Starting phenix.real_space_refine on Tue Aug 6 01:37:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/08_2024/6m67_30115.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/08_2024/6m67_30115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/08_2024/6m67_30115.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/08_2024/6m67_30115.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/08_2024/6m67_30115.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m67_30115/08_2024/6m67_30115.cif" } resolution = 3.6 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= 0.024 sd= 0.201 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 70 5.16 5 C 9975 2.51 5 N 2303 2.21 5 O 2590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14938 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "B" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "C" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "D" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "E" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "F" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Chain: "G" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2134 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain breaks: 1 Time building chain proxies: 9.41, per 1000 atoms: 0.63 Number of scatterers: 14938 At special positions: 0 Unit cell: (112.042, 112.042, 117.327, 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 70 16.00 O 2590 8.00 N 2303 7.00 C 9975 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.04 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.04 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.04 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.04 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.04 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.04 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.04 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.89 Conformation dependent library (CDL) restraints added in 2.6 seconds 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3612 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 7 sheets defined 72.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 removed outlier: 4.020A pdb=" N ILE A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.739A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS A 106 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 107 " --> pdb=" O TRP A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 108 through 131 removed outlier: 3.766A pdb=" N LEU A 115 " --> pdb=" O TYR A 111 " (cutoff:3.500A) Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 156 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 210 through 238 removed outlier: 4.788A pdb=" N CYS A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG A 217 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 removed outlier: 4.100A pdb=" N ASN A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 286 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 294 through 300 removed outlier: 5.063A pdb=" N VAL A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) Proline residue: A 298 - end of helix No H-bonds generated for 'chain 'A' and resid 294 through 300' Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 Processing helix chain 'A' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 59 removed outlier: 4.019A pdb=" N ILE B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.738A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 Processing helix chain 'B' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS B 106 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 107 " --> pdb=" O TRP B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 107' Processing helix chain 'B' and resid 108 through 131 removed outlier: 3.766A pdb=" N LEU B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS B 203 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 210 through 238 removed outlier: 4.788A pdb=" N CYS B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG B 217 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 removed outlier: 4.099A pdb=" N ASN B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 286 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 294 through 300 removed outlier: 5.063A pdb=" N VAL B 297 " --> pdb=" O THR B 294 " (cutoff:3.500A) Proline residue: B 298 - end of helix No H-bonds generated for 'chain 'B' and resid 294 through 300' Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 320 Processing helix chain 'B' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 59 removed outlier: 4.019A pdb=" N ILE C 41 " --> pdb=" O MET C 37 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.738A