Starting phenix.real_space_refine on Fri Mar 15 13:07:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/03_2024/6puz_20485_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/03_2024/6puz_20485.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/03_2024/6puz_20485_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/03_2024/6puz_20485_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/03_2024/6puz_20485_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/03_2024/6puz_20485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/03_2024/6puz_20485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/03_2024/6puz_20485_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puz_20485/03_2024/6puz_20485_updated.pdb" } resolution = 2.8 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= -0.007 sd= 1.021 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 72 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 7020 2.51 5 N 2044 2.21 5 O 2518 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ASP 25": "OD1" <-> "OD2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H ASP 41": "OD1" <-> "OD2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 167": "OD1" <-> "OD2" Residue "H ASP 202": "OD1" <-> "OD2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "H TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 253": "OD1" <-> "OD2" Residue "H ASP 270": "OD1" <-> "OD2" Residue "I ASP 229": "OD1" <-> "OD2" Residue "I ASP 253": "OD1" <-> "OD2" Residue "I ASP 270": "OD1" <-> "OD2" Residue "J TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 229": "OD1" <-> "OD2" Residue "J ASP 232": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11702 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2052 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Chain: "B" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1901 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 7, 'TRANS': 232} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 534 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "D" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 399 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 44} Chain: "E" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 371 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Conformer: "B" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} bond proxies already assigned to first conformer: 369 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' MG': 2, ' ZN': 1, 'XXJ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "G" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2052 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 9, 'TRANS': 252} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Chain: "H" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1901 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 7, 'TRANS': 232} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 534 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 3, 'TRANS': 61} Chain: "J" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 399 Classifications: {'peptide': 48} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 44} Chain: "K" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "L" Number of atoms: 371 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Conformer: "B" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} bond proxies already assigned to first conformer: 369 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 39 Unusual residues: {' MG': 2, ' ZN': 1, 'XXJ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "L" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 317 SG CYS A 40 26.691 45.365 55.574 1.00 11.56 S ATOM 338 SG CYS A 43 30.143 46.397 54.077 1.00 5.74 S ATOM 2351 SG CYS B 40 49.793 121.387 26.507 1.00 87.46 S ATOM 2374 SG CYS B 43 48.405 120.462 30.308 1.00 90.05 S ATOM 6168 SG CYS G 40 64.949 87.355 55.574 1.00 11.56 S ATOM 6189 SG CYS G 43 61.497 86.323 54.077 1.00 5.74 S ATOM 8202 SG CYS H 40 41.847 11.333 26.507 1.00 87.46 S ATOM 8225 SG CYS H 43 43.235 12.258 30.308 1.00 90.05 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.40 ... (40 atoms not shown) pdb=" C4 B DA F 21 " occ=0.60 residue: pdb=" P A DA L 21 " occ=0.40 ... (40 atoms not shown) pdb=" C4 B DA L 21 " occ=0.60 Time building chain proxies: 10.61, per 1000 atoms: 0.91 Number of scatterers: 11702 At special positions: 0 Unit cell: (92.43, 133.51, 86.