Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 12 02:05:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/10_2023/8ihr_35453_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/10_2023/8ihr_35453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/10_2023/8ihr_35453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/10_2023/8ihr_35453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/10_2023/8ihr_35453_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ihr_35453/10_2023/8ihr_35453_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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 Zn 16 6.06 5 S 72 5.16 5 C 15184 2.51 5 N 4424 2.21 5 O 4528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 312": "OE1" <-> "OE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 312": "OE1" <-> "OE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "F GLU 115": "OE1" <-> "OE2" Residue "G GLU 115": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "H GLU 115": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 24224 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3014 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' ZN': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Time building chain proxies: 12.02, per 1000 atoms: 0.50 Number of scatterers: 24224 At special positions: 0 Unit cell: (138.55, 138.55, 103.7, 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) Zn 16 29.99 S 72 16.00 O 4528 8.00 N 4424 7.00 C 15184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 75 " distance=2.03 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS G 75 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS H 75 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.03 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 501 " - pdb=" NE2 HIS A 85 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 251 " pdb="ZN ZN A 502 " - pdb=" NE2 HIS A 271 " pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 83 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 85 " pdb=" ZN B 502 " pdb="ZN ZN B 502 " - pdb=" NE2 HIS B 271 " pdb="ZN ZN B 502 " - pdb=" ND1 HIS B 251 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 83 " pdb="ZN ZN C 501 " - pdb=" NE2 HIS C 85 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" ND1 HIS C 251 " pdb="ZN ZN C 502 " - pdb=" NE2 HIS C 271 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 83 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 85 " pdb=" ZN D 502 " pdb="ZN ZN D 502 " - pdb=" NE2 HIS D 271 " pdb="ZN ZN D 502 " - pdb=" ND1 HIS D 251 " pdb=" ZN E 501 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 83 " pdb="ZN ZN E 501 " - pdb=" NE2 HIS E 85 " pdb=" ZN E 502 " pdb="ZN ZN E 502 " - pdb=" ND1 HIS E 251 " pdb="ZN ZN E 502 " - pdb=" NE2 HIS E 271 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 83 " pdb="ZN ZN F 501 " - pdb=" NE2 HIS F 85 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 251 " pdb="ZN ZN F 502 " - pdb=" NE2 HIS F 271 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 83 " pdb="ZN ZN G 501 " - pdb=" NE2 HIS G 85 " pdb=" ZN G 502 " pdb="ZN ZN G 502 " - pdb=" ND1 HIS G 251 " pdb="ZN ZN G 502 " - pdb=" NE2 HIS G 271 " pdb=" ZN H 501 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 83 " pdb="ZN ZN H 501 " - pdb=" NE2 HIS H 85 " pdb=" ZN H 502 " pdb="ZN ZN H 502 " - pdb=" ND1 HIS H 251 " pdb="ZN ZN H 502 " - pdb=" NE2 HIS H 271 " 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 32 sheets defined 38.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 Creating SS restraints... Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.531A pdb=" N GLU A 97 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ASP A 98 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 120 removed outlier: 4.036A pdb=" N GLY A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 255 through 264 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 312 through 334 Proline residue: A 316 - end of helix removed outlier: 4.435A pdb=" N ALA A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLN A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 removed outlier: 3.705A pdb=" N VAL A 361 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 362 " --> pdb=" O TYR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 4.676A pdb=" N HIS A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 Processing helix chain 'B' and resid 94 through 100 removed outlier: 4.438A pdb=" N ASP B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE B 99 " --> pdb=" O TYR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 120 removed outlier: 4.043A pdb=" N GLY B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 142 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.502A pdb=" N ASP B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 264 Processing helix chain 'B' and resid 277 through 286 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 312 through 334 Proline residue: B 316 - end of helix removed outlier: 4.420A pdb=" N ALA B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 367 through 382 removed outlier: 4.700A pdb=" N HIS B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 380 