through 336 removed outlier: 3.686A pdb=" N GLY H 351 " --> pdb=" O LEU H 336 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASP H 356 " --> pdb=" O TYR H 388 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR H 388 " --> pdb=" O ASP H 356 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N SER H 391 " --> pdb=" O PRO H 379 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL H 393 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N THR H 377 " --> pdb=" O VAL H 393 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 363 through 366 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.541A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 44 through 48 removed outlier: 6.674A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.752A pdb=" N SER L 139 " --> pdb=" O THR L 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR L 174 " --> pdb=" O ASP L 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.554A pdb=" N LYS L 206 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AB9, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.544A pdb=" N THR A 119 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 95 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 51 " --> pdb=" O TRP A 38 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 40 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N TRP A 49 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.544A pdb=" N THR A 119 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 95 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N CYS A 97 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TRP A 115 " --> pdb=" O CYS A 97 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N HIS A 99 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 113 " --> pdb=" O HIS A 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 132 through 136 removed outlier: 3.926A pdb=" N THR A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 140 through 141 removed outlier: 3.620A pdb=" N VAL A 161 " --> pdb=" O TYR A 203 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 159 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 172 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 231 through 235 removed outlier: 5.711A pdb=" N VAL A 247 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 284 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 240 through 242 removed outlier: 3.711A pdb=" N SER A 325 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 300 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 274 " --> pdb=" O PHE A 260 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.145A pdb=" N TYR A 388 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 332 through 336 removed outlier: 6.145A pdb=" N TYR A 388 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 362 through 366 Processing sheet with id=AC9, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.655A pdb=" N TYR B 85 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.655A pdb=" N TYR B 85 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AD3, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.388A pdb=" N TYR B 174 " --> pdb=" O ASP B 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 155 through 156 436 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1887 1.30 - 1.43: 3082 1.43 - 1.56: 6816 1.56 - 1.69: 0 1.69 - 1.82: 44 Bond restraints: 11829 Sorted by residual: bond pdb=" CA CYS H 352 " pdb=" C CYS H 352 " ideal model delta sigma weight residual 1.522 1.395 0.126 1.21e-02 6.83e+03 1.08e+02 bond pdb=" C PRO A 361 " pdb=" O PRO A 361 " ideal model delta sigma weight residual 1.235 1.178 0.057 7.90e-03 1.60e+04 5.16e+01 bond pdb=" C PRO A 359 " pdb=" O PRO A 359 " ideal model delta sigma weight residual 1.233 1.169 0.064 1.10e-02 8.26e+03 3.39e+01 bond pdb=" N CYS H 352 " pdb=" CA CYS H 352 " ideal model delta sigma weight residual 1.454 1.386 0.069 1.27e-02 6.20e+03 2.92e+01 bond pdb=" CA SER H 389 " pdb=" CB SER H 389 " ideal model delta sigma weight residual 1.535 1.433 0.102 1.90e-02 2.77e+03 2.88e+01 ... (remaining 11824 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 15669 2.85 - 5.71: 402 5.71 - 8.56: 43 8.56 - 11.41: 10 11.41 - 14.26: 2 Bond angle restraints: 16126 Sorted by residual: angle pdb=" C PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta sigma weight residual 111.23 96.97 14.26 1.28e+00 6.10e-01 1.24e+02 angle pdb=" C PRO A 361 " pdb=" CA PRO A 361 " pdb=" CB PRO A 361 " ideal model delta sigma weight residual 111.87 103.74 8.13 8.40e-01 1.42e+00 9.37e+01 angle pdb=" C THR A 372 " pdb=" CA THR A 372 " pdb=" CB THR A 372 " ideal model delta sigma weight residual 110.81 122.95 -12.14 1.73e+00 3.34e-01 4.93e+01 angle pdb=" CA PRO H 338 " pdb=" C PRO H 338 " pdb=" O PRO H 338 " ideal model delta sigma weight residual 119.34 109.12 10.22 1.47e+00 4.63e-01 4.84e+01 angle pdb=" C PRO H 335 " pdb=" CA PRO H 335 " pdb=" CB PRO H 335 " ideal model delta sigma weight residual 110.98 102.28 8.70 1.31e+00 5.83e-01 4.42e+01 ... (remaining 16121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 6859 23.42 - 46.83: 347 46.83 - 70.25: 36 70.25 - 93.67: 10 93.67 - 117.09: 5 Dihedral angle restraints: 7257 sinusoidal: 2891 harmonic: 4366 Sorted by residual: dihedral pdb=" C PRO A 331 " pdb=" N PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta harmonic sigma weight residual -120.70 -102.15 -18.55 0 2.50e+00 1.60e-01 5.51e+01 dihedral pdb=" C PRO A 359 " pdb=" N PRO A 359 " pdb=" CA PRO A 359 " pdb=" CB PRO A 359 " ideal model delta harmonic sigma weight residual -120.70 -105.80 -14.90 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CB CYS A 251 " pdb=" SG CYS A 251 " pdb=" SG CYS A 302 " pdb=" CB CYS A 302 " ideal model delta sinusoidal sigma weight residual 93.00 143.82 -50.82 1 1.00e+01 1.00e-02 3.54e+01 ... (remaining 7254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1796 0.154 - 0.308: 58 0.308 - 0.462: 9 0.462 - 0.616: 0 0.616 - 0.770: 2 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CA CYS H 352 " pdb=" N CYS H 352 " pdb=" C CYS H 352 " pdb=" CB CYS H 352 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA THR A 372 " pdb=" N THR A 372 " pdb=" C THR A 372 " pdb=" CB THR A 372 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.48e+00 ... (remaining 1862 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO H 338 " 0.028 2.00e-02 2.50e+03 6.20e-02 3.84e+01 pdb=" C PRO H 338 " -0.107 2.00e-02 2.50e+03 pdb=" O PRO H 338 " 0.040 2.00e-02 2.50e+03 pdb=" N CYS H 339 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 246 " 0.001 2.00e-02 2.50e+03 4.04e-02 2.04e+01 pdb=" CG ASN A 246 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 246 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A 246 " 0.050 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 335 " -0.015 2.00e-02 2.50e+03 3.09e-02 9.54e+00 pdb=" C PRO H 335 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO H 335 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU H 336 " -0.018 2.00e-02 2.50e+03 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 673 2.72 - 3.27: 11207 3.27 - 3.81: 16916 3.81 - 4.36: 19939 4.36 - 4.90: 36296 Nonbonded interactions: 85031 Sorted by model distance: nonbonded pdb=" OE2 GLU A 6 " pdb=" N GLY A 118 " model vdw 2.179 3.120 nonbonded pdb=" NZ LYS B 168 " pdb=" OD1 ASN B 172 " model vdw 2.197 3.120 nonbonded pdb=" NH2 ARG H 68 " pdb=" OD2 ASP H 91 " model vdw 2.219 3.120 nonbonded pdb=" NZ LYS H 130 " pdb=" OG1 THR A 70 " model vdw 2.246 3.120 nonbonded pdb=" OE2 GLU H 265 " pdb=" NH2 ARG H 301 " model vdw 2.318 3.120 ... (remaining 85026 