Starting phenix.real_space_refine on Tue Aug 6 04:25:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/08_2024/8ib2_35329.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/08_2024/8ib2_35329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/08_2024/8ib2_35329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/08_2024/8ib2_35329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/08_2024/8ib2_35329.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ib2_35329/08_2024/8ib2_35329.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 113 5.16 5 C 9608 2.51 5 N 2568 2.21 5 O 2930 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 ASP 363": "OD1" <-> "OD2" Residue "5 GLU 374": "OE1" <-> "OE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F ASP 154": "OD1" <-> "OD2" Residue "F ASP 157": "OD1" <-> "OD2" Residue "F GLU 316": "OE1" <-> "OE2" Residue "F GLU 334": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15229 Number of models: 1 Model: "" Number of chains: 11 Chain: "5" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 549 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2909 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.32, per 1000 atoms: 0.55 Number of scatterers: 15229 At special positions: 0 Unit cell: (108.23, 93.16, 190.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 113 16.00 P 10 15.00 O 2930 8.00 N 2568 7.00 C 9608 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: 5.38 Conformation dependent library (CDL) restraints added in 2.8 seconds 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 30 sheets defined 48.4% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain '5' and resid 344 through 349 removed outlier: 3.906A pdb=" N LEU 5 348 " --> pdb=" O PRO 5 344 " (cutoff:3.500A) Processing helix chain '5' and resid 372 through 381 Processing helix chain '5' and resid 383 through 390 removed outlier: 3.556A pdb=" N LEU 5 390 " --> pdb=" O GLU 5 386 " (cutoff:3.500A) Processing helix chain '5' and resid 391 through 402 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.756A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 127 removed outlier: 4.259A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.524A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.569A pdb=" N SER B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.915A pdb=" N ARG B 254 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 255' Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.944A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.870A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.653A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 306' Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.826A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.054A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.567A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.582A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.965A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.558A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 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 202 through 216 removed outlier: 3.926A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 removed outlier: 4.082A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix No H-bonds generated for 'chain 'C' and resid 252 through 260' Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.782A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.853A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.682A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 removed outlier: 4.075A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.738A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 79 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.730A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.967A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.731A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.810A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.512A pdb=" N LEU D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.960A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.691A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.120A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.801A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 356 removed outlier: 6.316A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE D 352 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET D 355 " --> pdb=" O PHE D 352 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 