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 Processing helix chain 'C' and resid 94 through 100 removed outlier: 4.440A pdb=" N ASP C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 120 removed outlier: 4.043A pdb=" N GLY C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 142 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 191 through 203 Processing helix chain 'C' and resid 231 through 243 removed outlier: 3.503A pdb=" N ASP C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 264 Processing helix chain 'C' and resid 277 through 286 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 312 through 334 Proline residue: C 316 - end of helix removed outlier: 4.420A pdb=" N ALA C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE C 325 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N SER C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'C' and resid 367 through 382 removed outlier: 4.700A pdb=" N HIS C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN C 380 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'D' and resid 94 through 100 removed outlier: 4.439A pdb=" N ASP D 98 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE D 99 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 120 removed outlier: 4.044A pdb=" N GLY D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 142 Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 191 through 203 Processing helix chain 'D' and resid 231 through 243 removed outlier: 3.502A pdb=" N ASP D 243 " --> pdb=" O ASP D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 264 Processing helix chain 'D' and resid 277 through 286 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 312 through 334 Proline residue: D 316 - end of helix removed outlier: 4.419A pdb=" N ALA D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE D 325 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER D 326 " --> pdb=" O GLY D 322 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLN D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 Processing helix chain 'D' and resid 367 through 382 removed outlier: 4.700A pdb=" N HIS D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN D 380 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 413 Processing helix chain 'E' and resid 94 through 100 removed outlier: 5.452A pdb=" N ASP E 98 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG E 100 " --> pdb=" O GLU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 119 removed outlier: 4.163A pdb=" N GLY E 112 " --> pdb=" O PHE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 142 Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 191 through 203 Processing helix chain 'E' and resid 231 through 243 Processing helix chain 'E' and resid 255 through 264 Processing helix chain 'E' and resid 277 through 286 Processing helix chain 'E' and resid 294 through 305 removed outlier: 3.985A pdb=" N ALA E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 334 Proline residue: E 316 - end of helix removed outlier: 4.531A pdb=" N ALA E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N SER E 326 " --> pdb=" O GLY E 322 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 Processing helix chain 'E' and resid 367 through 382 removed outlier: 3.537A pdb=" N ALA E 374 " --> pdb=" O ALA E 370 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N HIS E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN E 380 " --> pdb=" O VAL E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 413 Processing helix chain 'F' and resid 94 through 100 removed outlier: 5.450A pdb=" N ASP F 98 " --> pdb=" O TYR F 95 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG F 100 " --> pdb=" O GLU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 119 removed outlier: 4.164A pdb=" N GLY F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 142 Processing helix chain 'F' and resid 172 through 178 Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 231 through 243 Processing helix chain 'F' and resid 255 through 264 Processing helix chain 'F' and resid 277 through 286 Processing helix chain 'F' and resid 294 through 305 removed outlier: 3.991A pdb=" N ALA F 305 " --> pdb=" O THR F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 334 Proline residue: F 316 - end of helix removed outlier: 4.528A pdb=" N ALA F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LEU F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE F 325 " --> pdb=" O ILE F 321 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N SER F 326 " --> pdb=" O GLY F 322 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 Processing helix chain 'F' and resid 367 through 382 removed outlier: 3.539A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS F 377 " --> pdb=" O ALA F 373 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN F 380 " --> pdb=" O VAL F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 413 Processing helix chain 'G' and resid 94 through 100 removed outlier: 5.450A pdb=" N ASP G 98 " --> pdb=" O TYR G 95 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG G 100 " --> pdb=" O GLU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 119 removed outlier: 4.164A