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 1 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 426 or resid 501)) selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' } 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: 2.190 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.250 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 : 0.008 0.126 11829 Z= 0.518 Angle : 0.977 14.264 16126 Z= 0.624 Chirality : 0.069 0.770 1865 Planarity : 0.005 0.062 2064 Dihedral : 13.715 117.086 4424 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.65 % Favored : 94.22 % Rotamer: Outliers : 0.94 % Allowed : 1.57 % Favored : 97.49 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 3.85 % 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: -0.56 (0.23), residues: 1504 helix: 0.24 (0.40), residues: 178 sheet: 0.32 (0.23), residues: 553 loop : -1.03 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 256 HIS 0.005 0.001 HIS H 99 PHE 0.035 0.002 PHE A 358 TYR 0.040 0.002 TYR A 357 ARG 0.006 0.001 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 154 ASP cc_start: 0.7848 (t0) cc_final: 0.7599 (t0) REVERT: H 256 TRP cc_start: 0.7843 (t60) cc_final: 0.7637 (t-100) REVERT: H 257 MET cc_start: 0.7819 (mpp) cc_final: 0.7349 (mpp) REVERT: L 200 GLU cc_start: 0.7704 (pp20) cc_final: 0.7417 (pp20) REVERT: A 336 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9046 (pp) REVERT: A 341 ARG cc_start: 0.5812 (OUTLIER) cc_final: 0.5018 (tpp-160) REVERT: A 357 TYR cc_start: 0.8367 (p90) cc_final: 0.7530 (p90) REVERT: B 130 ASN cc_start: 0.8460 (m-40) cc_final: 0.7907 (t0) REVERT: D 288 GLN cc_start: 0.8515 (tp40) cc_final: 0.8274 (tp40) REVERT: D 294 ILE cc_start: 0.8587 (mm) cc_final: 0.8334 (tt) REVERT: C 230 THR cc_start: 0.9337 (m) cc_final: 0.9021 (p) REVERT: C 290 ASP cc_start: 0.7646 (m-30) cc_final: 0.7142 (m-30) outliers start: 12 outliers final: 4 residues processed: 186 average time/residue: 0.2301 time to fit residues: 61.7475 Evaluate side-chains 145 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.082829 restraints weight = 22271.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.086124 restraints weight = 11022.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.088209 restraints weight = 7297.526| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11829 Z= 0.254 Angle : 0.661 8.641 16126 Z= 0.335 Chirality : 0.045 0.211 1865 Planarity : 0.005 0.038 2064 Dihedral : 9.276 103.578 1851 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.02 % Allowed : 8.07 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.50 (0.23), residues: 1504 helix: 0.08 (0.39), residues: 187 sheet: 0.41 (0.24), residues: 553 loop : -0.98 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 272 HIS 0.004 0.001 HIS L 199 PHE 0.027 0.001 PHE A 358 TYR 0.014 0.001 TYR A 228 ARG 0.004 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 1.343 Fit side-chains REVERT: H 256 TRP cc_start: 0.8119 (t60) cc_final: 0.7821 (t-100) REVERT: H 257 MET cc_start: 0.7973 (mpp) cc_final: 0.7745 (mpp) REVERT: H 353 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.8006 (tp) REVERT: L 130 ASN cc_start: 0.8956 (t0) cc_final: 0.8687 (t0) REVERT: A 336 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8512 (pp) REVERT: A 409 ASN cc_start: 0.8584 (m-40) cc_final: 0.8347 (m-40) REVERT: B 130 ASN cc_start: 0.8502 (m-40) cc_final: 0.7893 (t0) REVERT: B 140 ASP cc_start: 0.8290 (m-30) cc_final: 0.8080 (m-30) REVERT: B 168 LYS cc_start: 0.8434 (tptt) cc_final: 0.8032 (tptt) REVERT: D 279 ASP cc_start: 0.8224 (p0) cc_final: 0.7986 (p0) REVERT: D 288 GLN cc_start: 0.8244 (tp40) cc_final: 0.7925 (tp40) REVERT: C 219 ASP cc_start: 0.6934 (t70) cc_final: 0.6732 (t70) REVERT: C 290 ASP cc_start: 0.8102 (m-30) cc_final: 0.7329 (m-30) outliers start: 13 outliers final: 7 residues processed: 171 average time/residue: 0.2215 time to fit residues: 55.1745 Evaluate side-chains 155 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain D residue 223 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 41 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.103269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.078783 restraints weight = 22433.