348 through 356' Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.543A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.626A pdb=" N GLU E 93 " --> pdb=" O THR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 4.037A pdb=" N GLU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.541A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.737A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 4.119A pdb=" N ARG E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 257' Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.066A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.718A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 348 through 349 No H-bonds generated for 'chain 'E' and resid 348 through 349' Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.677A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.023A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 removed outlier: 3.583A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 92 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.690A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 3.839A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 251 through 256 removed outlier: 3.962A pdb=" N PHE F 255 " --> pdb=" O ASN F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 262 removed outlier: 3.643A pdb=" N LEU F 261 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.074A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.509A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 removed outlier: 3.920A pdb=" N GLY F 343 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 349 " --> pdb=" O ILE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 355 Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.405A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.841A pdb=" N THR B 106 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B 132 " --> pdb=" O ILE B 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 178 removed outlier: 7.477A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.736A pdb=" N ALA B 170 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 239 through 241 Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.725A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA C 135 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.566A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.641A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 239 through 241 Processing sheet with id=AB4, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.559A pdb=" N LEU D 104 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR D 106 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET D 132 " --> pdb=" O ILE D 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.505A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 239 through 241 Processing sheet with id=AC1, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.018A pdb=" N THR E 106 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N ALA E 135 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.407A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 239 through 241 Processing sheet with id=AC7, first strand: chain 'F' and resid 29 through 32 removed outlier: 4.175A pdb=" N THR F 106 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASN F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA F 135 " --> pdb=" O VAL F 103 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET F 132 " --> pdb=" O ILE F 357 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.507A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N MET F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 239 through 241 667 hydrogen bonds defined for protein. 1764 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: 6.00 Time building geometry restraints manager: 6.00 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: 4945 1.34 - 1.46: 3223 1.46 - 1.58: 7187 1.58 - 1.70: 15 1.70 - 1.82: 196 Bond restraints: 15566 Sorted by residual: bond pdb=" CA VAL F 43 " pdb=" CB VAL F 43 " ideal model delta sigma weight residual 1.531 1.551 -0.020 1.11e-02 8.12e+03 3.32e+00 bond pdb=" CB GLN B 354 " pdb=" CG GLN B 354 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CB ASN C 252 " pdb=" CG ASN C 252 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.83e+00 bond pdb=" CA THR E 201 " pdb=" CB THR E 201 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.42e+00 bond pdb=" CG GLN B 354 " pdb=" CD GLN B 354 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.41e+00 ... (remaining 15561 not shown) Histogram of bond angle deviations from ideal: 96.88 - 104.69: 349 104.69 - 112.51: 7972 112.51 - 120.33: 6441 120.33 - 128.14: 6233 128.14 - 135.96: 110 Bond angle restraints: 21105 Sorted by residual: angle pdb=" C GLY B 42 " pdb=" N VAL B 43 " pdb=" CA VAL B 43 " ideal model delta sigma weight residual 121.97 128.58 -6.61 1.80e+00 3.09e-01 1.35e+01 angle pdb=" CB GLN B 354 " pdb=" CG GLN B 354 " pdb=" CD GLN B 354 " ideal model delta sigma weight residual 112.60 118.46 -5.86 1.70e+00 3.46e-01 1.19e+01 angle pdb=" CA GLU E 364 " pdb=" CB GLU E 364 " pdb=" CG GLU E 364 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" CB MET 5 365 " pdb=" CG MET 5 365 " pdb=" SD MET 5 365 " ideal model delta sigma weight residual 112.70 103.03 9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" N GLU D 83 " pdb=" CA GLU D 83 " pdb=" CB GLU D 83 " ideal model delta sigma weight residual 110.28 115.17 -4.89 1.55e+00 4.16e-01 9.95e+00 ... (remaining 21100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8466 17.94 - 35.89: 768 35.89 - 53.83: 119 53.83 - 71.77: 21 71.77 - 89.72: 12 Dihedral angle restraints: 9386 sinusoidal: 3808 harmonic: 5578 Sorted by residual: dihedral pdb=" CA VAL D 152 " pdb=" C VAL D 152 " pdb=" N MET D 153 " pdb=" CA MET D 153 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA GLN F 353 " pdb=" C GLN F 353 " pdb=" N GLN F 354 " pdb=" CA GLN F 354 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 -134.83 74.83 1 2.00e+01 2.50e-03 1.77e+01 ... (remaining 9383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1846 0.054 - 0.107: 401 0.107 - 0.161: 86 0.161 - 0.215: 3 0.215 - 0.268: 2 Chirality restraints: 2338 Sorted by residual: chirality pdb=" CB ILE F 250 " pdb=" CA ILE F 250 " pdb=" CG1 ILE F 250 " pdb=" CG2 ILE F 250 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB ILE D 250 " pdb=" CA ILE D 250 " pdb=" CG1 ILE D 250 " pdb=" CG2 ILE D 250 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA MET C 123 " pdb=" N MET C 123 " pdb=" C MET C 123 " pdb=" CB MET C 123 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2335 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP 5 363 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.59e+00 pdb=" CG ASP 5 363 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP 5 363 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP 5 363 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO C 112 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO E 243 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " 0.024 5.00e-02 4.00e+02 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2432 2.77 - 3.30: 13542 3.30 - 3.83: 23805 3.83 - 4.37: 27944 4.37 - 4.90: 49784 Nonbonded interactions: 117507 Sorted by model distance: nonbonded pdb=" OG1 THR F 202 " pdb=" OE1 GLU F 205 " model vdw 2.232 3.040 nonbonded pdb=" OG SER F 141 " pdb=" OG SER F 300 " model vdw 2.262 3.040 nonbonded pdb=" OD1 ASP F 157 " pdb=" O3' ADP F 401 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASP B 157 " pdb=" O3' ADP B 401 " model vdw 2.319 3.040 nonbonded pdb=" NZ LYS C 213 " pdb=" O2' ADP C 401 " model vdw 2.329 3.120 ... (remaining 117502 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.720 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 42.940 Find NCS groups from input model: 0.530 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.003 0.043 15566 Z= 0.200 Angle : 0.688 10.786 21105 Z= 0.354 Chirality : 0.047 0.268 2338 Planarity : 0.005 0.062 2700 Dihedral : 13.903 89.718 5810 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.01 (0.19), residues: 1919 helix: -0.37 (0.18), residues: 750 sheet: 0.74 (0.28), residues: 332 loop : 0.26 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 356 HIS 0.003 0.001 HIS E 371 PHE 0.026 0.001 PHE E 124 TYR 0.009 0.001 TYR E 143 ARG 0.009 0.000 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.743 Fit side-chains revert: symmetry clash REVERT: 5 376 PHE cc_start: 0.8161 (t80) cc_final: 0.7868 (t80) REVERT: B 122 ILE cc_start: 0.7942 (mt) cc_final: 0.7682 (mt) REVERT: B 195 GLU cc_start: 0.7678 (tp30) cc_final: 0.7418 (tp30) REVERT: C 72 GLU cc_start: 0.7447 (pp20) cc_final: 0.7214 (pp20) REVERT: C 269 MET cc_start: 0.8282 (mtt) cc_final: 0.7882 (mtp) REVERT: D 117 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7692 (mt-10) REVERT: E 296 ASN cc_start: 0.8844 (m-40) cc_final: 0.8389 (m-40) REVERT: E 313 MET cc_start: 0.8058 (tpp) cc_final: 0.7709 (tpp) REVERT: F 16 MET cc_start: 0.8169 (mmp) cc_final: 0.7950 (mmm) REVERT: F 113 LYS cc_start: 0.7382 (mtmt) cc_final: 0.6828 (pttm) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2443 time to fit residues: 73.2863 Evaluate side-chains 152 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN F 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15566 Z= 0.212 Angle : 0.575 7.710 21105 Z= 0.281 Chirality : 0.045 0.163 2338 Planarity : 0.004 0.049 2700 Dihedral : 6.454 84.629 2159 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.79 % Allowed : 5.98 % Favored : 93.23 % 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: 0.51 (0.20), residues: 1919 helix: 0.32 (0.19), residues: 784 sheet: 0.54 (0.28), residues: 331 loop : 0.53 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 356 HIS 0.004 0.001 HIS C 88 PHE 0.008 0.001 PHE C 255 TYR 0.012 0.001 TYR 5 345 ARG 0.003 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 1.718 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8673 (mt) cc_final: 0.8444 (mt) REVERT: B 117 GLU cc_start: 0.8667 (mt-10) cc_final: 0.7607 (tt0) REVERT: B 132 MET cc_start: 0.8406 (ppp) cc_final: 0.8151 (tmm) REVERT: C 227 MET cc_start: 0.8536 (mmm) cc_final: 0.7797 (tpp) REVERT: D 128 ASN cc_start: 0.9273 (m110) cc_final: 0.9055 (m110) REVERT: D 283 MET cc_start: 0.8560 (mmt) cc_final: 0.7958 (mmt) REVERT: D 313 MET cc_start: 0.9042 (tpp) cc_final: 0.8528 (ttm) REVERT: E 296 ASN cc_start: 0.8765 (m-40) cc_final: 0.8234 (m-40) REVERT: E 313 MET cc_start: 0.8134 (tpp) cc_final: 0.7818 (tpp) REVERT: F 16 MET cc_start: 0.8243 (mmp) cc_final: 0.7971 (mmm) REVERT: F 82 MET cc_start: 0.9052 (tpt) cc_final: 0.8713 (tpt) REVERT: F 113 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7144 (pttm) outliers start: 13 outliers final: 9 residues processed: 159 average time/residue: 0.2261 time to fit residues: 57.3479 Evaluate side-chains 147 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 272 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 144 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15566 Z= 0.169 Angle : 0.536 7.291 21105 Z= 0.257 Chirality : 0.044 0.140 2338 Planarity : 0.004 0.046 2700 Dihedral : 6.183 86.960 2159 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.85 % Allowed : 7.80 % Favored : 91.34 % 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: 0.79 (0.20), residues: 1919 helix: 0.72 (0.19), residues: 784 sheet: 0.47 (0.28), residues: 331 loop : 0.57 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.003 0.001 HIS E 87 PHE 0.008 0.001 PHE 5 380 TYR 0.009 0.001 TYR 5 345 ARG 0.002 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 1.797 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8631 (mt) cc_final: 0.8400 (mt) REVERT: 5 363 ASP cc_start: 0.8197 (t0) cc_final: 0.7967 (t0) REVERT: 5 395 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7679 (mtm180) REVERT: B 117 GLU cc_start: 0.8648 (mt-10) cc_final: 0.7632 (tt0) REVERT: B 132 MET cc_start: 0.8571 (ppp) cc_final: 0.8279 (tmm) REVERT: C 82 MET cc_start: 0.8426 (tpp) cc_final: 0.8214 (tpt) REVERT: C 227 MET cc_start: 0.8522 (mmm) cc_final: 0.7799 (tpp) REVERT: D 132 MET cc_start: 0.8615 (ppp) cc_final: 0.8330 (ppp) REVERT: D 227 MET cc_start: 0.8529 (mmm) cc_final: 0.8151 (tpt) REVERT: D 283 MET cc_start: 0.8507 (mmt) cc_final: 0.8091 (mpp) REVERT: D 313 MET cc_start: 0.9011 (tpp) cc_final: 0.8545 (ttm) REVERT: E 296 ASN cc_start: 0.8732 (m-40) cc_final: 0.8474 (m-40) REVERT: E 313 MET cc_start: 0.8075 (tpp) cc_final: 0.7781 (tpp) REVERT: E 326 LYS cc_start: 0.8668 (tttt) cc_final: 0.8313 (pttp) REVERT: F 16 MET cc_start: 0.8222 (mmp) cc_final: 0.7738 (mmm) REVERT: F 82 MET cc_start: 0.8999 (tpt) cc_final: 0.8646 (tpt) REVERT: F 113 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7101 (pttt) REVERT: F 132 MET cc_start: 0.7908 (tmm) cc_final: 0.7568 (tmm) REVERT: F 328 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7763 (mmpt) outliers start: 14 outliers final: 10 residues processed: 165 average time/residue: 0.2567 time to fit residues: 66.0713 Evaluate side-chains 154 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain E residue 346 LEU Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN D 121 GLN F 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15566 Z= 0.149 Angle : 0.523 7.952 21105 Z= 0.249 Chirality : 0.043 0.139 2338 Planarity : 0.004 0.045 2700 Dihedral : 5.988 88.231 2159 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.16 % Allowed : 8.96 % Favored : 89.88 % 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: 1.01 (0.20), residues: 1919 helix: 1.11 (0.20), residues: 771 sheet: 0.32 (0.28), residues: 355 loop : 0.61 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 340 HIS 0.002 0.000 HIS E 87 PHE 0.016 0.001 PHE 5 376 TYR 0.013 0.001 TYR 5 345 ARG 0.002 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.745 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8538 (mt) REVERT: 5 363 ASP cc_start: 0.8118 (t0) cc_final: 0.7878 (t0) REVERT: 5 395 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7728 (mtm180) REVERT: B 117 GLU cc_start: 0.8672 (mt-10) cc_final: 0.7611 (tt0) REVERT: B 132 MET cc_start: 0.8614 (ppp) cc_final: 0.8213 (tmm) REVERT: C 227 MET cc_start: 0.8568 (mmm) cc_final: 0.7824 (tpp) REVERT: D 227 MET cc_start: 0.8504 (mmm) cc_final: 0.8121 (tpt) REVERT: D 283 MET cc_start: 0.8429 (mmt) cc_final: 0.8059 (mpp) REVERT: D 313 MET cc_start: 0.8991 (tpp) cc_final: 0.8544 (ttm) REVERT: E 132 MET cc_start: 0.8209 (ttp) cc_final: 0.7670 (ttp) REVERT: E 296 ASN cc_start: 0.8655 (m-40) cc_final: 0.8404 (m-40) REVERT: E 313 MET cc_start: 0.8061 (tpp) cc_final: 0.7783 (tpp) REVERT: E 326 LYS cc_start: 0.8749 (tttt) cc_final: 0.8380 (pttp) REVERT: F 16 MET cc_start: 0.8084 (mmp) cc_final: 0.7582 (mmm) REVERT: F 82 MET cc_start: 0.8992 (tpt) cc_final: 0.8657 (tpt) REVERT: F 113 LYS cc_start: 0.7819 (mtmt) cc_final: 0.7166 (pttt) REVERT: F 132 MET cc_start: 0.7914 (tmm) cc_final: 0.7582 (tmm) REVERT: F 328 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7759 (mmpt) outliers start: 19 outliers final: 15 residues processed: 164 average time/residue: 0.2353 time to fit residues: 60.6540 Evaluate side-chains 160 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 143 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 348 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 127 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN E 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 0.044 15566 Z= 0.305 Angle : 0.596 8.681 21105 Z= 0.290 Chirality : 0.046 0.218 2338 Planarity : 0.004 0.046 2700 Dihedral : 6.100 87.643 2159 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.71 % Allowed : 10.49 % Favored : 87.80 % 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: 0.92 (0.20), residues: 1919 helix: 1.00 (0.20), residues: 777 sheet: 0.37 (0.28), residues: 331 loop : 0.53 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 340 HIS 0.005 0.001 HIS E 87 PHE 0.010 0.001 PHE B 200 TYR 0.010 0.001 TYR E 143 ARG 0.003 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.792 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8543 (mt) REVERT: 5 365 MET cc_start: 0.8332 (tpp) cc_final: 0.8006 (tpp) REVERT: 5 396 ASN cc_start: 0.8515 (m-40) cc_final: 0.8233 (m-40) REVERT: B 117 GLU cc_start: 0.8726 (mt-10) cc_final: 0.7693 (tt0) REVERT: B 163 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7566 (p) REVERT: C 227 MET cc_start: 0.8674 (mmm) cc_final: 0.7936 (tpp) REVERT: D 227 MET cc_start: 0.8547 (mmm) cc_final: 0.8140 (tpt) REVERT: E 305 MET cc_start: 0.9060 (mmt) cc_final: 0.8667 (mmt) REVERT: E 313 MET cc_start: 0.8298 (tpp) cc_final: 0.8003 (tpp) REVERT: F 113 LYS cc_start: 0.7879 (mtmt) cc_final: 0.7225 (pttt) REVERT: F 153 MET cc_start: 0.8540 (ttp) cc_final: 0.8318 (tmm) REVERT: F 328 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7829 (mmpt) outliers start: 28 outliers final: 19 residues processed: 163 average time/residue: 0.2375 time to fit residues: 61.0902 Evaluate side-chains 163 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 348 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.4980 chunk 166 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15566 Z= 0.135 Angle : 0.521 9.592 21105 Z= 0.248 Chirality : 0.043 0.201 2338 Planarity : 0.004 0.046 2700 Dihedral : 5.850 87.036 2159 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.16 % Allowed : 11.34 % Favored : 87.50 % 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: 1.09 (0.20), residues: 1919 helix: 1.15 (0.20), residues: 789 sheet: 0.39 (0.29), residues: 331 loop : 0.65 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 340 HIS 0.002 0.000 HIS D 101 PHE 0.009 0.001 PHE 5 376 TYR 0.007 0.001 TYR F 53 ARG 0.002 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 153 time to evaluate : 1.782 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8527 (mt) REVERT: 5 365 MET cc_start: 0.8106 (tpp) cc_final: 0.7617 (tpp) REVERT: 5 395 