pdb=" N SER C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 87 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS C 106 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 107 " --> pdb=" O TRP C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 107' Processing helix chain 'C' and resid 108 through 131 removed outlier: 3.765A pdb=" N LEU C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 156 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 210 through 238 removed outlier: 4.788A pdb=" N CYS C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG C 217 " --> pdb=" O TYR C 213 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 221 " --> pdb=" O ARG C 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 238 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 removed outlier: 4.100A pdb=" N ASN C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 275 through 277 No H-bonds generated for 'chain 'C' and resid 275 through 277' Processing helix chain 'C' and resid 278 through 286 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 294 through 300 removed outlier: 5.063A pdb=" N VAL C 297 " --> pdb=" O THR C 294 " (cutoff:3.500A) Proline residue: C 298 - end of helix No H-bonds generated for 'chain 'C' and resid 294 through 300' Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 320 Processing helix chain 'C' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 59 removed outlier: 4.019A pdb=" N ILE D 41 " --> pdb=" O MET D 37 " (cutoff:3.500A) Proline residue: D 46 - end of helix removed outlier: 3.739A pdb=" N SER D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 87 Processing helix chain 'D' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS D 106 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 107 " --> pdb=" O TRP D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 107' Processing helix chain 'D' and resid 108 through 131 removed outlier: 3.766A pdb=" N LEU D 115 " --> pdb=" O TYR D 111 " (cutoff:3.500A) Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 156 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.681A pdb=" N LYS D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 210 through 238 removed outlier: 4.787A pdb=" N CYS D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG D 217 " --> pdb=" O TYR D 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 218 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU D 221 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 238 " --> pdb=" O TYR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 4.100A pdb=" N ASN D 255 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 274 Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 286 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 294 through 300 removed outlier: 5.064A pdb=" N VAL D 297 " --> pdb=" O THR D 294 " (cutoff:3.500A) Proline residue: D 298 - end of helix No H-bonds generated for 'chain 'D' and resid 294 through 300' Processing helix chain 'D' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 320 Processing helix chain 'D' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 59 removed outlier: 4.019A pdb=" N ILE E 41 " --> pdb=" O MET E 37 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.739A pdb=" N SER E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 87 Processing helix chain 'E' and resid 103 through 107 removed outlier: 4.529A pdb=" N HIS E 106 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 107 " --> pdb=" O TRP E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 107' Processing helix chain 'E' and resid 108 through 131 removed outlier: 3.766A pdb=" N LEU E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 156 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 210 through 238 removed outlier: 4.788A pdb=" N CYS E 216 " --> pdb=" O LYS E 212 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG E 217 " --> pdb=" O TYR E 213 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 221 " --> pdb=" O ARG E 217 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE E 235 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER E 238 " --> pdb=" O TYR E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 256 removed outlier: 4.099A pdb=" N ASN E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 274 Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 286 Processing helix chain 'E' and resid 287 through 293 Processing helix chain 'E' and resid 294 through 300 removed outlier: 5.064A pdb=" N VAL E 297 " --> pdb=" O THR E 294 " (cutoff:3.500A) Proline residue: E 298 - end of helix No H-bonds generated for 'chain 'E' and resid 294 through 