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081840 restraints weight = 11080.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.083840 restraints weight = 7393.154| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11829 Z= 0.421 Angle : 0.690 8.918 16126 Z= 0.348 Chirality : 0.045 0.211 1865 Planarity : 0.004 0.038 2064 Dihedral : 9.015 100.362 1847 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.35 % Allowed : 10.34 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.64 (0.22), residues: 1504 helix: 0.07 (0.39), residues: 187 sheet: 0.23 (0.23), residues: 582 loop : -1.06 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 187 HIS 0.005 0.001 HIS H 99 PHE 0.028 0.002 PHE H 334 TYR 0.038 0.002 TYR A 357 ARG 0.003 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: H 104 ASN cc_start: 0.8770 (p0) cc_final: 0.8515 (p0) REVERT: H 256 TRP cc_start: 0.8222 (t60) cc_final: 0.7567 (t-100) REVERT: H 257 MET cc_start: 0.8066 (mpp) cc_final: 0.7770 (mpp) REVERT: H 336 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8806 (pp) REVERT: H 420 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7541 (m-30) REVERT: L 130 ASN cc_start: 0.9080 (t0) cc_final: 0.8794 (t0) REVERT: A 409 ASN cc_start: 0.8689 (m-40) cc_final: 0.8397 (m-40) REVERT: B 130 ASN cc_start: 0.8585 (m-40) cc_final: 0.7934 (t0) REVERT: D 279 ASP cc_start: 0.8227 (p0) cc_final: 0.7990 (p0) REVERT: D 288 GLN cc_start: 0.8354 (tp40) cc_final: 0.8032 (tp40) REVERT: C 219 ASP cc_start: 0.7149 (t70) cc_final: 0.6932 (t70) REVERT: C 290 ASP cc_start: 0.8040 (m-30) cc_final: 0.7276 (m-30) outliers start: 30 outliers final: 25 residues processed: 163 average time/residue: 0.2369 time to fit residues: 56.2496 Evaluate side-chains 163 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 107 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.077037 restraints weight = 22519.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.080055 restraints weight = 11181.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.081997 restraints weight = 7468.176| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 11829 Z= 0.527 Angle : 0.737 9.475 16126 Z= 0.372 Chirality : 0.046 0.216 1865 Planarity : 0.005 0.038 2064 Dihedral : 8.981 96.004 1847 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.13 % Allowed : 11.82 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.84 (0.22), residues: 1504 helix: -0.09 (0.38), residues: 187 sheet: 0.06 (0.22), residues: 583 loop : -1.15 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 49 HIS 0.007 0.002 HIS H 99 PHE 0.023 0.002 PHE A 358 TYR 0.027 0.002 TYR A 357 ARG 0.003 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: H 104 ASN cc_start: 0.8791 (p0) cc_final: 0.8415 (p0) REVERT: H 336 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8914 (pp) REVERT: H 353 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8495 (tp) REVERT: H 420 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: L 130 ASN cc_start: 0.9064 (t0) cc_final: 0.8788 (t0) REVERT: A 409 ASN cc_start: 0.8646 (m-40) cc_final: 0.8398 (m-40) REVERT: B 41 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: B 130 ASN cc_start: 0.8658 (m-40) cc_final: 0.8004 (t0) REVERT: D 279 ASP cc_start: 0.8225 (p0) cc_final: 0.8010 (p0) REVERT: D 288 GLN cc_start: 0.8482 (tp40) cc_final: 0.8168 (tp40) REVERT: C 290 ASP cc_start: 0.7992 (m-30) cc_final: 0.7242 (m-30) outliers start: 40 outliers final: 30 residues processed: 165 average time/residue: 0.2294 time to fit residues: 55.5646 Evaluate side-chains 168 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 267 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 115 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.076230 restraints weight = 22525.