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 36 16.00 P 72 15.00 Mg 4 11.99 F 4 9.00 O 2518 8.00 N 2044 7.00 C 7020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.58 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " pdb=" ZN G 303 " pdb="ZN ZN G 303 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 303 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 40 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 43 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 40 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " Number of angles added : 2 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2276 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 20 sheets defined 39.5% alpha, 20.5% beta 30 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 5.52 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 removed outlier: 3.797A pdb=" N ASP A 6 " --> pdb=" O LEU A 2 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 31 through 39 Processing helix chain 'A' and resid 94 through 107 removed outlier: 3.613A pdb=" N TYR A 99 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 122 No H-bonds generated for 'chain 'A' and resid 119 through 122' Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 145 through 165 removed outlier: 5.497A pdb=" N VAL A 150 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 196 through 218 Processing helix chain 'B' and resid 5 through 15 WARNING: missing atoms! Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'B' and resid 94 through 107 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 151 through 168 removed outlier: 5.338A pdb=" N ASP B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 185 Processing helix chain 'B' and resid 196 through 220 removed outlier: 3.685A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 222 removed outlier: 3.614A pdb=" N ASN C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.797A pdb=" N ASP G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 31 through 39 Processing helix chain 'G' and resid 94 through 107 removed outlier: 3.613A pdb=" N TYR G 99 " --> pdb=" O GLN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 122 No H-bonds generated for 'chain 'G' and resid 119 through 122' Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 145 through 165 removed outlier: 5.497A pdb=" N VAL G 150 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU G 152 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 185 Processing helix chain 'G' and resid 196 through 218 Processing helix chain 'H' and resid 5 through 15 WARNING: missing atoms! Processing helix chain 'H' and resid 19 through 25 Processing helix chain 'H' and resid 30 through 39 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 94 through 107 Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 151 through 168 removed outlier: 5.338A pdb=" N ASP H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN H 168 " --> pdb=" O GLN H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 185 Processing helix chain 'H' and resid 196 through 220 removed outlier: 3.685A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 222 removed outlier: 3.614A pdb=" N ASN I 222 " --> pdb=" O THR I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 264 No H-bonds generated for 'chain 'I' and resid 262 through 264' Processing helix chain 'J' and resid 262 through 264 No H-bonds generated for 'chain 'J' and resid 262 through 264' Processing sheet with id= A, first strand: chain 'A' and resid 86 through 89 removed outlier: 4.222A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR A 112 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU A 63 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS A 114 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N CYS A 65 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYS A 136 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR A 115 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU A 138 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 224 through 227 Processing sheet with id= C, first strand: chain 'A' and resid 256 through 261 removed outlier: 6.536A pdb=" N GLN A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU A 241 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 84 through 89 removed outlier: 4.274A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR B 112 " --> pdb=" O TRP B 61 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU B 63 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N HIS B 114 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N CYS B 65 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS B 136 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 223 through 227 Processing sheet with id= F, first strand: chain 'B' and resid 256 through 261 removed outlier: 6.234A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 