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7803 (mtm180) REVERT: B 117 GLU cc_start: 0.8682 (mt-10) cc_final: 0.7622 (tt0) REVERT: C 227 MET cc_start: 0.8602 (mmm) cc_final: 0.7828 (tpp) REVERT: D 227 MET cc_start: 0.8488 (mmm) cc_final: 0.8089 (tpt) REVERT: D 283 MET cc_start: 0.8551 (tpp) cc_final: 0.7476 (mpp) REVERT: E 305 MET cc_start: 0.9026 (mmt) cc_final: 0.8685 (mmp) REVERT: E 313 MET cc_start: 0.8164 (tpp) cc_final: 0.7879 (tpp) REVERT: F 113 LYS cc_start: 0.7718 (mtmt) cc_final: 0.7060 (pttt) REVERT: F 328 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7730 (mmpt) outliers start: 19 outliers final: 13 residues processed: 164 average time/residue: 0.2613 time to fit residues: 67.8802 Evaluate side-chains 162 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 348 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 3.9990 chunk 20 optimal weight: 0.0000 chunk 105 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 155 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN F 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15566 Z= 0.137 Angle : 0.519 9.691 21105 Z= 0.245 Chirality : 0.043 0.172 2338 Planarity : 0.004 0.047 2700 Dihedral : 5.670 85.929 2159 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.34 % Allowed : 11.59 % Favored : 87.07 % 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: 1.27 (0.20), residues: 1919 helix: 1.28 (0.20), residues: 792 sheet: 0.45 (0.29), residues: 331 loop : 0.77 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 340 HIS 0.002 0.000 HIS F 161 PHE 0.007 0.001 PHE B 255 TYR 0.006 0.001 TYR F 53 ARG 0.001 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.868 Fit side-chains revert: symmetry clash REVERT: 5 348 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8503 (mt) REVERT: B 117 GLU cc_start: 0.8664 (mt-10) cc_final: 0.7584 (tt0) REVERT: B 132 MET cc_start: 0.8873 (tmm) cc_final: 0.8517 (tmm) REVERT: C 227 MET cc_start: 0.8593 (mmm) cc_final: 0.7800 (tpp) REVERT: D 227 MET cc_start: 0.8509 (mmm) cc_final: 0.8135 (tpt) REVERT: D 283 MET cc_start: 0.8595 (tpp) cc_final: 0.7402 (mpp) REVERT: E 132 MET cc_start: 0.8194 (ttp) cc_final: 0.7581 (ttp) REVERT: F 113 LYS cc_start: 0.7677 (mtmt) cc_final: 0.7061 (pttt) REVERT: F 328 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7548 (mmpt) outliers start: 22 outliers final: 14 residues processed: 174 average time/residue: 0.2582 time to fit residues: 69.1556 Evaluate side-chains 167 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 348 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 328 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15566 Z= 0.301 Angle : 0.608 9.946 21105 Z= 0.293 Chirality : 0.046 0.149 2338 Planarity : 0.004 0.049 2700 Dihedral : 5.839 84.010 2159 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.34 % Allowed : 12.20 % Favored : 86.46 % 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: 1.12 (0.20), residues: 1919 helix: 1.29 (0.20), residues: 758 sheet: 0.38 (0.28), residues: 331 loop : 0.57 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 340 HIS 0.005 0.001 HIS E 87 PHE 0.010 0.001 PHE B 200 TYR 0.012 0.001 TYR C 143 ARG 0.003 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.737 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8509 (mt) REVERT: 5 365 MET cc_start: 0.8303 (tpp) cc_final: 0.7808 (tpp) REVERT: 5 396 ASN cc_start: 0.8603 (m-40) cc_final: 0.8314 (m-40) REVERT: B 113 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8127 (mttp) REVERT: B 117 GLU cc_start: 0.8714 (mt-10) cc_final: 0.7660 (tt0) REVERT: B 132 MET cc_start: 0.8669 (tmm) cc_final: 0.8303 (tmm) REVERT: B 163 VAL cc_start: 0.7744 (OUTLIER) cc_final: 0.7519 (p) REVERT: B 313 MET cc_start: 0.8632 (ttp) cc_final: 0.8383 (ttp) REVERT: C 227 MET cc_start: 0.8699 (mmm) cc_final: 0.7926 (tpp) REVERT: D 227 MET cc_start: 0.8562 (mmm) cc_final: 0.8162 (tpt) REVERT: D 283 MET cc_start: 0.8671 (tpp) cc_final: 0.7420 (mpp) REVERT: E 132 MET cc_start: 0.8307 (ttp) cc_final: 0.7683 (ttp) REVERT: E 305 MET cc_start: 0.9037 (mmt) cc_final: 0.8627 (mmt) REVERT: E 325 MET cc_start: 0.7513 (mmt) cc_final: 0.6965 (mmt) REVERT: F 113 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7196 (pttt) REVERT: F 201 THR cc_start: 0.9111 (p) cc_final: 0.8865 (t) outliers start: 22 outliers final: 18 residues processed: 160 average time/residue: 0.2414 time to fit residues: 60.0659 Evaluate side-chains 164 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 348 