Starting phenix.real_space_refine on Fri Jan 19 15:11:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puy_20484/01_2024/6puy_20484_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puy_20484/01_2024/6puy_20484.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puy_20484/01_2024/6puy_20484_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/6puy_20484/01_2024/6puy_20484_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puy_20484/01_2024/6puy_20484_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puy_20484/01_2024/6puy_20484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puy_20484/01_2024/6puy_20484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puy_20484/01_2024/6puy_20484_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6puy_20484/01_2024/6puy_20484_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= 0.040 sd= 0.741 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 34 5.16 5 C 7036 2.51 5 N 2038 2.21 5 O 2592 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 PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ASP 256": "OD1" <-> "OD2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B ASP 64": "OD1" <-> "OD2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 232": "OD1" <-> "OD2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "G PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G GLU 138": "OE1" <-> "OE2" Residue "G TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G ASP 256": "OD1" <-> "OD2" Residue "H GLU 13": "OE1" <-> "OE2" Residue "H ASP 64": "OD1" <-> "OD2" Residue "H ASP 116": "OD1" <-> "OD2" Residue "H ASP 202": "OD1" <-> "OD2" Residue "H ASP 207": "OD1" <-> "OD2" Residue "H PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 232": "OD1" <-> "OD2" Residue "J PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 229": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 11784 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2045 Classifications: {'peptide': 261} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1915 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 543 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "D" Number of atoms: 396 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Conformer: "B" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} bond proxies already assigned to first conformer: 388 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'OZ1': 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: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "G" Number of atoms: 2045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2045 Classifications: {'peptide': 261} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Chain: "H" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1915 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 543 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "J" Number of atoms: 396 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Conformer: "B" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} bond proxies already assigned to first conformer: 388 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' ZN': 1, 'OZ1': 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: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "J" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "K" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "L" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 318 SG CYS A 40 27.337 46.228 53.451 1.00 30.33 S ATOM 341 SG CYS A 43 30.837 47.289 51.877 1.00 18.13 S ATOM 2363 SG CYS B 40 51.089 121.213 23.188 1.00118.66 S ATOM 2386 SG CYS B 43 48.727 122.056 26.707 1.00 80.08 S ATOM 6210 SG CYS G 40 65.883 88.072 53.451 1.00 30.33 S ATOM 6233 SG CYS G 43 62.383 87.011 51.877 1.00 18.13 S ATOM 8255 SG CYS H 40 42.131 13.087 23.188 1.00118.66 S ATOM 8278 SG CYS H 43 44.493 12.244 26.707 1.00 80.08 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.35 ... (40 atoms not shown) pdb=" C4 B DA F 21 " occ=0.65 residue: pdb=" P A DA L 21 " occ=0.35 ... (40 atoms not shown) pdb=" C4 B DA L 21 " occ=0.65 Time building chain proxies: 7.12, per 1000 atoms: 0.60 Number of scatterers: 11784 At special positions: 0 Unit cell: (94.01, 135.09, 85.32, 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 34 16.00 P 72 15.00 Mg 4 11.99 F 4 9.00 O 2592 8.00 N 2038 7.00 C 7036 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: 4.69 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb=" ZN G 303 " pdb="ZN ZN G 303 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 303 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 40 " pdb="ZN ZN G 303 " - pdb=" SG CYS G 43 " pdb=" ZN H 500 " pdb="ZN ZN H 500 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 500 " - pdb=" ND1 HIS H 16 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 43 " pdb="ZN ZN H 500 " - pdb=" SG CYS H 40 " Number of angles added : 6 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 18 sheets defined 40.9% alpha, 21.4% beta 32 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 5.