224 through 227 Processing sheet with id= H, first strand: chain 'C' and resid 256 through 261 removed outlier: 6.177A pdb=" N GLN C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU C 241 " --> pdb=" O GLN C 252 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 224 through 227 Processing sheet with id= J, first strand: chain 'D' and resid 256 through 261 removed outlier: 6.653A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 86 through 89 removed outlier: 4.222A pdb=" N VAL G 72 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR G 112 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU G 63 " --> pdb=" O THR G 112 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS G 114 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N CYS G 65 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYS G 136 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR G 115 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU G 138 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 224 through 227 Processing sheet with id= M, first strand: chain 'G' and resid 256 through 261 removed outlier: 6.536A pdb=" N GLN G 252 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N LEU G 241 " --> pdb=" O GLN G 252 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 84 through 89 removed outlier: 4.274A pdb=" N VAL H 72 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR H 112 " --> pdb=" O TRP H 61 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU H 63 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N HIS H 114 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N CYS H 65 " --> pdb=" O HIS H 114 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LYS H 136 " --> pdb=" O VAL H 113 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 223 through 227 Processing sheet with id= P, first strand: chain 'H' and resid 256 through 261 removed outlier: 6.234A pdb=" N GLN H 252 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU H 241 " --> pdb=" O GLN H 252 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 224 through 227 Processing sheet with id= R, first strand: chain 'I' and resid 256 through 261 removed outlier: 6.177A pdb=" N GLN I 252 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU I 241 " --> pdb=" O GLN I 252 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 224 through 227 Processing sheet with id= T, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.653A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 7.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1698 1.31 - 1.43: 3432 1.43 - 1.56: 6418 1.56 - 1.69: 136 1.69 - 1.81: 54 Bond restraints: 11738 Sorted by residual: bond pdb=" O3' DC L 20 " pdb=" P B DA L 21 " ideal model delta sigma weight residual 1.607 1.421 0.186 1.50e-02 4.44e+03 1.54e+02 bond pdb=" O3' DC F 20 " pdb=" P B DA F 21 " ideal model delta sigma weight residual 1.607 1.421 0.186 1.50e-02 4.44e+03 1.54e+02 bond pdb=" C ASP G 116 " pdb=" N ASN G 117 " ideal model delta sigma weight residual 1.334 1.270 0.064 1.24e-02 6.50e+03 2.67e+01 bond pdb=" C ASP A 116 " pdb=" N ASN A 117 " ideal model delta sigma weight residual 1.334 1.270 0.064 1.24e-02 6.50e+03 2.67e+01 bond pdb=" O3' DG F 19 " pdb=" P DC F 20 " ideal model delta sigma weight residual 1.607 1.540 0.067 1.50e-02 4.44e+03 2.01e+01 ... (remaining 11733 not shown) Histogram of bond angle deviations from ideal: 97.41 - 104.73: 428 104.73 - 112.05: 5844 112.05 - 119.37: 4048 119.37 - 126.69: 5390 126.69 - 134.01: 430 Bond angle restraints: 16140 Sorted by residual: angle pdb=" O LYS A 127 " pdb=" C LYS A 127 " pdb=" N ALA A 128 " ideal model delta sigma weight residual 122.15 115.50 6.65 1.14e+00 7.69e-01 3.40e+01 angle pdb=" O LYS G 127 " pdb=" C LYS G 127 " pdb=" N ALA G 128 " ideal model delta sigma weight residual 122.15 115.50 6.65 1.14e+00 7.69e-01 3.40e+01 angle pdb=" C LYS A 127 " pdb=" N ALA A 128 " pdb=" CA ALA A 128 " ideal model delta sigma weight residual 120.29 128.30 -8.01 1.42e+00 4.96e-01 3.19e+01 angle pdb=" C LYS G 127 " pdb=" N ALA G 128 " pdb=" CA ALA G 128 " ideal model delta sigma weight residual 120.29 128.30 -8.01 1.42e+00 4.96e-01 3.19e+01 angle pdb=" N SER A 123 " pdb=" CA SER A 123 " pdb=" C SER A 123 " ideal model delta sigma weight residual 110.41 117.14 -6.73 1.23e+00 6.61e-01 3.00e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 6324 32.69 - 65.37: 486 65.37 - 98.06: 26 98.06 - 130.75: 0 130.75 - 163.43: 2 Dihedral angle restraints: 6838 sinusoidal: 3312 harmonic: 3526 Sorted by residual: dihedral pdb=" CA ARG J 228 " pdb=" C ARG J 228 " pdb=" N ASP J 229 " pdb=" CA