Starting phenix.real_space_refine on Tue Aug 6 18:31:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo5_7119/08_2024/6bo5_7119.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo5_7119/08_2024/6bo5_7119.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/6bo5_7119/08_2024/6bo5_7119.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo5_7119/08_2024/6bo5_7119.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo5_7119/08_2024/6bo5_7119.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bo5_7119/08_2024/6bo5_7119.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= 0.000 sd= 0.004 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 96 5.16 5 C 11280 2.51 5 N 2900 2.21 5 O 2960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17236 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4309 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'CIS': 3, 'PTRANS': 18, 'TRANS': 535} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 4309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4309 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'CIS': 3, 'PTRANS': 18, 'TRANS': 535} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Chain: "D" Number of atoms: 4309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4309 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'CIS': 3, 'PTRANS': 18, 'TRANS': 535} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 4309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4309 Classifications: {'peptide': 557} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'CIS': 3, 'PTRANS': 18, 'TRANS': 535} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 110 Time building chain proxies: 9.77, per 1000 atoms: 0.57 Number of scatterers: 17236 At special positions: 0 Unit cell: (136.53, 136.53, 110.7, 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 96 16.00 O 2960 8.00 N 2900 7.00 C 11280 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: 6.79 Conformation dependent library (CDL) restraints added in 3.5 seconds 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4192 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 4 sheets defined 59.3% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 143 removed outlier: 3.895A pdb=" N LEU A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.994A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 183 Processing helix chain 'A' and resid 212 through 220 removed outlier: 4.294A pdb=" N THR A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 279 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 370 through 374 removed outlier: 4.053A pdb=" N VAL A 373 " --> pdb=" O HIS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 387 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 393 through 413 Processing helix chain 'A' and resid 428 through 460 removed outlier: 3.598A pdb=" N SER A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 492 removed outlier: 4.171A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 513 removed outlier: 4.130A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU A 513 " --> pdb=" O TRP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 536 through 557 removed outlier: 3.547A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 556 " --> pdb=" O ALA A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 602 Processing helix chain 'A' and resid 623 through 649 Processing helix chain 'A' and resid 651 through 675 removed outlier: 4.289A pdb=" N ASN A 655 " --> pdb=" O HIS A 651 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP A 657 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS A 661 " --> pdb=" O TRP A 657 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 675 " --> pdb=" O MET A 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.895A pdb=" N LEU B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.993A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 Processing helix chain 'B' and resid 212 through 220 removed outlier: 4.295A pdb=" N THR B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 279 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 370 through 374 removed outlier: 4.053A pdb=" N VAL B 373 " --> pdb=" O HIS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 387 Processing helix chain 'B' and resid 389 through 392 Processing helix chain 'B' and resid 393 through 413 Processing helix chain 'B' and resid 428 through 460 removed outlier: 3.598A pdb=" N SER B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 492 removed outlier: 4.171A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 513 removed outlier: 4.130A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU B 513 " --> pdb=" O TRP B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 536 Processing helix chain 'B' and resid 536 through 557 removed outlier: 3.548A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 556 " --> pdb=" O ALA B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 602 Processing helix chain 'B' and resid 623 through 649 Processing helix chain 'B' and resid 651 through 675 removed outlier: 4.289A pdb=" N ASN B 655 " --> pdb=" O HIS B 651 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS B 661 " --> pdb=" O TRP B 657 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR B 675 " --> pdb=" O MET B 671 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 