pdb=" N GLY G 112 " --> pdb=" O PHE G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 142 Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 191 through 203 Processing helix chain 'G' and resid 231 through 243 Processing helix chain 'G' and resid 255 through 264 Processing helix chain 'G' and resid 277 through 286 Processing helix chain 'G' and resid 294 through 305 removed outlier: 3.985A pdb=" N ALA G 305 " --> pdb=" O THR G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 334 Proline residue: G 316 - end of helix removed outlier: 4.528A pdb=" N ALA G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE G 325 " --> pdb=" O ILE G 321 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER G 326 " --> pdb=" O GLY G 322 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N GLN G 327 " --> pdb=" O ALA G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 361 Processing helix chain 'G' and resid 367 through 382 removed outlier: 3.537A pdb=" N ALA G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N HIS G 377 " --> pdb=" O ALA G 373 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA G 378 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA G 379 " --> pdb=" O THR G 375 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN G 380 " --> pdb=" O VAL G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 413 Processing helix chain 'H' and resid 94 through 100 removed outlier: 5.451A pdb=" N ASP H 98 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG H 100 " --> pdb=" O GLU H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 119 removed outlier: 4.163A pdb=" N GLY H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 142 Processing helix chain 'H' and resid 172 through 178 Processing helix chain 'H' and resid 191 through 203 Processing helix chain 'H' and resid 231 through 243 Processing helix chain 'H' and resid 255 through 264 Processing helix chain 'H' and resid 277 through 286 Processing helix chain 'H' and resid 294 through 305 removed outlier: 3.993A pdb=" N ALA H 305 " --> pdb=" O THR H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 333 Proline residue: H 316 - end of helix removed outlier: 4.527A pdb=" N ALA H 323 " --> pdb=" O ALA H 319 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LEU H 324 " --> pdb=" O ARG H 320 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE H 325 " --> pdb=" O ILE H 321 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER H 326 " --> pdb=" O GLY H 322 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLN H 327 " --> pdb=" O ALA H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 363 removed outlier: 4.027A pdb=" N GLU H 362 " --> pdb=" O TYR H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 382 removed outlier: 3.540A pdb=" N ALA H 374 " --> pdb=" O ALA H 370 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS H 377 " --> pdb=" O ALA H 373 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA H 378 " --> pdb=" O ALA H 374 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA H 379 " --> pdb=" O THR H 375 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN H 380 " --> pdb=" O VAL H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 409 through 413 Processing sheet with id= A, first strand: chain 'A' and resid 66 through 70 removed outlier: 6.361A pdb=" N ALA A 47 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.571A pdb=" N PHE A 417 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS A 420 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 149 through 152 removed outlier: 7.082A pdb=" N TRP A 79 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL A 125 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP A 81 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP A 127 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 249 through 251 removed outlier: 6.561A pdb=" N SER A 268 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP A 289 " --> pdb=" O ILE A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 66 through 70 removed outlier: 6.364A pdb=" N ALA B 47 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 74 through 77 removed outlier: 3.571A pdb=" N PHE B 417 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS B 420 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 149 through 152 removed outlier: 7.082A pdb=" N TRP B 79 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL B 125 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP B 81 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ASP B 127 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 249 through 251 removed outlier: 6.559A pdb=" N SER B 268 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP B 289 " --> pdb=" O ILE B 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 66 through 70 removed outlier: 6.363A pdb=" N ALA C 47 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.570A pdb=" N PHE C 417 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS C 420 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE C 424 " --> pdb=" O LYS C 420 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 149 through 152 removed outlier: 7.084A pdb=" N TRP C 79 