300' Processing helix chain 'E' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 59 removed outlier: 4.020A pdb=" N ILE F 41 " --> pdb=" O MET F 37 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.738A pdb=" N SER F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 87 Processing helix chain 'F' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS F 106 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS F 107 " --> pdb=" O TRP F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 107' Processing helix chain 'F' and resid 108 through 131 removed outlier: 3.765A pdb=" N LEU F 115 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 156 Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS F 203 " --> pdb=" O TYR F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 210 through 238 removed outlier: 4.788A pdb=" N CYS F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG F 217 " --> pdb=" O TYR F 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU F 218 " --> pdb=" O ILE F 214 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU F 221 " --> pdb=" O ARG F 217 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE F 235 " --> pdb=" O LEU F 231 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 238 " --> pdb=" O TYR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 256 removed outlier: 4.100A pdb=" N ASN F 255 " --> pdb=" O GLY F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 274 Processing helix chain 'F' and resid 275 through 277 No H-bonds generated for 'chain 'F' and resid 275 through 277' Processing helix chain 'F' and resid 278 through 286 Processing helix chain 'F' and resid 287 through 293 Processing helix chain 'F' and resid 294 through 300 removed outlier: 5.064A pdb=" N VAL F 297 " --> pdb=" O THR F 294 " (cutoff:3.500A) Proline residue: F 298 - end of helix No H-bonds generated for 'chain 'F' and resid 294 through 300' Processing helix chain 'F' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 59 removed outlier: 4.019A pdb=" N ILE G 41 " --> pdb=" O MET G 37 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.738A pdb=" N SER G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 103 through 107 removed outlier: 4.528A pdb=" N HIS G 106 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS G 107 " --> pdb=" O TRP G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 103 through 107' Processing helix chain 'G' and resid 108 through 131 removed outlier: 3.765A pdb=" N LEU G 115 " --> pdb=" O TYR G 111 " (cutoff:3.500A) Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 156 Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 198 through 203 removed outlier: 3.682A pdb=" N LYS G 203 " --> pdb=" O TYR G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 209 No H-bonds generated for 'chain 'G' and resid 207 through 209' Processing helix chain 'G' and resid 210 through 238 removed outlier: 4.787A pdb=" N CYS G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG G 217 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU G 218 " --> pdb=" O ILE G 214 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU G 221 " --> pdb=" O ARG G 217 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE G 235 " --> pdb=" O LEU G 231 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER G 236 " --> pdb=" O GLY G 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER G 238 " --> pdb=" O TYR G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 256 removed outlier: 4.100A pdb=" N ASN G 255 " --> pdb=" O GLY G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 274 Processing helix chain 'G' and resid 275 through 277 No H-bonds generated for 'chain 'G' and resid 275 through 277' Processing helix chain 'G' and resid 278 through 286 Processing helix chain 'G' and resid 287 through 293 Processing helix chain 'G' and resid 294 through 300 removed outlier: 5.063A pdb=" N VAL G 297 " --> pdb=" O THR G 294 " (cutoff:3.500A) Proline residue: G 298 - end of helix No H-bonds generated for 'chain 'G' and resid 294 through 300' Processing helix chain 'G' and resid 311 through 316 removed outlier: 3.925A pdb=" N ASP G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 320 Processing helix chain 'G' and resid 329 through 336 removed outlier: 4.076A pdb=" N GLU G 336 " --> pdb=" O ASN G 332 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER A 65 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.522A pdb=" N SER B 65 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER C 65 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER D 65 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER E 65 " --> pdb=" O LYS E 266 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER F 65 " --> pdb=" O LYS F 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.523A pdb=" N SER G 65 " --> pdb=" O LYS G 266 " (cutoff:3.500A) 736 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 6.