143 removed outlier: 3.894A pdb=" N LEU D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.994A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 212 through 220 removed outlier: 4.295A pdb=" N THR D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 279 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 370 through 374 removed outlier: 4.053A pdb=" N VAL D 373 " --> pdb=" O HIS D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 387 Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 393 through 413 Processing helix chain 'D' and resid 428 through 460 removed outlier: 3.598A pdb=" N SER D 432 " --> pdb=" O THR D 428 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR D 447 " --> pdb=" O LEU D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 492 removed outlier: 4.171A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 513 removed outlier: 4.130A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU D 513 " --> pdb=" O TRP D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 536 Processing helix chain 'D' and resid 536 through 557 removed outlier: 3.548A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL D 556 " --> pdb=" O ALA D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 602 Processing helix chain 'D' and resid 623 through 649 Processing helix chain 'D' and resid 651 through 675 removed outlier: 4.289A pdb=" N ASN D 655 " --> pdb=" O HIS D 651 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP D 657 " --> pdb=" O ALA D 653 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS D 661 " --> pdb=" O TRP D 657 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR D 675 " --> pdb=" O MET D 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 143 removed outlier: 3.896A pdb=" N LEU C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.994A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 212 through 220 removed outlier: 4.294A pdb=" N THR C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 279 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 370 through 374 removed outlier: 4.053A pdb=" N VAL C 373 " --> pdb=" O HIS C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 387 Processing helix chain 'C' and resid 389 through 392 Processing helix chain 'C' and resid 393 through 413 Processing helix chain 'C' and resid 428 through 460 removed outlier: 3.598A pdb=" N SER C 432 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 447 " --> pdb=" O LEU C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 492 removed outlier: 4.171A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 513 removed outlier: 4.130A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C 513 " --> pdb=" O TRP C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 536 Processing helix chain 'C' and resid 536 through 557 removed outlier: 3.547A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 556 " --> pdb=" O ALA C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 602 Processing helix chain 'C' and resid 623 through 649 Processing helix chain 'C' and resid 651 through 675 removed outlier: 4.289A pdb=" N ASN C 655 " --> pdb=" O HIS C 651 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 661 " --> pdb=" O TRP C 657 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR C 675 " --> pdb=" O MET C 671 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.538A pdb=" N LEU A 689 " --> pdb=" O SER A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 331 removed outlier: 3.537A pdb=" N LEU B 689 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 329 through 331 removed outlier: 3.537A pdb=" N LEU D 689 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 329 through 331 removed outlier: 3.537A pdb=" N LEU C 689 " --> pdb=" O SER C 341 " (cutoff:3.500A) 897 hydrogen bonds defined for protein. 2655 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: 4.81 Time building geometry restraints manager: 7.48 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: 5355 1.34 - 1.46: 3620 1.46 - 1.58: 8533 1.58 - 1.69: 0 1.69 - 1.81: 148 Bond restraints: 17656 Sorted by residual: bond pdb=" C GLN B 324 " pdb=" N PRO B 325 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.34e-02 1.83e+03 1.16e+01 bond pdb=" C GLN D 324 " pdb=" N PRO D 325 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.34e-02 1.83e+03 1.16e+01 bond pdb=" C GLN A 324 " pdb=" N PRO A 325 " ideal model delta sigma weight residual 1.334 1.413 -0.079 2.34e-02 1.83e+03 1.15e+01 bond pdb=" C GLN C 324 " pdb=" N PRO C 325 " ideal model delta sigma weight residual 1.334 1.413 -0.079 2.34e-02 1.83e+03 1.15e+01 bond pdb=" CA PHE A 519 " pdb=" CB PHE A 519 " ideal model delta sigma weight residual 1.521 1.564 -0.043 1.48e-02 4.57e+03 8.42e+00 ... (remaining 17651 not shown) Histogram of bond angle deviations from ideal: 98.95 - 105.96: 328 105.96 - 112.98: 9190 112.98 - 119.99: 6486 119.99 - 127.01: 7776 127.01 - 134.03: 232 Bond angle restraints: 24012 Sorted by residual: angle pdb=" N VAL B 621 " pdb=" CA VAL B 621 " pdb=" C VAL B 621 " ideal model delta sigma weight residual 111.09 125.63 -14.54 1.25e+00 6.40e-01 1.35e+02 angle pdb=" N VAL C 621 " pdb=" CA VAL C 621 " pdb=" C VAL C 621 " ideal model delta sigma weight residual 111.09 125.63 -14.54 1.25e+00 6.40e-01 1.35e+02 angle pdb=" N VAL A 621 " pdb=" CA VAL A 621 " pdb=" C