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.079283 restraints weight = 11169.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.081265 restraints weight = 7411.465| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11829 Z= 0.266 Angle : 0.630 9.797 16126 Z= 0.315 Chirality : 0.044 0.209 1865 Planarity : 0.004 0.038 2064 Dihedral : 8.619 93.380 1847 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.90 % Allowed : 13.86 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.59 (0.23), residues: 1504 helix: 0.02 (0.39), residues: 186 sheet: 0.34 (0.23), residues: 577 loop : -1.08 (0.24), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 49 HIS 0.004 0.001 HIS H 99 PHE 0.015 0.001 PHE H 334 TYR 0.023 0.001 TYR A 357 ARG 0.002 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: H 104 ASN cc_start: 0.8760 (p0) cc_final: 0.8386 (p0) REVERT: H 336 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8714 (pp) REVERT: H 353 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7989 (tp) REVERT: H 420 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7412 (m-30) REVERT: L 130 ASN cc_start: 0.9126 (t0) cc_final: 0.8863 (t0) REVERT: A 409 ASN cc_start: 0.8694 (m-40) cc_final: 0.8330 (m-40) REVERT: B 130 ASN cc_start: 0.8631 (m-40) cc_final: 0.7957 (t0) REVERT: B 168 LYS cc_start: 0.8446 (tppt) cc_final: 0.8099 (tptt) REVERT: D 279 ASP cc_start: 0.8156 (p0) cc_final: 0.7920 (p0) REVERT: D 288 GLN cc_start: 0.8354 (tp40) cc_final: 0.8013 (tp40) REVERT: C 290 ASP cc_start: 0.7990 (m-30) cc_final: 0.7251 (m-30) outliers start: 37 outliers final: 25 residues processed: 167 average time/residue: 0.2294 time to fit residues: 56.9537 Evaluate side-chains 162 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 315 HIS ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.105132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.080453 restraints weight = 22557.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.083661 restraints weight = 11091.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.085710 restraints weight = 7350.560| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11829 Z= 0.230 Angle : 0.615 10.286 16126 Z= 0.305 Chirality : 0.043 0.213 1865 Planarity : 0.004 0.036 2064 Dihedral : 8.220 88.396 1847 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.29 % Allowed : 14.17 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.54 (0.23), residues: 1504 helix: 0.02 (0.39), residues: 187 sheet: 0.37 (0.23), residues: 571 loop : -1.01 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 49 HIS 0.004 0.001 HIS H 99 PHE 0.012 0.001 PHE H 334 TYR 0.020 0.001 TYR A 357 ARG 0.001 0.000 ARG A 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.333 Fit side-chains revert: symmetry clash REVERT: H 104 ASN cc_start: 0.8794 (p0) cc_final: 0.8407 (p0) REVERT: H 256 TRP cc_start: 0.8221 (t60) cc_final: 0.7772 (t-100) REVERT: H 336 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8593 (pp) REVERT: H 353 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7771 (tp) REVERT: H 420 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: L 130 ASN cc_start: 0.9151 (t0) cc_final: 0.8875 (t0) REVERT: A 409 ASN cc_start: 0.8671 (m-40) cc_final: 0.8306 (m-40) REVERT: B 78 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8191 (mp10) REVERT: B 130 ASN cc_start: 0.8617 (m-40) cc_final: 0.7930 (t0) REVERT: B 140 ASP cc_start: 0.8314 (m-30) cc_final: 0.8098 (m-30) REVERT: B 168 LYS cc_start: 0.8435 (tppt) cc_final: 