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4336 1.34 - 1.46: 3078 1.46 - 1.57: 7811 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 15309 Sorted by residual: bond pdb=" C PRO A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.74e+00 bond pdb=" C PRO C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.335 1.358 -0.022 1.36e-02 5.41e+03 2.74e+00 bond pdb=" C PRO B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 1.335 1.358 -0.022 1.36e-02 5.41e+03 2.65e+00 bond pdb=" C PRO G 123 " pdb=" N PRO G 124 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.64e+00 bond pdb=" C PRO F 123 " pdb=" N PRO F 124 " ideal model delta sigma weight residual 1.335 1.357 -0.022 1.36e-02 5.41e+03 2.61e+00 ... (remaining 15304 not shown) Histogram of bond angle deviations from ideal: 100.76 - 107.42: 512 107.42 - 114.09: 8507 114.09 - 120.75: 7066 120.75 - 127.41: 4564 127.41 - 134.08: 176 Bond angle restraints: 20825 Sorted by residual: angle pdb=" N THR D 314 " pdb=" CA THR D 314 " pdb=" C THR D 314 " ideal model delta sigma weight residual 114.56 108.03 6.53 1.27e+00 6.20e-01 2.65e+01 angle pdb=" N THR B 314 " pdb=" CA THR B 314 " pdb=" C THR B 314 " ideal model delta sigma weight residual 114.56 108.04 6.52 1.27e+00 6.20e-01 2.64e+01 angle pdb=" N THR C 314 " pdb=" CA THR C 314 " pdb=" C THR C 314 " ideal model delta sigma weight residual 114.56 108.04 6.52 1.27e+00 6.20e-01 2.63e+01 angle pdb=" N THR F 314 " pdb=" CA THR F 314 " pdb=" C THR F 314 " ideal model delta sigma weight residual 114.56 108.05 6.51 1.27e+00 6.20e-01 2.63e+01 angle pdb=" N THR A 314 " pdb=" CA THR A 314 " pdb=" C THR A 314 " ideal model delta sigma weight residual 114.56 108.05 6.51 1.27e+00 6.20e-01 2.63e+01 ... (remaining 20820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.17: 6873 10.17 - 20.35: 1296 20.35 - 30.52: 560 30.52 - 40.70: 315 40.70 - 50.87: 70 Dihedral angle restraints: 9114 sinusoidal: 3563 harmonic: 5551 Sorted by residual: dihedral pdb=" CA LYS D 107 " pdb=" C LYS D 107 " pdb=" N PHE D 108 " pdb=" CA PHE D 108 " ideal model delta harmonic sigma weight residual 180.00 -151.71 -28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS F 107 " pdb=" C LYS F 107 " pdb=" N PHE F 108 " pdb=" CA PHE F 108 " ideal model delta harmonic sigma weight residual 180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS B 107 " pdb=" C LYS B 107 " pdb=" N PHE B 108 " pdb=" CA PHE B 108 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 9111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1619 0.051 - 0.103: 649 0.103 - 0.154: 159 0.154 - 0.206: 37 0.206 - 0.257: 7 Chirality restraints: 2471 Sorted by residual: chirality pdb=" CA PHE B 109 " pdb=" N PHE B 109 " pdb=" C PHE B 109 " pdb=" CB PHE B 109 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA PHE F 109 " pdb=" N PHE F 109 " pdb=" C PHE F 109 " pdb=" CB PHE F 109 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA PHE E 109 " pdb=" N PHE E 109 " pdb=" C PHE E 109 " pdb=" CB PHE E 109 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2468 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 312 " 0.050 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO B 313 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 312 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.87e+00 pdb=" N PRO C 313 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO C 313 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 313 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 312 " 0.050 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO G 313 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO G 313 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 313 " 0.041 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3522 2.78 - 3.31: 13875 3.31 - 3.84: 25008 3.84 - 4.37: 27524 4.37 - 4.90: 44939 Nonbonded interactions: 114868 Sorted by model distance: nonbonded pdb=" O PHE A 72 " pdb=" OG SER B 71 " model vdw 2.247 3.040 nonbonded pdb=" O PHE F 72 " pdb=" OG SER G 71 " model vdw 2.248 3.040 nonbonded pdb=" OG SER A 71 " pdb=" O PHE G 72 " model vdw 2.285 3.040 nonbonded pdb=" O SER B 241 " pdb=" OG SER B 241 " model vdw 2.300 3.040 nonbonded pdb=" O SER C 241 " pdb=" OG SER C 241 " model vdw 2.300 3.040 ... (remaining 114863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 41.660 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 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 : 0.006 0.059 15309 Z= 0.352 Angle : 1.137 9.158 20825 Z= 0.599 Chirality : 0.059 0.257 2471 Planarity : 0.010 0.075 2520 Dihedral : 14.949 50.872 5460 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % 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: -4.86 (0.16), residues: 1827 helix: -3.29 (0.10), residues: 1141 sheet: None (None), residues: 0 loop : -2.81 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.008 0.003 HIS A 106 PHE 0.028 0.002 PHE A 109 TYR 0.015 0.002 TYR E 234 ARG 0.008 0.001 ARG E 254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7104 (mt0) cc_final: 0.6873 (mt0) REVERT: A 75 ARG cc_start: 0.7158 (tpp-160) cc_final: 0.6899 (ttt90) REVERT: A 214 ILE cc_start: 0.6695 (tp) cc_final: 0.6422 (mp) REVERT: B 242 ASP cc_start: 0.7776 (t70) cc_final: 0.7389 (m-30) REVERT: C 83 TYR cc_start: 0.7734 (t80) cc_final: 0.7192 (t80) REVERT: C 214 ILE cc_start: 0.6891 (tp) cc_final: 0.6659 (pt) REVERT: C 242 ASP cc_start: 0.7566 (t70) cc_final: 0.7241 (m-30) REVERT: D 83 TYR cc_start: 0.7572 (t80) cc_final: 0.6937 (t80) REVERT: D 214 ILE cc_start: 0.7314 (tp) cc_final: 0.7037 (mt) REVERT: D 242 ASP cc_start: 0.7656 (t70) cc_final: 0.7298 (m-30) REVERT: D 262 GLN cc_start: 0.7828 (pm20) cc_final: 0.7572 (pp30) REVERT: D 279 ILE cc_start: 0.8170 (mt) cc_final: 0.7906 (mt) REVERT: E 83 TYR cc_start: 0.7590 (t80) cc_final: 0.7356 (t80) REVERT: E 214 ILE cc_start: 0.6888 (tp) cc_final: 0.6578 (pt) REVERT: E 242 ASP cc_start: 0.7434 (t70) cc_final: 0.7195 (m-30) REVERT: F 279 ILE cc_start: 0.8288 (mt) cc_final: 0.8033 (mt) REVERT: G 124 PRO cc_start: 0.9038 (Cg_exo) cc_final: 0.8753 (Cg_endo) REVERT: G 199 TYR cc_start: 0.7883 (m-80) cc_final: 0.7659 (m-10) REVERT: G 214 ILE cc_start: 0.7012 (tp) cc_final: 0.6704 (mt) REVERT: G 299 PHE cc_start: 0.7160 (t80) cc_final: 0.6938 (t80) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.2555 time to fit residues: 146.2348 Evaluate side-chains 243 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 55 optimal weight: 0.0060 chunk 86 optimal weight: 0.1980 chunk 106 optimal weight: 8.9990 chunk 165 optimal weight: 0.0060 overall best weight: 0.4412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 GLN A 280 ASN B 56 GLN B 90 GLN B 280 ASN C 56 GLN C 76 GLN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 280 ASN F 56 GLN F 76 GLN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN G 280 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15309 Z= 0.190 Angle : 0.779 9.394 20825 Z= 0.395 Chirality : 0.045 0.194 2471 Planarity : 0.007 0.060 2520 Dihedral : 6.436 22.724 1981 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 1.24 % Allowed : 17.61 % Favored : 81.15 % 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: -3.63 (0.17), residues: 1827 helix: -1.66 (0.14), residues: 1113 sheet: -3.05 (0.43), residues: 91 loop : -3.52 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 127 HIS 0.002 0.001 HIS B 106 PHE 0.027 0.001 PHE D 299 TYR 0.025 0.002 TYR E 121 ARG 0.003 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 289 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8992 (mt) cc_final: 0.8316 (tt) REVERT: A 150 TYR cc_start: 0.6755 (m-10) cc_final: 0.5123 (m-80) REVERT: C 57 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8184 (mm-30) REVERT: C 119 LEU cc_start: 0.8747 (mp) cc_final: 0.8037 (tt) REVERT: D 119 LEU cc_start: 0.8908 (mt) cc_final: 0.8107 (tt) REVERT: D 127 TRP cc_start: 0.7682 (t60) cc_final: 0.7336 (t60) REVERT: D 262 GLN cc_start: 0.7726 (pm20) cc_final: 0.7435 (pp30) REVERT: D 279 ILE cc_start: 0.8054 (mt) cc_final: 0.7761 (mt) REVERT: D 299 PHE cc_start: 0.6574 (t80) cc_final: 0.6324 (t80) REVERT: E 85 TRP cc_start: 0.8265 (t60) cc_final: 0.8002 (t-100) REVERT: E 119 LEU cc_start: 0.8743 (mp) cc_final: 0.8068 (tt) REVERT: E 214 ILE cc_start: 0.6795 (tp) cc_final: 0.6550 (pt) REVERT: F 199 TYR cc_start: 0.7135 (m-10) cc_final: 0.6782 (m-10) REVERT: F 279 ILE cc_start: 0.8155 (mt) cc_final: 0.7869 (mt) REVERT: F 299 PHE cc_start: 0.7031 (t80) cc_final: 0.6824 (t80) REVERT: F 307 LYS cc_start: 0.7764 (mptt) cc_final: 0.7497 (mptt) REVERT: G 119 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8470 (tt) REVERT: G 124 PRO cc_start: 0.9037 (Cg_exo) cc_final: 0.8697 (Cg_endo) REVERT: G 128 ARG cc_start: 0.8425 (ttm110) cc_final: 0.7852 (mtp-110) REVERT: G 214 ILE cc_start: 0.7037 (tp) cc_final: 0.6818 (mt) REVERT: G 307 LYS cc_start: 0.7751 (mptt) cc_final: 0.7520 (mptt) outliers start: 21 outliers final: 3 residues processed: 307 average time/residue: 0.2535 time to fit residues: 117.3777 Evaluate side-chains 235 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain F residue 76 GLN Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain G residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 178 optimal weight: 0.3980 chunk 147 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN C 90 GLN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 90 GLN ** G 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15309 Z= 0.191 Angle : 0.746 9.986 20825 Z= 0.373 Chirality : 0.044 0.191 2471 Planarity : 0.006 0.049 2520 Dihedral : 5.840 25.730 1981 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 2.90 % Allowed : 20.04 % Favored : 77.06 % 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: -2.47 (0.19), residues: 1827 helix: -0.69 (0.15), residues: 1141 sheet: -2.38 (0.45), residues: 91 loop : -3.30 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 85 HIS 0.004 0.001 HIS F 106 PHE 0.021 0.001 PHE B 320 TYR 0.027 0.002 TYR E 121 ARG 0.003 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.4042 (OUTLIER) cc_final: 0.1278 (mt) REVERT: A 119 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8275 (tt) REVERT: A 147 ASP cc_start: 0.6526 (p0) cc_final: 0.6178 (p0) REVERT: A 150 TYR cc_start: 0.6834 (m-10) cc_final: 0.5278 (m-80) REVERT: B 57 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 103 LEU cc_start: 0.4257 (OUTLIER) cc_final: 0.1682 (mt) REVERT: C 57 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8097 (mm-30) REVERT: C 230 TYR cc_start: 0.6779 (t80) cc_final: 0.6464 (t80) REVERT: C 262 GLN cc_start: 0.6400 (pp30) cc_final: 0.6194 (pp30) REVERT: C 310 GLU cc_start: 0.6199 (mt-10) cc_final: 0.5677 (pm20) REVERT: D 119 LEU cc_start: 0.8949 (mt) cc_final: 0.8194 (tt) REVERT: D 127 TRP cc_start: 0.7662 (t60) cc_final: 0.7453 (t60) REVERT: D 262 GLN cc_start: 0.7689 (pm20) cc_final: 0.7348 (pp30) REVERT: D 279 ILE cc_start: 0.8121 (mt) cc_final: 0.7806 (mt) REVERT: D 299 PHE cc_start: 0.6664 (t80) cc_final: 0.6365 (t80) REVERT: E 83 TYR cc_start: 0.7564 (t80) cc_final: 0.7281 (t80) REVERT: E 119 LEU cc_start: 0.8645 (mp) cc_final: 0.8007 (tt) REVERT: F 57 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8170 (mm-30) REVERT: F 103 LEU cc_start: 0.4769 (OUTLIER) cc_final: 0.2128 (mt) REVERT: F 279 ILE cc_start: 0.8124 (mt) cc_final: 0.7873 (mt) REVERT: G 128 ARG cc_start: 0.8405 (ttm110) cc_final: 0.7880 (mtp-110) outliers start: 49 outliers final: 29 residues processed: 281 average time/residue: 0.2453 time to fit residues: 103.9010 Evaluate side-chains 247 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 2.9990 chunk 124 optimal weight: 0.0000 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 0.0970 chunk 79 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 GLN A 280 ASN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 GLN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15309 Z= 0.171 Angle : 0.723 10.430 20825 Z= 0.359 Chirality : 0.043 0.177 2471 Planarity : 0.006 0.045 2520 Dihedral : 5.504 20.752 1981 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 3.08 % Allowed : 23.12 % Favored : 73.80 % 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: -2.07 (0.20), residues: 1827 helix: -0.32 (0.16), residues: 1134 sheet: -2.22 (0.46), residues: 91 loop : -3.25 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 85 HIS 0.003 0.001 HIS F 106 PHE 0.026 0.001 PHE G 126 TYR 0.024 0.002 TYR C 121 ARG 0.004 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 243 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8269 (tt) REVERT: A 128 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7601 (ttm170) REVERT: A 150 TYR cc_start: 0.6865 (m-10) cc_final: 0.5320 (m-80) REVERT: B 57 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8070 (mm-30) REVERT: B 119 LEU cc_start: 0.8908 (mt) cc_final: 0.8382 (tt) REVERT: B 237 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6945 (tp) REVERT: C 57 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8091 (mm-30) REVERT: C 262 GLN cc_start: 0.6456 (pp30) cc_final: 0.6248 (pp30) REVERT: D 262 GLN cc_start: 0.7722 (pm20) cc_final: 0.7340 (pp30) REVERT: D 299 PHE cc_start: 0.6677 (t80) cc_final: 0.6284 (t80) REVERT: D 310 GLU cc_start: 0.6206 (mt-10) cc_final: 0.5536 (pm20) REVERT: E 63 GLN cc_start: 0.6246 (tp40) cc_final: 0.5620 (mp10) REVERT: E 83 TYR cc_start: 0.7584 (t80) cc_final: 0.7292 (t80) REVERT: E 109 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.6726 (t80) REVERT: E 119 LEU cc_start: 0.8621 (mp) cc_final: 0.8011 (tt) REVERT: E 230 TYR cc_start: 0.6716 (t80) cc_final: 0.6364 (t80) REVERT: E 237 LEU cc_start: 0.7581 (tt) cc_final: 0.7313 (tp) REVERT: F 199 TYR cc_start: 0.6998 (m-80) cc_final: 0.6715 (m-80) REVERT: F 274 GLN