ASP J 229 " ideal model delta harmonic sigma weight residual 180.00 -155.53 -24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ARG D 228 " pdb=" C ARG D 228 " pdb=" N ASP D 229 " pdb=" CA ASP D 229 " ideal model delta harmonic sigma weight residual -180.00 -155.53 -24.47 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA TYR I 271 " pdb=" C TYR I 271 " pdb=" N GLY I 272 " pdb=" CA GLY I 272 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 6835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 958 0.037 - 0.074: 518 0.074 - 0.111: 204 0.111 - 0.149: 62 0.149 - 0.186: 22 Chirality restraints: 1764 Sorted by residual: chirality pdb=" CB ILE G 60 " pdb=" CA ILE G 60 " pdb=" CG1 ILE G 60 " pdb=" CG2 ILE G 60 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA ILE A 268 " pdb=" N ILE A 268 " pdb=" C ILE A 268 " pdb=" CB ILE A 268 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.13e-01 ... (remaining 1761 not shown) Planarity restraints: 1768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 158 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C LEU G 158 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU G 158 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS G 159 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 158 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C LEU A 158 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU A 158 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS A 159 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 156 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.77e+00 pdb=" C LYS A 156 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS A 156 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 157 " 0.016 2.00e-02 2.50e+03 ... (remaining 1765 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 6 0.98 - 1.96: 2 1.96 - 2.94: 4750 2.94 - 3.92: 32416 3.92 - 4.90: 64492 Warning: very small nonbonded interaction distances. Nonbonded interactions: 101666 Sorted by model distance: nonbonded pdb=" O HOH A 457 " pdb=" O HOH K 113 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 469 " pdb=" O HOH K 114 " model vdw 0.000 2.440 nonbonded pdb=" O HOH E 114 " pdb=" O HOH G 469 " model vdw 0.000 2.440 nonbonded pdb=" O HOH E 113 " pdb=" O HOH G 457 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 491 " pdb=" O HOH G 476 " model vdw 0.006 2.440 ... (remaining 101661 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' and (resid 3 through 8 or (resid 9 and (name N or name CA or name C o \ r name CB or name CG or name CD or name OE1 or name NE2)) or resid 10 through 44 \ or resid 57 through 139 or resid 150 through 269)) selection = (chain 'B' and (resid 3 through 9 or (resid 10 and (name N or name CA or name C \ or name CB or name CG or name CD or name OE1 or name OE2)) or resid 11 through 2 \ 8 or (resid 29 and (name N or name CA or name C or name CB or name CG or name CD \ )) or resid 30 through 41 or (resid 42 and (name N or name CA or name C or name \ CB or name CG or name CD or name CE or name NZ )) or (resid 43 and (name N or n \ ame CA or name C or name CB or name SG )) or resid 44 through 66 or (resid 67 an \ d (name N or name CA or name C or name CB or name CG or name ND1 or name CD2 or \ name CE1 or name NE2)) or resid 68 through 77 or (resid 78 and (name N or name C \ A or name C or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2)) or resid 79 through 80 or (resid 81 and (name N or name CA or name C or name \ CB or name OG )) or resid 82 through 83 or (resid 84 and (name N or name CA or \ name C or name CB or name CG1 or name CG2 or name CD1)) or resid 85 through 228 \ or resid 236 through 269)) selection = (chain 'G' and (resid 3 through 8 or (resid 9 and (name N or name CA or name C o \ r name CB or name CG or name CD or name OE1 or name NE2)) or resid 10 through 44 \ or resid 57 through 139 or resid 150 through 269)) selection = (chain 'H' and (resid 3 through 9 or (resid 10 and (name N or name CA or name C \ or name CB or name CG or name CD or name OE1 or name OE2)) or resid 11 through 2 \ 8 or (resid 29 and (name N or name CA or name C or name CB or name CG or name CD \ )) or resid 30 through 41 or (resid 42 and (name N or name CA or name C or name \ CB or name CG or name CD or name CE or name NZ )) or (resid 43 and (name N or n \ ame CA or name C or name CB or name SG )) or resid 44 through 66 or (resid 67 an \ d (name N or name CA or name C or name CB or name CG or name ND1 or name CD2 or \ name CE1 or name NE2)) or resid 68 through 77 or (resid 78 and (name N or name C \ A or name C or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2)) or