0.8080 (tptt) REVERT: D 279 ASP cc_start: 0.8088 (p0) cc_final: 0.7848 (p0) REVERT: D 288 GLN cc_start: 0.8301 (tp40) cc_final: 0.7956 (tp40) REVERT: C 290 ASP cc_start: 0.7978 (m-30) cc_final: 0.7167 (m-30) outliers start: 42 outliers final: 28 residues processed: 173 average time/residue: 0.2238 time to fit residues: 56.9295 Evaluate side-chains 172 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 102 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 42 optimal weight: 0.0980 chunk 61 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.111027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.086531 restraints weight = 22663.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.090240 restraints weight = 11823.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091099 restraints weight = 7088.138| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11829 Z= 0.182 Angle : 0.593 11.041 16126 Z= 0.291 Chirality : 0.042 0.231 1865 Planarity : 0.004 0.036 2064 Dihedral : 7.662 79.388 1845 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.58 % Allowed : 14.80 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.37 (0.23), residues: 1504 helix: 0.14 (0.39), residues: 187 sheet: 0.52 (0.23), residues: 562 loop : -0.92 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 49 HIS 0.003 0.001 HIS H 99 PHE 0.011 0.001 PHE H 334 TYR 0.018 0.001 TYR A 357 ARG 0.001 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: H 104 ASN cc_start: 0.8801 (p0) cc_final: 0.8462 (p0) REVERT: H 256 TRP cc_start: 0.8156 (t60) cc_final: 0.7814 (t-100) REVERT: H 336 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8633 (pp) REVERT: H 353 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7969 (tp) REVERT: H 420 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: L 130 ASN cc_start: 0.9093 (t0) cc_final: 0.8813 (t0) REVERT: A 409 ASN cc_start: 0.8687 (m-40) cc_final: 0.8301 (m-40) REVERT: B 78 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8262 (mp10) REVERT: B 130 ASN cc_start: 0.8635 (m-40) cc_final: 0.7943 (t0) REVERT: B 140 ASP cc_start: 0.8427 (m-30) cc_final: 0.8181 (m-30) REVERT: B 168 LYS cc_start: 0.8420 (tppt) cc_final: 0.8078 (tptt) REVERT: D 229 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8981 (tp) REVERT: D 288 GLN cc_start: 0.8359 (tp40) cc_final: 0.8013 (tp40) REVERT: C 290 ASP cc_start: 0.7930 (m-30) cc_final: 0.7124 (m-30) outliers start: 33 outliers final: 26 residues processed: 171 average time/residue: 0.2209 time to fit residues: 56.1712 Evaluate side-chains 169 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 78 ASN Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 364 VAL Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 87 CYS Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain L residue 153 ASP Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 109 optimal weight: 0.0970 chunk 31 optimal weight: 0.0980 chunk 144 optimal weight: 0.0030 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.112563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.087510 restraints weight = 22679.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.090780 restraints weight = 11320.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.092909 restraints weight = 7503.153| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11829 Z= 0.154 Angle : 0.587 11.546 16126 Z= 0.288 Chirality : 0.042 0.237 1865 Planarity : 0.004 0.035 2064 Dihedral : 7.027 69.371 1844 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.11 % Allowed : 15.58 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -0.23 (0.23), residues: 1504 helix: 0.17 (0.39), residues: 181 sheet: 0.62 (0.23), residues: 564 loop : -0.81 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 212 HIS 0.002 0.000 HIS H 99 PHE 0.017 0.001 PHE C 204 TYR 