cc_start: 0.7810 (tt0) cc_final: 0.7571 (tt0) REVERT: F 279 ILE cc_start: 0.8100 (mt) cc_final: 0.7866 (mt) REVERT: G 103 LEU cc_start: 0.4099 (OUTLIER) cc_final: 0.1673 (mt) REVERT: G 128 ARG cc_start: 0.8383 (ttm110) cc_final: 0.7852 (mtp-110) REVERT: G 226 LEU cc_start: 0.8513 (mm) cc_final: 0.8095 (tt) REVERT: G 299 PHE cc_start: 0.6985 (t80) cc_final: 0.6644 (t80) outliers start: 52 outliers final: 27 residues processed: 274 average time/residue: 0.2587 time to fit residues: 107.5399 Evaluate side-chains 245 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 214 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 274 GLN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15309 Z= 0.183 Angle : 0.728 10.671 20825 Z= 0.358 Chirality : 0.044 0.245 2471 Planarity : 0.006 0.044 2520 Dihedral : 5.381 23.715 1981 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.85 % Allowed : 24.60 % Favored : 71.55 % 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: -1.77 (0.20), residues: 1827 helix: -0.12 (0.16), residues: 1141 sheet: -2.02 (0.49), residues: 91 loop : -3.10 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 127 HIS 0.004 0.001 HIS F 106 PHE 0.024 0.001 PHE A 320 TYR 0.026 0.001 TYR C 121 ARG 0.002 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 236 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7891 (mm-30) REVERT: A 103 LEU cc_start: 0.4286 (OUTLIER) cc_final: 0.1634 (mt) REVERT: A 128 ARG cc_start: 0.7913 (ttt-90) cc_final: 0.7479 (ttm170) REVERT: A 234 TYR cc_start: 0.6809 (t80) cc_final: 0.6347 (t80) REVERT: B 57 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8097 (mm-30) REVERT: B 103 LEU cc_start: 0.4250 (OUTLIER) cc_final: 0.1752 (mt) REVERT: B 119 LEU cc_start: 0.8816 (mt) cc_final: 0.8331 (tt) REVERT: C 57 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8120 (mm-30) REVERT: C 128 ARG cc_start: 0.8352 (ttm170) cc_final: 0.7968 (ttm170) REVERT: C 262 GLN cc_start: 0.6498 (pp30) cc_final: 0.6272 (pp30) REVERT: C 274 GLN cc_start: 0.7776 (tt0) cc_final: 0.7470 (tt0) REVERT: C 310 GLU cc_start: 0.6214 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: D 262 GLN cc_start: 0.7603 (pm20) cc_final: 0.7255 (pp30) REVERT: D 299 PHE cc_start: 0.6736 (t80) cc_final: 0.6402 (t80) REVERT: E 83 TYR cc_start: 0.7618 (t80) cc_final: 0.7230 (t80) REVERT: E 103 LEU cc_start: 0.5198 (OUTLIER) cc_final: 0.2529 (mt) REVERT: E 109 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.6956 (t80) REVERT: E 237 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6840 (tp) REVERT: F 85 TRP cc_start: 0.8025 (t60) cc_final: 0.7437 (t60) REVERT: F 103 LEU cc_start: 0.4579 (OUTLIER) cc_final: 0.2024 (mt) REVERT: F 199 TYR cc_start: 0.7005 (m-80) cc_final: 0.6666 (m-80) REVERT: F 274 GLN cc_start: 0.7824 (tt0) cc_final: 0.7608 (tt0) REVERT: F 279 ILE cc_start: 0.8134 (mt) cc_final: 0.7895 (mt) REVERT: G 103 LEU cc_start: 0.4123 (OUTLIER) cc_final: 0.1672 (mt) REVERT: G 128 ARG cc_start: 0.8371 (ttm110) cc_final: 0.7839 (mtp-110) REVERT: G 226 LEU cc_start: 0.8602 (mm) cc_final: 0.8140 (tt) REVERT: G 299 PHE cc_start: 0.6992 (t80) cc_final: 0.6620 (t80) outliers start: 65 outliers final: 37 residues processed: 279 average time/residue: 0.2628 time to fit residues: 110.8701 Evaluate side-chains 250 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 205 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 235 PHE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 109 PHE Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 0.6980 chunk 146 optimal weight: 0.0010 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 GLN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 15309 Z= 0.226 Angle : 0.754 10.695 20825 Z= 0.373 Chirality : 0.045 0.254 2471 Planarity : 0.005 0.042 2520 Dihedral : 5.453 22.964 1981 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 4.56 % Allowed : 25.01 % Favored : 70.42 % 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: -1.74 (0.20), residues: 1827 helix: -0.08 (0.16), residues: 1162 sheet: -1.82 (0.50), residues: 91 loop : -3.26 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 127 HIS 0.006 0.001 HIS F 106 PHE 0.028 0.001 PHE F 299 TYR 0.027 0.002 TYR C 121 ARG 0.004 0.000 ARG A 254 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3654 Ramachandran restraints generated. 