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 12 through 15 No H-bonds generated for 'chain 'A' and resid 12 through 15' Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 30 through 39 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 94 through 106 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 168 removed outlier: 5.558A pdb=" N VAL A 150 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG A 166 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP A 167 " --> pdb=" O GLN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 196 through 220 removed outlier: 3.797A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 removed outlier: 4.383A pdb=" N ASP B 6 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 30 through 38 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: 5.510A pdb=" N ASP B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 5.648A 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 Processing helix chain 'C' and resid 214 through 222 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 10 Processing helix chain 'G' and resid 12 through 15 No H-bonds generated for 'chain 'G' and resid 12 through 15' Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 30 through 39 Processing helix chain 'G' and resid 41 through 43 No H-bonds generated for 'chain 'G' and resid 41 through 43' Processing helix chain 'G' and resid 94 through 106 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 168 removed outlier: 5.558A pdb=" N VAL G 150 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU G 152 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG G 166 " --> pdb=" O GLY G 163 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASP G 167 " --> pdb=" O GLN G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 185 Processing helix chain 'G' and resid 190 through 192 No H-bonds generated for 'chain 'G' and resid 190 through 192' Processing helix chain 'G' and resid 196 through 220 removed outlier: 3.797A pdb=" N ILE G 220 " --> pdb=" O GLN G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 15 removed outlier: 4.383A pdb=" N ASP H 6 " --> pdb=" O LEU H 2 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'H' and resid 19 through 25 Processing helix chain 'H' and resid 30 through 38 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: 5.510A pdb=" N ASP H 167 " --> pdb=" O GLY H 163 " (cutoff:3.500A) removed outlier: 5.648A 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 Processing helix chain 'I' and resid 214 through 222 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 84 through 89 removed outlier: 4.212A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR A 112 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU A 63 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS A 114 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N CYS A 65 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS A 136 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR A 115 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU A 138 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 265 through 267 removed outlier: 3.593A pdb=" N VAL A 225 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 250 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYS A 244 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 84 through 89 removed outlier: 4.266A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR B 112 " --> pdb=" O TRP B 61 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU B 63 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS B 114 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N CYS B 65 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS B 136 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 223 through 227 Processing sheet with id= E, first strand: chain 'B' and resid 256 through 261 removed outlier: 6.012A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 224 through 227 Processing sheet with id= G, first strand: chain 'C' and resid 256 through 261 removed outlier: 6.543A pdb=" N GLN C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU C 241 " --> pdb=" O GLN C 252 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 224 through 227 Processing sheet with id= I, first strand: chain 'D' and resid 256 through 261 removed outlier: 6.688A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 84 through 89 removed outlier: 4.212A pdb=" N VAL G 72 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR G 112 " --> pdb=" O TRP G 61 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU G 63 " --> pdb=" O THR G 112 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS G 114 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N CYS G 65 " --> pdb=" O HIS G 114 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS G 136 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR G 115 " --> pdb=" O LYS G 136 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU G 138 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 265 through 267 removed outlier: 3.593A pdb=" N VAL G 225 " --> pdb=" O ALA G 239 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL G 250 " --> pdb=" O LEU G 242 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYS G 244 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 84 through 89 removed outlier: 4.266A pdb=" N VAL H 72 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR H 112 " --> pdb=" O TRP H 61 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU H 63 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS H 114 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N CYS H 65 " --> pdb=" O HIS H 114 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS H 136 " --> pdb=" O VAL H 113 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 223 through 227 Processing sheet with id= N, first strand: chain 'H' and resid 256 through 261 removed outlier: 6.012A pdb=" N GLN H 252 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU H 241 " --> pdb=" O GLN H 252 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 224 through 227 Processing sheet with id= P, first strand: chain 'I' and resid 256 through 261 removed outlier: 6.543A pdb=" N GLN I 252 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU I 241 " --> pdb=" O GLN I 252 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 224 through 227 Processing sheet with id= R, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.688A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 3.75 Time building geometry restraints manager: 5.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1686 1.26 - 1.40: 3060 1.40 - 1.53: 6528 1.53 - 1.67: 434 1.67 - 1.80: 50 Bond restraints: 11758 Sorted by residual: bond pdb=" CAV OZ1 A 304 " pdb=" NAU OZ1 A 304 " ideal model delta sigma weight residual 0.779 1.336 -0.557 2.00e-02 2.50e+03 7.75e+02 bond pdb=" CAV OZ1 G 304 " pdb=" NAU OZ1 G 304 " ideal model delta sigma weight residual 0.779 1.336 -0.557 2.00e-02 2.50e+03 7.75e+02 bond pdb=" CAM OZ1 G 304 " pdb=" CAV OZ1 G 304 " ideal model delta sigma weight residual 1.698 1.386 0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" CAM OZ1 A 304 " pdb=" CAV OZ1 A 304 " ideal model delta sigma weight residual 1.698 1.386 0.312 2.00e-02 2.50e+03 2.43e+02 bond pdb=" CAT OZ1 G 304 " pdb=" NAU OZ1 G 304 " ideal model delta sigma weight residual 1.588 1.328 0.260 2.00e-02 2.50e+03 1.69e+02 ... (remaining 11753 not shown) Histogram of bond angle deviations from ideal: 98.63 - 105.72: 552 105.72 - 112.80: 6318 112.80 - 119.88: 4074 119.88 - 126.97: 4880 126.97 - 134.05: 346 Bond angle restraints: 16170 Sorted by residual: angle pdb=" N SER A 123 " pdb=" CA SER A 123 " pdb=" C SER A 123 " ideal model delta sigma weight residual 110.41 117.19 -6.78 1.23e+00 6.61e-01 3.04e+01 angle pdb=" N SER G 123 " pdb=" CA SER G 123 " pdb=" C SER G 123 " ideal model delta sigma weight residual 110.41 117.19 -6.78 1.23e+00 6.61e-01 3.04e+01 angle pdb=" C3' DC L 20 " pdb=" O3' DC L 20 " pdb=" P B DA L 21 " ideal model delta sigma weight residual 120.20 127.21 -7.01 1.50e+00 4.44e-01 2.19e+01 angle pdb=" C3' DC F 20 " pdb=" O3' DC F 20 " pdb=" P B DA F 21 " ideal model delta sigma weight residual 120.20 127.21 -7.01 1.50e+00 4.44e-01 2.19e+01 angle pdb=" CAK OZ1 A 304 " pdb=" CAM OZ1 A 304 " pdb=" CAN OZ1 A 304 " ideal model delta sigma weight residual 106.72 118.96 -12.24 3.00e+00 1.11e-01 1.66e+01 ... (remaining 16165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.11: 5848 20.11 - 40.21: 620 40.21 - 60.32: 352 60.32 - 80.43: 20 80.43 - 100.54: 10 Dihedral angle restraints: 6850 sinusoidal: 3314 harmonic: 3536 Sorted by residual: 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 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA TYR C 271 " pdb=" C TYR C 271 " pdb=" N GLY C 272 " pdb=" CA GLY C 272 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA TYR G 194 " pdb=" C TYR G 194 " pdb=" N SER G 195 " pdb=" CA SER G 195 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 6847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 812 0.035 - 0.070: 602 0.070 - 0.106: 248 0.106 - 0.141: 74 0.141 - 0.176: 32 Chirality restraints: 1768 Sorted by residual: chirality pdb=" CA ASN A 120 " pdb=" N ASN A 120 " pdb=" C ASN A 120 " pdb=" CB ASN A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA ASN G 120 " pdb=" N ASN G 120 " pdb=" C ASN G 120 " pdb=" CB ASN G 120 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA THR G 122 " pdb=" N THR G 122 " pdb=" C THR G 122 " pdb=" CB THR G 122 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 1765 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 162 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.50e+00 pdb=" C ILE A 162 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 162 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 163 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 162 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.50e+00 pdb=" C ILE G 162 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE G 162 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY G 163 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 156 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.63e+00 pdb=" C LYS G 156 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS G 156 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU G 157 " -0.016 2.00e-02 2.50e+03 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 16 0.98 - 1.96: 12 1.96 - 2.94: 4822 2.94 - 3.92: 32469 3.92 - 4.90: 65198 Warning: very small nonbonded interaction distances. Nonbonded interactions: 102517 Sorted by model distance: nonbonded pdb=" O HOH D 316 " pdb=" O HOH G 508 " model vdw 0.000 2.440 nonbonded pdb=" O HOH D 317 " pdb=" O HOH G 459 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 475 " pdb=" O HOH L 114 " model vdw 0.000 2.440 nonbonded pdb=" O HOH F 114 " pdb=" O HOH G 475 " model vdw 0.000 2.440 nonbonded pdb=" O HOH A 508 " pdb=" O HOH J 316 " model vdw 0.000 2.440 ... (remaining 102512 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 