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL C 125 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP C 81 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ASP C 127 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 249 through 251 removed outlier: 6.559A pdb=" N SER C 268 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP C 289 " --> pdb=" O ILE C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.364A pdb=" N ALA D 47 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ILE D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 74 through 77 removed outlier: 3.565A pdb=" N PHE D 417 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS D 420 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 149 through 152 removed outlier: 7.084A pdb=" N TRP D 79 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL D 125 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP D 81 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP D 127 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 249 through 251 removed outlier: 6.560A pdb=" N SER D 268 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP D 289 " --> pdb=" O ILE D 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.644A pdb=" N GLN E 53 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA E 47 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.583A pdb=" N PHE E 417 " --> pdb=" O ALA E 400 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS E 420 " --> pdb=" O ILE E 424 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE E 424 " --> pdb=" O LYS E 420 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 149 through 152 removed outlier: 7.096A pdb=" N TRP E 79 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL E 125 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP E 81 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP E 127 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 249 through 251 removed outlier: 6.636A pdb=" N SER E 268 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP E 289 " --> pdb=" O ILE E 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 66 through 70 removed outlier: 3.638A pdb=" N GLN F 53 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA F 47 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 74 through 77 removed outlier: 3.581A pdb=" N PHE F 417 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS F 420 " --> pdb=" O ILE F 424 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 149 through 152 removed outlier: 7.095A pdb=" N TRP F 79 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL F 125 " --> pdb=" O TRP F 79 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP F 81 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP F 127 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 249 through 251 removed outlier: 6.633A pdb=" N SER F 268 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP F 289 " --> pdb=" O ILE F 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 66 through 70 removed outlier: 3.645A pdb=" N GLN G 53 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA G 47 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.583A pdb=" N PHE G 417 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS G 420 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE G 424 " --> pdb=" O LYS G 420 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 149 through 152 removed outlier: 7.098A pdb=" N TRP G 79 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL G 125 " --> pdb=" O TRP G 79 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP G 81 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP G 127 " --> pdb=" O ASP G 81 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 249 through 251 removed outlier: 6.635A pdb=" N SER G 268 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP G 289 " --> pdb=" O ILE G 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'H' and resid 66 through 70 removed outlier: 3.647A pdb=" N GLN H 53 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA H 47 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.582A pdb=" N PHE H 417 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS H 420 " --> pdb=" O ILE H 424 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE H 424 " --> pdb=" O LYS H 420 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 149 through 152 removed outlier: 7.096A pdb=" N TRP H 79 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL H 125 " --> pdb=" O TRP H 79 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP H 81 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP H 127 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 249 through 251 removed outlier: 6.638A pdb=" N SER H 268 " --> pdb=" O ALA H 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP H 289 " --> pdb=" O ILE H 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF 900 hydrogen bonds defined for protein. 2355 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: 8.18 Time building geometry restraints manager: 10.