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 272 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 5.9990 chunk 176 optimal weight: 0.0870 chunk 160 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 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 : 0.004 0.039 15566 Z= 0.242 Angle : 0.578 10.668 21105 Z= 0.276 Chirality : 0.045 0.158 2338 Planarity : 0.004 0.047 2700 Dihedral : 5.802 82.683 2159 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.40 % Allowed : 12.74 % Favored : 85.85 % 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: 1.13 (0.20), residues: 1919 helix: 1.30 (0.20), residues: 758 sheet: 0.35 (0.28), residues: 331 loop : 0.58 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 340 HIS 0.004 0.001 HIS E 87 PHE 0.008 0.001 PHE 5 387 TYR 0.009 0.001 TYR F 53 ARG 0.003 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3838 Ramachandran restraints generated. 1919 Oldfield, 0 Emsley, 1919 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.750 Fit side-chains REVERT: 5 348 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8239 (mt) REVERT: 5 365 MET cc_start: 0.8364 (tpp) cc_final: 0.7963 (tpp) REVERT: 5 396 ASN cc_start: 0.8607 (m-40) cc_final: 0.8302 (m-40) REVERT: B 113 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8109 (mttp) REVERT: B 117 GLU cc_start: 0.8692 (mt-10) cc_final: 0.7641 (tt0) REVERT: B 132 MET cc_start: 0.8707 (tmm) cc_final: 0.8328 (tmm) REVERT: B 163 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7502 (p) REVERT: B 369 ILE cc_start: 0.9078 (tp) cc_final: 0.8821 (tt) REVERT: C 227 MET cc_start: 0.8682 (mmm) cc_final: 0.7908 (tpp) REVERT: D 132 MET cc_start: 0.8700 (ppp) cc_final: 0.8362 (ppp) REVERT: D 227 MET cc_start: 0.8533 (mmm) cc_final: 0.8142 (tpt) REVERT: D 283 MET cc_start: 0.8669 (tpp) cc_final: 0.7531 (mpp) REVERT: E 25 ASP cc_start: 0.7732 (t0) cc_final: 0.7518 (t0) REVERT: E 325 MET cc_start: 0.7388 (mmt) cc_final: 0.6884 (mmt) REVERT: F 113 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7118 (pttt) REVERT: F 201 THR cc_start: 0.9105 (p) cc_final: 0.8861 (t) outliers start: 23 outliers final: 17 residues processed: 170 average time/residue: 0.2550 time to fit residues: 66.9917 Evaluate side-chains 168 residues out of total 1640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 348 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain F residue 272 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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: 71.2265 > 50: distance: 38 - 69: 34.213 distance: 61 - 69: 33.797 distance: 69 - 70: 32.913 distance: 70 - 71: 9.354 distance: 70 - 73: 31.876 distance: 71 - 72: 11.290 distance: 73 - 74: 35.499 distance: 74 - 75: 9.017 distance: 74 - 76: 40.795 distance: 77 - 78: 48.881 distance: 78 - 79: 64.667 distance: 78 - 81: 33.079 distance: 79 - 86: 24.003 distance: 81 - 82: 38.180 distance: 82 - 83: 48.154 distance: 83 - 84: 56.804 distance: 83 - 85: 39.516 distance: 86 - 87: 32.562 distance: 87 - 88: 46.450 distance: 87 - 90: 25.145 distance: 88 - 89: 7.151 distance: 88 - 94: 9.854 distance: 90 - 91: 52.462 distance: 91 - 92: 24.566 distance: 91 - 93: 51.644 distance: 94 - 95: 37.931 distance: 95 - 96: 28.913 distance: 95 - 98: 12.120 distance: 96 - 97: 38.554 distance: 96 - 105: 39.205 distance: 98 - 99: 68.159 distance: 99 - 100: 13.039 distance: 100 - 101: 28.321 distance: 101 - 102: 14.129 distance: 102 - 103: 47.717 distance: 102 - 104: 60.431 distance: 105 - 106: 10.941 distance: 106 - 107: 31.652 distance: 106 - 109: 12.330 distance: 107 - 112: 44.067 distance: 109 - 110: 40.311 distance: 109 - 111: 34.669 distance: 112 - 113: 21.887 distance: 113 - 114: 14.683 distance: 113 - 116: 19.091 distance: 117 - 118: 38.122 distance: 117 - 123: 48.647 distance: 118 - 119: 4.622 distance: 118 - 121: 53.291 distance: 119 - 120: 57.425 distance: 119 - 124: 40.625 distance: 121 - 122: 39.468 distance: 122 - 123: 12.583 distance: 124 - 125: 39.032 distance: 125 - 126: 32.485 distance: 126 - 127: 25.763 distance: 126 - 133: 35.177 distance: 130 - 131: 27.052 distance: 134 - 137: 34.529 distance: 135 - 142: 59.353 distance: 137 - 138: 3.466 distance: 138 - 139: 28.512 distance: 139 - 140: 27.495 distance: 139 - 141: 45.664 distance: 142 - 143: 35.549 distance: 143 - 144: 40.645 distance: 143 - 146: 58.165 distance: 144 - 145: 55.977 distance: 144 - 152: 35.274 distance: 146 - 147: 15.790 distance: 147 - 148: 40.835 distance: 147 - 149: 56.368 distance: 149 - 151: 42.730 distance: 150 - 151: 40.596