Starting phenix.real_space_refine on Sat Dec 9 23:20:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/12_2023/7l6u_23208.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/12_2023/7l6u_23208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/12_2023/7l6u_23208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/12_2023/7l6u_23208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/12_2023/7l6u_23208.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l6u_23208/12_2023/7l6u_23208.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 8255 2.51 5 N 2115 2.21 5 O 2275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 30": "OE1" <-> "OE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 53": "OD1" <-> "OD2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 97": "OD1" <-> "OD2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 97": "OD1" <-> "OD2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 97": "OD1" <-> "OD2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E ARG 163": "NH1" <-> "NH2" Residue "E PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12675 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "B" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "D" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Chain: "E" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2535 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 14, 'TRANS': 296} Time building chain proxies: 6.77, per 1000 atoms: 0.53 Number of scatterers: 12675 At special positions: 0 Unit cell: (92.064, 93.16, 121.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 2275 8.00 N 2115 7.00 C 8255 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: 5.00 Conformation dependent library (CDL) restraints added in 2.3 seconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 38.3% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS A 54 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 202 through 207 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR A 237 " --> pdb=" O GLN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 removed outlier: 3.709A pdb=" N GLN A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Proline residue: A 305 - end of helix removed outlier: 3.541A pdb=" N THR A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS B 54 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN B 68 " --> pdb=" O GLU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 237 " --> pdb=" O GLN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 removed outlier: 3.709A pdb=" N GLN B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 305 - end of helix removed outlier: 3.541A pdb=" N THR B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS C 54 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 209 through 220 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 237 " --> pdb=" O GLN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 321 removed outlier: 4.260A pdb=" N GLN C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Proline residue: C 305 - end of helix removed outlier: 3.541A pdb=" N THR C 321 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS D 54 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.664A pdb=" N ASN D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 227 through 253 removed outlier: 3.832A pdb=" N PHE D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR D 237 " --> pdb=" O GLN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 321 removed outlier: 4.261A pdb=" N GLN D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) Proline residue: D 305 - end of helix removed outlier: 3.541A pdb=" N THR D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.928A pdb=" N LYS E 54 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.663A pdb=" N ASN E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 202 through 207 Processing helix chain 'E' and resid 209 through 220 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 227 through 253 removed outlier: 3.833A pdb=" N PHE E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR E 237 " --> pdb=" O GLN E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 285 removed outlier: 3.710A pdb=" N GLN E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 321 removed outlier: 4.260A pdb=" N GLN E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Proline residue: E 305 - end of helix removed outlier: 3.541A pdb=" N THR E 321 " --> pdb=" O ILE E 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 6.286A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL A 14 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER A 143 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A 16 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 145 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 18 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.780A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.780A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL B 14 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER B 143 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 16 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE B 145 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE B 18 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL C 14 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER C 143 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 16 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE C 145 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 18 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.285A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL D 14 " --> pdb=" O ARG D 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER D 143 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL D 16 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE D 145 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE D 18 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.286A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL E 14 " --> pdb=" O ARG E 141 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER E 143 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL E 16 " --> pdb=" O SER E 143 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE E 145 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE E 18 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.779A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 5.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3037 1.33 - 1.45: 2787 1.45 - 1.57: 7141 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 13015 Sorted by residual: bond pdb=" C VAL A 58 " pdb=" N GLU A 59 " ideal model delta sigma weight residual 1.332 1.221 0.112 1.40e-02 5.10e+03 6.36e+01 bond pdb=" C VAL C 58 " pdb=" N GLU C 59 " ideal model delta sigma weight residual 1.332 1.222 0.111 1.40e-02 5.10e+03 6.23e+01 bond pdb=" C VAL D 58 " pdb=" N GLU D 59 " ideal model delta sigma weight residual 1.332 1.222 0.110 1.40e-02 5.10e+03 6.19e+01 bond pdb=" C VAL E 58 " pdb=" N GLU E 59 " ideal model delta sigma weight residual 1.332 1.223 0.110 1.40e-02 5.10e+03 6.13e+01 bond pdb=" C VAL B 58 " pdb=" N GLU B 59 " ideal model delta sigma weight residual 1.332 1.223 0.109 1.40e-02 5.10e+03 6.11e+01 ... (remaining 13010 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.77: 375 106.77 - 113.59: 7169 113.59 - 120.40: 5097 120.40 - 127.22: 4929 127.22 - 134.04: 165 Bond angle restraints: 17735 Sorted by residual: angle pdb=" N VAL A 291 " pdb=" CA VAL A 291 " pdb=" C VAL A 291 " ideal model delta sigma weight residual 113.71 107.58 6.13 9.50e-01 1.11e+00 4.17e+01 angle pdb=" N VAL B 291 " pdb=" CA VAL B 291 " pdb=" C VAL B 291 " ideal model delta sigma weight residual 113.71 107.61 6.10 9.50e-01 1.11e+00 4.12e+01 angle pdb=" N VAL E 291 " pdb=" CA VAL E 291 " pdb=" C VAL E 291 " ideal model delta sigma weight residual 113.71 107.62 6.09 9.50e-01 1.11e+00 4.11e+01 angle pdb=" N VAL D 291 " pdb=" CA VAL D 291 " pdb=" C VAL D 291 " ideal model delta sigma weight residual 113.71 107.63 6.08 9.50e-01 1.11e+00 4.10e+01 angle pdb=" N VAL C 291 " pdb=" CA VAL C 291 " pdb=" C VAL C 291 " ideal model delta sigma weight residual 113.71 107.64 6.07 9.50e-01 1.11e+00 4.09e+01 ... (remaining 17730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 6653 15.94 - 31.89: 751 31.89 - 47.83: 175 47.83 - 63.78: 26 63.78 - 79.72: 10 Dihedral angle restraints: 7615 sinusoidal: 3060 harmonic: 4555 Sorted by residual: dihedral pdb=" CA GLN C 182 " pdb=" C GLN C 182 " pdb=" N PRO C 183 " pdb=" CA PRO C 183 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLN A 182 " pdb=" C GLN A 182 " pdb=" N PRO A 183 " pdb=" CA PRO A 183 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA GLN D 182 " pdb=" C GLN D 182 " pdb=" N PRO D 183 " pdb=" CA PRO D 183 " ideal model delta harmonic sigma weight residual 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 7612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1519 0.059 - 0.117: 396 0.117 - 0.176: 55 0.176 - 0.235: 0 0.235 - 0.293: 5 Chirality restraints: 1975 Sorted by residual: chirality pdb=" CA GLU B 59 " pdb=" N GLU B 59 " pdb=" C GLU B 59 " pdb=" CB GLU B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA GLU D 59 " pdb=" N GLU D 59 " pdb=" C GLU D 59 " pdb=" CB GLU D 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1972 not shown) Planarity restraints: 2260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 59 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C GLU A 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU A 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN A 60 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 59 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU B 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU B 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN B 60 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 59 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C GLU E 59 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU E 59 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN E 60 " -0.021 2.00e-02 2.50e+03 ... (remaining 2257 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 4737 2.87 - 3.38: 11474 3.38 - 3.89: 19850 3.89 - 4.39: 22253 4.39 - 4.90: 40341 Nonbonded interactions: 98655 Sorted by model distance: nonbonded pdb=" OH TYR D 33 " pdb=" O VAL D 127 " model vdw 2.365 2.440 nonbonded pdb=" OH TYR E 33 " pdb=" O VAL E 127 " model vdw 2.365 2.440 nonbonded pdb=" OH TYR A 33 " pdb=" O VAL A 127 " model vdw 2.365 2.440 nonbonded pdb=" OH TYR B 33 " pdb=" O VAL B 127 " model vdw 2.365 2.440 nonbonded pdb=" OH TYR C 33 " pdb=" O VAL C 127 " model vdw 2.366 2.440 ... (remaining 98650 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' } 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: 0.490 