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4626 1.32 - 1.45: 6097 1.45 - 1.57: 13853 1.57 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 24704 Sorted by residual: bond pdb=" NZ KCX E 210 " pdb=" CX KCX E 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX A 210 " pdb=" CX KCX A 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX D 210 " pdb=" CX KCX D 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" NZ KCX G 210 " pdb=" CX KCX G 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" NZ KCX H 210 " pdb=" CX KCX H 210 " ideal model delta sigma weight residual 1.411 1.327 0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 24699 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.24: 733 106.24 - 113.18: 12950 113.18 - 120.12: 9041 120.12 - 127.07: 10495 127.07 - 134.01: 277 Bond angle restraints: 33496 Sorted by residual: angle pdb=" N VAL C 347 " pdb=" CA VAL C 347 " pdb=" C VAL C 347 " ideal model delta sigma weight residual 111.67 101.21 10.46 9.50e-01 1.11e+00 1.21e+02 angle pdb=" N VAL A 347 " pdb=" CA VAL A 347 " pdb=" C VAL A 347 " ideal model delta sigma weight residual 111.67 101.42 10.25 9.50e-01 1.11e+00 1.16e+02 angle pdb=" N GLY C 346 " pdb=" CA GLY C 346 " pdb=" C GLY C 346 " ideal model delta sigma weight residual 113.18 102.11 11.07 2.37e+00 1.78e-01 2.18e+01 angle pdb=" C GLN C 345 " pdb=" CA GLN C 345 " pdb=" CB GLN C 345 " ideal model delta sigma weight residual 109.72 117.46 -7.74 1.66e+00 3.63e-01 2.17e+01 angle pdb=" C GLN B 345 " pdb=" CA GLN B 345 " pdb=" CB GLN B 345 " ideal model delta sigma weight residual 109.72 117.43 -7.71 1.66e+00 3.63e-01 2.16e+01 ... (remaining 33491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 12882 17.58 - 35.16: 1251 35.16 - 52.74: 368 52.74 - 70.33: 86 70.33 - 87.91: 29 Dihedral angle restraints: 14616 sinusoidal: 5656 harmonic: 8960 Sorted by residual: dihedral pdb=" CA GLY D 346 " pdb=" C GLY D 346 " pdb=" N VAL D 347 " pdb=" CA VAL D 347 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA GLN D 345 " pdb=" C GLN D 345 " pdb=" N GLY D 346 " pdb=" CA GLY D 346 " ideal model delta harmonic sigma weight residual -180.00 -158.59 -21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLY F 272 " pdb=" C GLY F 272 " pdb=" N THR F 273 " pdb=" CA THR F 273 " ideal model delta harmonic sigma weight residual 180.00 -159.31 -20.69 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 14613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2988 0.057 - 0.114: 610 0.114 - 0.171: 68 0.171 - 0.229: 6 0.229 - 0.286: 8 Chirality restraints: 3680 Sorted by residual: chirality pdb=" CA VAL G 347 " pdb=" N VAL G 347 " pdb=" C VAL G 347 " pdb=" CB VAL G 347 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA VAL E 347 " pdb=" N VAL E 347 " pdb=" C VAL E 347 " pdb=" CB VAL E 347 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA VAL H 347 " pdb=" N VAL H 347 " pdb=" C VAL H 347 " pdb=" CB VAL H 347 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3677 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 55 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO G 56 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO G 56 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 56 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 374 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.05e+00 pdb=" C ALA E 374 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA E 374 " 0.017 2.00e-02 2.50e+03 pdb=" N THR E 375 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 374 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.04e+00 pdb=" C ALA G 374 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA G 374 " -0.017 2.00e-02 2.50e+03 pdb=" N THR G 375 " -0.016 2.00e-02 2.50e+03 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 412 2.69 - 3.24: 22041 3.24 - 3.80: 37679 3.80 - 4.35: 54855 4.35 - 4.90: 88642 Nonbonded interactions: 203629 Sorted by model distance: nonbonded pdb=" OQ2 KCX E 210 " pdb="ZN ZN E 501 " model vdw 2.138 2.230 nonbonded pdb=" OQ2 KCX F 210 " pdb="ZN ZN F 501 " model vdw 2.138 2.230 nonbonded pdb=" OQ2 KCX G 210 " pdb="ZN ZN G 501 " model vdw 2.139 2.230 nonbonded pdb=" OQ2 KCX H 210 " pdb="ZN ZN H 501 " model vdw 2.139 2.230 nonbonded pdb=" N GLN H 327 " pdb=" OE1 GLN H 327 " model vdw 2.216 2.520 ... (remaining 203624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 11.100 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 66.660 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.180 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 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 : 0.004 0.084 24704 Z= 0.239 Angle : 0.669 11.066 33496 Z= 0.401 Chirality : 0.048 0.286 3680 Planarity : 0.005 0.068 4464 Dihedral : 15.866 87.908 8912 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.70 % Allowed : 15.72 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.14), residues: 3136 helix: 0.21 (0.14), residues: 1344 sheet: -0.05 (0.24), residues: 400 loop : -0.90 (0.16), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 337 time to evaluate : 2.257 Fit side-chains outliers start: 17 outliers final: 17 residues processed: 351 average time/residue: 1.5207 time to fit residues: 605.5376 Evaluate side-chains 339 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 322 time to evaluate : 2.104 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.1838 