0.017 0.001 TYR A 357 ARG 0.008 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: H 104 ASN cc_start: 0.8763 (p0) cc_final: 0.8384 (p0) REVERT: H 256 TRP cc_start: 0.8158 (t60) cc_final: 0.7847 (t-100) REVERT: H 336 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8596 (pp) REVERT: H 420 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: L 96 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6378 (p90) REVERT: L 130 ASN cc_start: 0.9066 (t0) cc_final: 0.8793 (t0) REVERT: A 409 ASN cc_start: 0.8692 (m-40) cc_final: 0.8307 (m-40) REVERT: B 78 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8273 (mp10) REVERT: B 140 ASP cc_start: 0.8429 (m-30) cc_final: 0.8188 (m-30) REVERT: B 168 LYS cc_start: 0.8376 (tppt) cc_final: 0.8007 (tptt) REVERT: D 288 GLN cc_start: 0.8304 (tp40) cc_final: 0.7960 (tp40) REVERT: C 290 ASP cc_start: 0.7949 (m-30) cc_final: 0.7137 (m-30) outliers start: 27 outliers final: 20 residues processed: 164 average time/residue: 0.2230 time to fit residues: 53.7007 Evaluate side-chains 157 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 336 LEU Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 420 ASP Chi-restraints excluded: chain L residue 51 ILE Chi-restraints excluded: chain L residue 96 TYR Chi-restraints excluded: chain L residue 135 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 196 TYR Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 223 TYR Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain C residue 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.1541 > 50: distance: 17 - 101: 25.992 distance: 32 - 89: 36.841 distance: 35 - 86: 37.287 distance: 55 - 60: 31.123 distance: 60 - 61: 31.383 distance: 61 - 62: 31.832 distance: 62 - 63: 44.882 distance: 62 - 64: 41.896 distance: 64 - 65: 20.908 distance: 65 - 66: 23.639 distance: 65 - 68: 47.629 distance: 66 - 67: 25.679 distance: 66 - 73: 39.050 distance: 68 - 69: 62.834 distance: 69 - 70: 45.917 distance: 70 - 71: 33.511 distance: 70 - 72: 55.835 distance: 73 - 74: 33.616 distance: 74 - 75: 46.541 distance: 74 - 77: 50.926 distance: 75 - 76: 23.282 distance: 75 - 79: 23.274 distance: 77 - 78: 13.764 distance: 79 - 80: 4.736 distance: 79 - 85: 37.241 distance: 80 - 81: 44.390 distance: 80 - 83: 21.521 distance: 81 - 82: 3.897 distance: 81 - 86: 37.353 distance: 83 - 84: 41.715 distance: 84 - 85: 8.237 distance: 86 - 87: 25.086 distance: 87 - 88: 16.177 distance: 87 - 90: 46.346 distance: 88 - 89: 40.544 distance: 88 - 93: 40.774 distance: 90 - 91: 14.106 distance: 90 - 92: 25.251 distance: 93 - 94: 36.942 distance: 94 - 95: 10.501 distance: 94 - 97: 7.325 distance: 95 - 96: 29.249 distance: 95 - 101: 23.353 distance: 97 - 98: 41.221 distance: 98 - 99: 14.332 distance: 98 - 100: 19.538 distance: 101 - 102: 41.647 distance: 102 - 103: 41.657 distance: 102 - 105: 44.625 distance: 103 - 104: 8.987 distance: 103 - 109: 36.044 distance: 105 - 106: 43.339 distance: 106 - 107: 18.715 distance: 106 - 108: 16.174 distance: 109 - 110: 38.668 distance: 110 - 111: 33.925 distance: 110 - 113: 17.494 distance: 111 - 112: 26.765 distance: 111 - 117: 32.964 distance: 113 - 114: 26.388 distance: 113 - 115: 13.782 distance: 114 - 116: 29.446 distance: 117 - 118: 20.225 distance: 118 - 119: 19.121 distance: 118 - 121: 18.012 distance: 119 - 120: 24.135 distance: 119 - 129: 17.866 distance: 121 - 122: 12.608 distance: 122 - 123: 28.302 distance: 122 - 124: 5.332 distance: 123 - 125: 22.252 distance: 124 - 126: 5.833 distance: 125 - 127: 13.084 distance: 126 - 127: 12.162 distance: 127 - 128: 16.055 distance: 129 - 130: 35.414 distance: 130 - 131: 13.024 distance: 130 - 133: 14.979 distance: 131 - 132: 6.981 distance: 131 - 138: 25.730 distance: 133 - 134: 33.021 distance: 134 - 135: 31.195 distance: 135 - 136: 46.180 distance: 136 - 137: 44.343