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: 2.430 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 35.510 Find NCS groups from input model: 0.820 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.009 0.112 13015 Z= 0.590 Angle : 0.786 8.281 17735 Z= 0.454 Chirality : 0.054 0.293 1975 Planarity : 0.005 0.070 2260 Dihedral : 14.086 79.721 4675 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 0.72 % Allowed : 0.79 % Favored : 98.49 % 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: -1.06 (0.22), residues: 1545 helix: 0.42 (0.22), residues: 515 sheet: -0.18 (0.26), residues: 480 loop : -2.25 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 160 HIS 0.003 0.001 HIS D 285 PHE 0.025 0.002 PHE B 247 TYR 0.021 0.002 TYR A 248 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 1.399 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 117 average time/residue: 0.3088 time to fit residues: 49.8236 Evaluate side-chains 89 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1489 time to fit residues: 3.2281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.4980 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 90 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN D 251 ASN E 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13015 Z= 0.177 Angle : 0.584 6.978 17735 Z= 0.303 Chirality : 0.046 0.153 1975 Planarity : 0.004 0.053 2260 Dihedral : 4.918 26.393 1710 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.43 % Allowed : 3.53 % Favored : 96.04 % 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: -0.43 (0.22), residues: 1545 helix: 0.99 (0.23), residues: 535 sheet: 0.18 (0.26), residues: 480 loop : -2.06 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 43 HIS 0.003 0.001 HIS E 285 PHE 0.035 0.002 PHE C 142 TYR 0.013 0.001 TYR A 248 ARG 0.002 0.000 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 1.446 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 141 average time/residue: 0.3100 time to fit residues: 62.4477 Evaluate side-chains 102 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.434 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1124 time to fit residues: 2.2331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN B 89 ASN B 251 ASN C 89 ASN C 103 ASN C 251 ASN D 89 ASN D 138 GLN D 251 ASN E 89 ASN E 233 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 13015 Z= 0.493 Angle : 0.705 7.450 17735 Z= 0.366 Chirality : 0.051 0.191 1975 Planarity : 0.005 0.049 2260 Dihedral : 5.310 26.777 1710 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.50 % Allowed : 9.57 % Favored : 89.93 % 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: -0.72 (0.22), residues: 1545 helix: 0.64 (0.22), residues: 535 sheet: 0.08 (0.26), residues: 480 loop : -2.15 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 224 HIS 0.004 0.001 HIS E 285 PHE 0.037 0.002 PHE A 142 TYR 0.021 0.002 TYR A 248 ARG 0.002 0.000 ARG E 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.458 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 107 average time/residue: 0.2844 time to fit residues: 43.7842 Evaluate side-chains 83 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.462 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1155 time to fit residues: 2.2802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 149 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13015 Z= 0.272 Angle : 0.611 6.794 17735 Z= 0.317 Chirality : 0.047 0.152 1975 Planarity : 0.004 0.048 2260 Dihedral : 4.925 25.899 1710 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.94 % Allowed : 10.94 % Favored : 88.13 % 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: -0.45 (0.22), residues: 1545 helix: 0.87 (0.23), residues: 535 sheet: 0.28 (0.26), residues: 480 loop : -2.07 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 43 HIS 0.003 0.001 HIS B 285 PHE 0.030 0.002 PHE A 142 TYR 0.017 0.001 TYR C 248 ARG 0.001 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.466 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 114 average time/residue: 0.2732 time to fit residues: 45.0744 Evaluate side-chains 102 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1109 time to fit residues: 4.3485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.0030 chunk 134 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 ASN E 185 GLN E 251 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13015 Z= 0.227 Angle : 0.574 6.572 17735 Z= 0.296 Chirality : 0.045 0.149 1975 Planarity : 0.004 0.045 2260 Dihedral : 4.691 25.023 1710 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.43 % Allowed : 12.45 % Favored : 87.12 % 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: -0.23 (0.23), residues: 1545 helix: 1.07 (0.23), residues: 535 sheet: 0.42 (0.27), residues: 480 loop : -2.00 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 43 HIS 0.005 0.001 HIS C 285 PHE 0.027 0.002 PHE A 142 TYR 0.015 0.001 TYR C 248 ARG 0.001 0.000 ARG D 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.334 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 111 average time/residue: 0.2856 time to fit residues: 45.2706 Evaluate side-chains 91 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 1.474 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1338 time to fit residues: 2.7767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 149 optimal weight: 0.0970 chunk 124 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 