time to fit residues: 4.1429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN B 335 ASN C 335 ASN D 335 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.0377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24704 Z= 0.127 Angle : 0.480 7.283 33496 Z= 0.255 Chirality : 0.043 0.134 3680 Planarity : 0.004 0.045 4464 Dihedral : 4.665 34.085 3552 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.35 % Allowed : 14.27 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3136 helix: 0.44 (0.14), residues: 1344 sheet: 0.11 (0.25), residues: 400 loop : -0.82 (0.16), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 323 time to evaluate : 2.821 Fit side-chains outliers start: 57 outliers final: 38 residues processed: 349 average time/residue: 1.5005 time to fit residues: 593.4891 Evaluate side-chains 359 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 321 time to evaluate : 1.947 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 21 residues processed: 17 average time/residue: 0.3141 time to fit residues: 10.5410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.5980 chunk 87 optimal weight: 7.9990 chunk 235 optimal weight: 0.0970 chunk 192 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 283 optimal weight: 9.9990 chunk 306 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 281 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 227 optimal weight: 10.0000 overall best weight: 2.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 53 GLN A 335 ASN B 53 GLN B 335 ASN C 53 GLN C 335 ASN D 53 GLN D 335 ASN E 37 GLN F 37 GLN G 37 GLN H 37 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 24704 Z= 0.251 Angle : 0.575 8.689 33496 Z= 0.311 Chirality : 0.047 0.142 3680 Planarity : 0.005 0.046 4464 Dihedral : 5.127 35.608 3552 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.34 % Allowed : 14.40 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3136 helix: 0.21 (0.14), residues: 1344 sheet: -0.09 (0.24), residues: 400 loop : -0.89 (0.16), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 327 time to evaluate : 2.699 Fit side-chains outliers start: 81 outliers final: 42 residues processed: 365 average time/residue: 1.5315 time to fit residues: 634.3720 Evaluate side-chains 360 residues out of total 2424 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 318 time to evaluate : 2.654 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 24 residues processed: 18 average time/residue: 0.4960 time to fit residues: 16.4421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7319 > 50: distance: 95 - 115: 23.319 distance: 100 - 107: 18.383 distance: 107 - 108: 30.061 distance: 108 - 109: 44.542 distance: 108 - 111: 36.241 distance: 109 - 110: 39.589 distance: 109 - 115: 49.394 distance: 111 - 112: 13.291 distance: 112 - 113: 24.819 distance: 112 - 114: 12.355 distance: 115 - 116: 20.873 distance: 116 - 117: 22.366 distance: 116 - 119: 3.955 distance: 117 - 118: 24.878 distance: 117 - 126: 16.640 distance: 119 - 120: 15.987 distance: 120 - 121: 14.236 distance: 120 - 122: 7.502 distance: 121 - 123: 19.614 distance: 122 - 124: 15.077 distance: 123 - 125: 17.797 distance: 124 - 125: 16.084 distance: 126 - 127: 12.551 distance: 127 - 128: 25.052 distance: 127 - 130: 15.983 distance: 128 - 129: 25.266 distance: 128 - 137: 32.831 distance: 130 - 131: 8.604 distance: 131 - 132: 26.356 distance: 132 - 133: 13.900 distance: 133 - 134: 34.051 distance: 134 - 135: 33.642 distance: 134 - 136: 16.552 distance: 137 - 138: 12.297 distance: 138 - 139: 14.584 distance: 138 - 141: 16.371 distance: 139 - 140: 36.875 distance: 139 - 145: 35.525 distance: 141 - 142: 22.777 distance: 142 - 143: 14.393 distance: 142 - 144: 23.784 distance: 145 - 146: 26.938 distance: 146 - 147: 32.653 distance: 146 - 149: 9.379 distance: 147 - 148: 33.173 distance: 147 - 153: 44.642 distance: 149 - 150: 5.214 distance: 150 - 151: 31.166 distance: 150 - 152: 17.709 distance: 153 - 154: 30.226 distance: 153 - 159: 37.715 distance: 154 - 155: 35.173 distance: 154 - 157: 16.337 distance: 155 - 156: 36.254 distance: 155 - 160: 44.404 distance: 156 - 185: 12.640 distance: 157 - 158: 11.637 distance: 158 - 159: 24.119 distance: 160 - 161: 48.382 distance: 161 - 162: 59.732 distance: 161 - 164: 12.315 distance: 162 - 163: 43.965 distance: 162 - 167: 50.976 distance: 163 - 190: 13.305 distance: 164 - 165: 42.327 distance: 164 - 166: 27.115 distance: 167 - 168: 22.932 distance: 168 - 169: 23.500 distance: 168 - 171: 19.168 distance: 169 - 170: 7.038 distance: 169 - 175: 17.054 distance: 170 - 200: 12.643 distance: 171 - 172: 11.248 distance: 172 - 173: 8.490 distance: 172 - 174: 7.294 distance: 175 - 176: 22.542 distance: 176 - 177: 11.832 distance: 176 - 179: 12.276 distance: 177 - 178: 35.612 distance: 177 - 185: 25.890 distance: 178 - 211: 14.653 distance: 179 - 180: 22.325 distance: 180 - 181: 46.757 distance: 180 - 182: 55.970 distance: 181 - 183: 43.294 distance: 182 - 184: 50.335 distance: 183 - 184: 44.492 distance: 185 - 186: 27.826 distance: 186 - 187: 35.777 distance: 186 - 189: 32.525 distance: 187 - 188: 39.799 distance: 187 - 190: 23.964 distance: 188 - 216: 24.319