1 through 6 or (resid 7 and (name N or name CA or name C o \ r name CB or name CG or name CD or name CE or name NZ )) or resid 8 through 43 o \ r resid 57 through 140 or resid 150 through 268 or resid 303)) selection = (chain 'B' and (resid 1 through 7 or (resid 8 and (name N or name CA or name C o \ r name CB )) or resid 9 through 81 or (resid 82 and (name N or name CA or name C \ )) or resid 83 through 90 or (resid 91 and (name N or name CA or name C or name \ CB )) or resid 92 through 106 or (resid 107 and (name N or name CA or name C or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) o \ r resid 108 through 228 or resid 236 through 268 or resid 500)) selection = (chain 'G' and (resid 1 through 6 or (resid 7 and (name N or name CA or name C o \ r name CB or name CG or name CD or name CE or name NZ )) or resid 8 through 43 o \ r resid 57 through 140 or resid 150 through 268 or resid 303)) selection = (chain 'H' and (resid 1 through 7 or (resid 8 and (name N or name CA or name C o \ r name CB )) or resid 9 through 81 or (resid 82 and (name N or name CA or name C \ )) or resid 83 through 90 or (resid 91 and (name N or name CA or name C or name \ CB )) or resid 92 through 106 or (resid 107 and (name N or name CA or name C or \ name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) o \ r resid 108 through 228 or resid 236 through 268 or resid 500)) } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = (chain 'D' and (resid 222 through 230 or resid 232 through 268)) selection = (chain 'J' and (resid 222 through 230 or resid 232 through 268)) } 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=0.35 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: 2.050 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: 12.640 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 39.160 Find NCS groups from input model: 0.770 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 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 : 0.015 0.557 11758 Z= 0.844 Angle : 0.898 12.240 16170 Z= 0.510 Chirality : 0.056 0.176 1768 Planarity : 0.007 0.054 1778 Dihedral : 19.873 100.537 4570 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.19 % Allowed : 4.25 % Favored : 95.56 % 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: -3.07 (0.20), residues: 1202 helix: -2.19 (0.16), residues: 484 sheet: -1.37 (0.26), residues: 300 loop : -2.02 (0.26), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 132 HIS 0.004 0.001 HIS A 51 PHE 0.015 0.002 PHE G 100 TYR 0.022 0.003 TYR G 194 ARG 0.005 0.001 ARG J 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 196 time to evaluate : 1.480 Fit side-chains REVERT: B 228 ARG cc_start: 0.5962 (mtm180) cc_final: 0.5753 (ttt90) REVERT: H 228 ARG cc_start: 0.5961 (mtm180) cc_final: 0.5755 (ttt90) outliers start: 2 outliers final: 4 residues processed: 196 average time/residue: 1.5286 time to fit residues: 320.9354 Evaluate side-chains 148 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain G residue 120 ASN Chi-restraints excluded: chain J residue 240 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 60.1499 > 50: distance: 62 - 85: 4.709 distance: 67 - 93: 27.928 distance: 71 - 103: 8.220 distance: 76 - 85: 3.296 distance: 77 - 111: 11.720 distance: 85 - 86: 8.097 distance: 86 - 87: 14.556 distance: 86 - 89: 8.761 distance: 87 - 88: 33.310 distance: 87 - 93: 29.427 distance: 89 - 90: 16.206 distance: 89 - 91: 19.981 distance: 90 - 92: 10.634 distance: 93 - 94: 16.678 distance: 94 - 95: 15.641 distance: 94 - 97: 8.012 distance: 95 - 96: 18.212 distance: 95 - 103: 12.872 distance: 97 - 98: 8.531 distance: 98 - 99: 18.227 distance: 98 - 100: 10.806 distance: 99 - 101: 15.894 distance: 100 - 102: 17.016 distance: 101 - 102: 10.806 distance: 103 - 104: 7.616 distance: 105 - 106: 12.686 distance: 105 - 111: 15.704 distance: 108 - 110: 4.838 distance: 111 - 112: 11.264 distance: 112 - 113: 10.836 distance: 112 - 115: 11.954 distance: 113 - 114: 3.491 distance: 113 - 122: 31.887 distance: 115 - 116: 7.277 distance: 116 - 117: 4.879 distance: 116 - 118: 3.845 distance: 117 - 119: 6.459 distance: 118 - 120: 6.618 distance: 119 - 121: 9.657 distance: 120 - 121: 6.339 distance: 122 - 123: 7.455 distance: 123 - 124: 7.929 distance: 123 - 126: 4.916 distance: 124 - 125: 10.183 distance: 124 - 131: 10.021 distance: 126 - 127: 11.262 distance: 127 - 128: 11.225 distance: 128 - 129: 9.529 distance: 129 - 130: 7.959 distance: 131 - 132: 9.544 distance: 132 - 133: 11.360 distance: 133 - 134: 9.036 distance: 133 - 142: 7.145 distance: 135 - 136: 5.807 distance: 136 - 137: 16.596 distance: 137 - 138: 15.598 distance: 138 - 139: 29.728 distance: 139 - 140: 9.410 distance: 139 - 141: 5.535 distance: 142 - 143: 5.800 distance: 143 - 144: 6.241 distance: 143 - 146: 11.015 distance: 144 - 145: 14.929 distance: 144 - 151: 15.279 distance: 146 - 147: 33.150 distance: 147 - 148: 21.778 distance: 148 - 149: 25.602 distance: 149 - 150: 60.150 distance: 151 - 152: 5.795 distance: 152 - 153: 3.915 distance: 153 - 154: 4.083 distance: 153 - 155: 6.230 distance: 155 - 156: 6.497 distance: 156 - 157: 9.209 distance: 157 - 158: 9.129 distance: 157 - 159: 6.881 distance: 160 - 161: 4.607 distance: 160 - 163: 3.789 distance: 161 - 162: 5.751 distance: 163 - 164: 13.267 distance: 163 - 165: 7.824 distance: 164 - 166: 16.532