13015 Z= 0.297 Angle : 0.607 6.585 17735 Z= 0.314 Chirality : 0.047 0.150 1975 Planarity : 0.004 0.045 2260 Dihedral : 4.818 25.430 1710 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.72 % Allowed : 12.95 % Favored : 86.33 % 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: -0.23 (0.22), residues: 1545 helix: 1.04 (0.23), residues: 535 sheet: 0.45 (0.27), residues: 480 loop : -2.00 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 43 HIS 0.005 0.001 HIS E 285 PHE 0.027 0.002 PHE C 142 TYR 0.020 0.001 TYR C 248 ARG 0.003 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.473 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 105 average time/residue: 0.2816 time to fit residues: 43.1110 Evaluate side-chains 98 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 1.492 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1269 time to fit residues: 3.8997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13015 Z= 0.244 Angle : 0.580 6.883 17735 Z= 0.297 Chirality : 0.046 0.146 1975 Planarity : 0.004 0.043 2260 Dihedral : 4.676 25.003 1710 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.22 % Allowed : 13.60 % Favored : 86.19 % 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: -0.09 (0.22), residues: 1545 helix: 1.17 (0.23), residues: 535 sheet: 0.63 (0.27), residues: 475 loop : -2.01 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 224 HIS 0.005 0.001 HIS E 285 PHE 0.027 0.002 PHE C 142 TYR 0.018 0.001 TYR C 248 ARG 0.003 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.524 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 0.2962 time to fit residues: 43.4015 Evaluate side-chains 90 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1086 time to fit residues: 2.1822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13015 Z= 0.255 Angle : 0.588 6.538 17735 Z= 0.302 Chirality : 0.046 0.147 1975 Planarity : 0.004 0.043 2260 Dihedral : 4.699 24.964 1710 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.22 % Allowed : 14.46 % Favored : 85.32 % 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: -0.06 (0.22), residues: 1545 helix: 1.18 (0.23), residues: 535 sheet: 0.67 (0.27), residues: 475 loop : -2.02 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 224 HIS 0.005 0.001 HIS E 285 PHE 0.026 0.002 PHE C 142 TYR 0.018 0.001 TYR C 248 ARG 0.003 0.000 ARG A 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 1.541 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 98 average time/residue: 0.3010 time to fit residues: 41.8577 Evaluate side-chains 92 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1314 time to fit residues: 2.4174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 0.7980 chunk 130 optimal weight: 0.4980 chunk 139 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 131 optimal weight: 0.3980 chunk 138 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13015 Z= 0.184 Angle : 0.551 6.513 17735 Z= 0.282 Chirality : 0.045 0.142 1975 Planarity : 0.004 0.042 2260 Dihedral : 4.479 24.258 1710 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.29 % Allowed : 14.17 % Favored : 85.54 % 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: 0.14 (0.23), residues: 1545 helix: 1.43 (0.23), residues: 530 sheet: 0.80 (0.27), residues: 475 loop : -1.98 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 43 HIS 0.005 0.001 HIS B 285 PHE 0.024 0.001 PHE C 142 TYR 0.023 0.001 TYR C 248 ARG 0.001 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.586 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 108 average time/residue: 0.2708 time to fit residues: 42.8866 Evaluate side-chains 96 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 1.504 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1451 time to fit residues: 2.5344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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: 70.8045 > 50: distance: 74 - 78: 34.097 distance: 78 - 79: 46.684 distance: 79 - 80: 21.217 distance: 79 - 82: 23.234 distance: 82 - 83: 54.494 distance: 83 - 84: 23.751 distance: 83 - 85: 15.129 distance: 87 - 90: 7.335 distance: 88 - 89: 39.010 distance: 88 - 97: 31.444 distance: 90 - 91: 8.462 distance: 92 - 93: 25.043 distance: 93 - 94: 31.280 distance: 94 - 96: 36.691 distance: 97 - 98: 40.991 distance: 98 - 101: 39.328 distance: 99 - 100: 39.720 distance: 99 - 108: 26.903 distance: 108 - 109: 17.335 distance: 109 - 110: 41.499 distance: 109 - 112: 21.895 distance: 110 - 111: 13.857 distance: 110 - 114: 44.355 distance: 112 - 113: 28.658 distance: 122 - 123: 7.469 distance: 123 - 124: 31.426 distance: 123 - 126: 10.096 distance: 124 - 125: 39.685 distance: 124 - 130: 5.780 distance: 126 - 127: 4.390 distance: 126 - 128: 58.061 distance: 127 - 129: 4.077 distance: 130 - 131: 4.798 distance: 131 - 132: 40.700 distance: 135 - 136: 17.161 distance: 136 - 137: 23.386 distance: 136 - 138: 21.531 distance: 140 - 141: 19.736 distance: 141 - 142: 37.185 distance: 141 - 146: 45.635 distance: 143 - 144: 39.997 distance: 150 - 151: 26.541 distance: 151 - 152: 14.299 distance: 151 - 153: 12.331 distance: 152 - 154: 4.974 distance: 154 - 156: 13.137 distance: 155 - 156: 16.333 distance: 156 - 157: 23.898 distance: 158 - 159: 13.342 distance: 159 - 160: 3.073 distance: 159 - 162: 6.421 distance: 160 - 161: 9.468 distance: 160 - 165: 30.176 distance: 162 - 163: 6.636 distance: 162 - 164: 16.488