1827 Oldfield, 0 Emsley, 1827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 212 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7937 (mm-30) REVERT: A 103 LEU cc_start: 0.4241 (OUTLIER) cc_final: 0.1631 (mt) REVERT: A 128 ARG cc_start: 0.7906 (ttt-90) cc_final: 0.7464 (ttm170) REVERT: B 57 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8110 (mm-30) REVERT: B 103 LEU cc_start: 0.4596 (OUTLIER) cc_final: 0.1988 (mt) REVERT: C 57 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8138 (mm-30) REVERT: C 274 GLN cc_start: 0.8013 (tt0) cc_final: 0.7699 (tt0) REVERT: C 310 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5706 (pm20) REVERT: D 262 GLN cc_start: 0.7495 (pm20) cc_final: 0.7242 (pp30) REVERT: D 299 PHE cc_start: 0.6747 (t80) cc_final: 0.6442 (t80) REVERT: E 63 GLN cc_start: 0.6099 (tp40) cc_final: 0.5591 (mp10) REVERT: E 83 TYR cc_start: 0.7607 (t80) cc_final: 0.7301 (t80) REVERT: E 103 LEU cc_start: 0.5201 (OUTLIER) cc_final: 0.2586 (mt) REVERT: E 109 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7084 (t80) REVERT: E 237 LEU cc_start: 0.7200 (tt) cc_final: 0.6949 (tp) REVERT: F 103 LEU cc_start: 0.4704 (OUTLIER) cc_final: 0.2112 (mt) REVERT: F 199 TYR cc_start: 0.7162 (m-80) cc_final: 0.6833 (m-80) REVERT: F 226 LEU cc_start: 0.8392 (mm) cc_final: 0.8074 (tt) REVERT: F 274 GLN cc_start: 0.7922 (tt0) cc_final: 0.7668 (tt0) REVERT: G 103 LEU cc_start: 0.4419 (OUTLIER) cc_final: 0.1890 (mt) REVERT: G 107 LYS cc_start: 0.8370 (mttp) cc_final: 0.8024 (mtpp) REVERT: G 128 ARG cc_start: 0.8352 (ttm110) cc_final: 0.7826 (mtp-110) REVERT: G 226 LEU cc_start: 0.8708 (mm) cc_final: 0.8258 (tt) outliers start: 77 outliers final: 46 residues processed: 270 average time/residue: 0.2493 time to fit residues: 100.8043 Evaluate side-chains 251 residues out of total 1687 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 198 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 PHE Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 319 HIS Chi-restraints excluded: chain D residue 76 GLN Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 242 ASP Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 310 GLU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 109 PHE Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 235 PHE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain G residue 56 GLN Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 235 PHE Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 319 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 52.625 > 50: distance: 54 - 58: 20.460 distance: 58 - 59: 11.869 distance: 59 - 60: 36.083 distance: 59 - 62: 23.465 distance: 60 - 61: 4.302 distance: 60 - 66: 39.297 distance: 61 - 88: 16.201 distance: 62 - 63: 8.837 distance: 62 - 64: 13.272 distance: 63 - 65: 15.271 distance: 66 - 67: 23.625 distance: 67 - 68: 29.808 distance: 67 - 70: 24.635 distance: 68 - 69: 17.304 distance: 68 - 74: 12.986 distance: 70 - 71: 28.682 distance: 71 - 72: 14.665 distance: 71 - 73: 30.608 distance: 74 - 75: 24.695 distance: 74 - 80: 22.800 distance: 75 - 76: 17.244 distance: 75 - 78: 9.669 distance: 76 - 77: 15.407 distance: 76 - 81: 21.051 distance: 78 - 79: 14.299 distance: 79 - 80: 42.134 distance: 81 - 82: 21.639 distance: 82 - 83: 7.073 distance: 82 - 85: 15.011 distance: 83 - 84: 20.288 distance: 83 - 88: 6.710 distance: 85 - 86: 21.627 distance: 85 - 87: 7.013 distance: 88 - 89: 12.442 distance: 89 - 90: 14.026 distance: 89 - 92: 6.247 distance: 90 - 91: 5.252 distance: 90 - 99: 16.995 distance: 92 - 93: 7.862 distance: 93 - 94: 9.818 distance: 93 - 95: 5.678 distance: 94 - 96: 5.789 distance: 95 - 97: 6.105 distance: 96 - 98: 9.248 distance: 97 - 98: 6.773 distance: 99 - 100: 20.137 distance: 100 - 101: 15.936 distance: 100 - 103: 15.196 distance: 101 - 102: 17.099 distance: 101 - 107: 29.676 distance: 103 - 104: 14.483 distance: 104 - 105: 26.885 distance: 104 - 106: 8.949 distance: 107 - 108: 27.126 distance: 108 - 109: 17.912 distance: 108 - 111: 13.915 distance: 109 - 110: 29.578 distance: 109 - 114: 12.269 distance: 110 - 132: 17.641 distance: 111 - 112: 18.688 distance: 111 - 113: 38.992 distance: 114 - 115: 13.848 distance: 115 - 116: 35.246 distance: 115 - 118: 25.834 distance: 116 - 117: 5.558 distance: 116 - 122: 18.700 distance: 118 - 119: 36.317 distance: 119 - 120: 25.513 distance: 119 - 121: 15.024 distance: 122 - 123: 6.540 distance: 123 - 124: 8.853 distance: 123 - 126: 14.160 distance: 124 - 125: 19.444 distance: 124 - 132: 14.978 distance: 126 - 127: 11.973 distance: 127 - 128: 16.304 distance: 127 - 129: 26.691 distance: 128 - 130: 15.735 distance: 129 - 131: 16.827 distance: 130 - 131: 19.025 distance: 132 - 133: 17.976 distance: 133 - 134: 8.289 distance: 133 - 136: 7.996 distance: 134 - 135: 15.116 distance: 134 - 143: 7.507 distance: 136 - 137: 21.296 distance: 137 - 138: 14.417 distance: 137 - 139: 14.816 distance: 138 - 140: 3.092 distance: 139 - 141: 10.003 distance: 140 - 142: 5.132 distance: 141 - 142: 4.959