resid 79 through 80 or (resid 81 and (name N or name CA or name C or name \ CB or name OG )) or resid 82 through 83 or (resid 84 and (name N or name CA or \ name C or name CB or name CG1 or name CG2 or name CD1)) or resid 85 through 228 \ or resid 236 through 269)) } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = (chain 'F' and resid 5 through 20) selection = (chain 'L' and resid 5 through 20) } 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=0.40 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: 3.760 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: 12.750 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 47.830 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 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 0.186 11738 Z= 0.461 Angle : 0.856 9.784 16140 Z= 0.512 Chirality : 0.054 0.186 1764 Planarity : 0.007 0.053 1768 Dihedral : 19.789 163.433 4562 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.19 % Allowed : 3.09 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.67 (0.21), residues: 1198 helix: -2.09 (0.17), residues: 488 sheet: -0.71 (0.29), residues: 292 loop : -1.87 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 132 HIS 0.005 0.001 HIS B 12 PHE 0.014 0.003 PHE G 185 TYR 0.015 0.002 TYR H 83 ARG 0.007 0.000 ARG G 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 1.265 Fit side-chains TARDY: cannot create tardy model for: "GLU A 10 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN B 9 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 10 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN H 9 " (corrupted residue). Skipping it. REVERT: A 85 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 240 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8786 (ttmt) REVERT: G 85 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7771 (mt-10) REVERT: I 240 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8785 (ttmt) outliers start: 2 outliers final: 2 residues processed: 254 average time/residue: 1.4025 time to fit residues: 381.4590 Evaluate side-chains 216 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain G residue 120 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 63.6226 > 50: distance: 96 - 118: 4.422 distance: 102 - 126: 6.542 distance: 109 - 131: 26.937 distance: 113 - 135: 31.147 distance: 118 - 119: 7.069 distance: 119 - 120: 10.831 distance: 119 - 122: 11.681 distance: 120 - 121: 21.080 distance: 120 - 126: 13.324 distance: 122 - 123: 16.384 distance: 123 - 124: 9.481 distance: 123 - 125: 18.463 distance: 126 - 127: 7.957 distance: 127 - 128: 28.956 distance: 127 - 130: 16.196 distance: 128 - 129: 3.647 distance: 128 - 131: 19.802 distance: 131 - 132: 28.990 distance: 132 - 133: 42.149 distance: 133 - 134: 18.336 distance: 133 - 135: 46.405 distance: 135 - 136: 57.370 distance: 136 - 137: 17.981 distance: 136 - 139: 36.065 distance: 137 - 138: 27.058 distance: 137 - 146: 40.771 distance: 139 - 140: 22.764 distance: 140 - 141: 43.944 distance: 141 - 142: 26.580 distance: 142 - 143: 29.432 distance: 143 - 144: 23.013 distance: 143 - 145: 18.095 distance: 146 - 147: 29.385 distance: 147 - 148: 28.606 distance: 147 - 150: 26.769 distance: 148 - 149: 48.464 distance: 148 - 160: 39.442 distance: 150 - 151: 21.635 distance: 151 - 152: 3.204 distance: 151 - 153: 6.730 distance: 152 - 154: 9.396 distance: 153 - 155: 10.273 distance: 153 - 156: 6.144 distance: 154 - 155: 5.585 distance: 155 - 157: 4.872 distance: 156 - 158: 6.669 distance: 157 - 159: 8.590 distance: 158 - 159: 9.592 distance: 160 - 161: 27.319 distance: 160 - 166: 20.251 distance: 161 - 162: 37.102 distance: 161 - 164: 17.536 distance: 162 - 163: 5.885 distance: 162 - 167: 47.656 distance: 164 - 165: 22.076 distance: 165 - 166: 19.400 distance: 167 - 168: 4.243 distance: 168 - 169: 21.089 distance: 168 - 171: 23.322 distance: 169 - 170: 21.837 distance: 169 - 174: 6.326 distance: 171 - 172: 11.134 distance: 171 - 173: 14.912 distance: 174 - 175: 26.788 distance: 175 - 176: 23.652 distance: 175 - 178: 26.324 distance: 176 - 177: 23.534 distance: 176 - 183: 28.917 distance: 178 - 179: 23.323 distance: 179 - 180: 49.042 distance: 180 - 181: 10.916 distance: 181 - 182: 9.596 distance: 183 - 184: 35.609 distance: 184 - 185: 31.601 distance: 184 - 187: 14.250 distance: 185 - 186: 39.278 distance: 185 - 190: 35.957 distance: 187 - 188: 12.040 distance: 187 - 189: 26.167 distance: 190 - 191: 21.999 distance: 191 - 192: 30.520 distance: 191 - 194: 32.850 distance: 192 - 193: 5.775 distance: 192 - 197: 29.969 distance: 194 - 195: 50.706 distance: 194 - 196: 28.175