VAL A 621 " ideal model delta sigma weight residual 111.09 125.63 -14.54 1.25e+00 6.40e-01 1.35e+02 angle pdb=" N VAL D 621 " pdb=" CA VAL D 621 " pdb=" C VAL D 621 " ideal model delta sigma weight residual 111.09 125.63 -14.54 1.25e+00 6.40e-01 1.35e+02 angle pdb=" N VAL B 390 " pdb=" CA VAL B 390 " pdb=" C VAL B 390 " ideal model delta sigma weight residual 112.35 102.48 9.87 1.41e+00 5.03e-01 4.90e+01 ... (remaining 24007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.26: 9644 19.26 - 38.53: 524 38.53 - 57.79: 92 57.79 - 77.06: 16 77.06 - 96.32: 4 Dihedral angle restraints: 10280 sinusoidal: 3792 harmonic: 6488 Sorted by residual: dihedral pdb=" CA HIS B 363 " pdb=" C HIS B 363 " pdb=" N CYS B 364 " pdb=" CA CYS B 364 " ideal model delta harmonic sigma weight residual -180.00 -83.68 -96.32 0 5.00e+00 4.00e-02 3.71e+02 dihedral pdb=" CA HIS A 363 " pdb=" C HIS A 363 " pdb=" N CYS A 364 " pdb=" CA CYS A 364 " ideal model delta harmonic sigma weight residual -180.00 -83.70 -96.30 0 5.00e+00 4.00e-02 3.71e+02 dihedral pdb=" CA HIS C 363 " pdb=" C HIS C 363 " pdb=" N CYS C 364 " pdb=" CA CYS C 364 " ideal model delta harmonic sigma weight residual -180.00 -83.73 -96.27 0 5.00e+00 4.00e-02 3.71e+02 ... (remaining 10277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2504 0.092 - 0.184: 244 0.184 - 0.276: 9 0.276 - 0.368: 3 0.368 - 0.461: 4 Chirality restraints: 2764 Sorted by residual: chirality pdb=" CA VAL D 621 " pdb=" N VAL D 621 " pdb=" C VAL D 621 " pdb=" CB VAL D 621 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA VAL A 621 " pdb=" N VAL A 621 " pdb=" C VAL A 621 " pdb=" CB VAL A 621 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA VAL C 621 " pdb=" N VAL C 621 " pdb=" C VAL C 621 " pdb=" CB VAL C 621 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.27e+00 ... (remaining 2761 not shown) Planarity restraints: 2984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 519 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C PHE D 519 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE D 519 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN D 520 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 519 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C PHE C 519 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE C 519 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN C 520 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 519 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.69e+00 pdb=" C PHE A 519 " -0.045 2.00e-02 2.50e+03 pdb=" O PHE A 519 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN A 520 " 0.015 2.00e-02 2.50e+03 ... (remaining 2981 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4674 2.80 - 3.33: 16020 3.33 - 3.85: 27979 3.85 - 4.38: 31364 4.38 - 4.90: 51483 Nonbonded interactions: 131520 Sorted by model distance: nonbonded pdb=" O MET C 404 " pdb=" OG1 THR C 408 " model vdw 2.277 3.040 nonbonded pdb=" O MET D 404 " pdb=" OG1 THR D 408 " model vdw 2.277 3.040 nonbonded pdb=" O MET B 404 " pdb=" OG1 THR B 408 " model vdw 2.277 3.040 nonbonded pdb=" O MET A 404 " pdb=" OG1 THR A 408 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLN C 479 " pdb=" ND2 ASN C 511 " model vdw 2.295 3.120 ... (remaining 131515 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' } 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: 0.810 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 47.440 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.090 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 0.005 0.080 17656 Z= 0.301 Angle : 1.082 16.507 24012 Z= 0.587 Chirality : 0.055 0.461 2764 Planarity : 0.007 0.064 2984 Dihedral : 12.892 96.321 6088 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.11 % Favored : 90.53 % Rotamer: Outliers : 1.84 % Allowed : 6.67 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 2.24 % 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: -5.44 (0.12), residues: 2196 helix: -3.76 (0.08), residues: 1188 sheet: -2.75 (0.58), residues: 40 loop : -3.32 (0.16), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 496 HIS 0.007 0.002 HIS D 165 PHE 0.026 0.003 PHE B 209 TYR 0.032 0.003 TYR A 323 ARG 0.005 0.001 ARG B 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 348 time to evaluate : 2.114 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 433 MET cc_start: 0.6313 (ttp) cc_final: 0.6038 (mtp) REVERT: A 634 TYR cc_start: 0.7375 (t80) cc_final: 0.6973 (t80) REVERT: B 433 MET cc_start: 0.6309 (ttp) cc_final: 0.6022 (mtp) REVERT: D 433 MET cc_start: 0.6313 (ttp) cc_final: 0.6024 (mtp) REVERT: D 529 ILE cc_start: 0.8368 (pp) cc_final: 0.8154 (pt) REVERT: C 433 MET cc_start: 0.6311 (ttp) cc_final: 0.6023 (mtp) REVERT: C 529 ILE cc_start: 0.8365 (pp) cc_final: 0.8152 (pt) outliers start: 32 outliers final: 0 residues processed: 376 average time/residue: 0.3564 time to fit residues: 187.1876 Evaluate side-chains 169 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 112 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 172 optimal weight: 0.0980 chunk 66 optimal weight: 0.3980 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 0.2980 chunk 199 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS A 259 ASN A 286 GLN A 368 ASN B 251 HIS B 259 ASN B 286 GLN B 368 ASN D 251 HIS D 259 ASN D 286 GLN D 368 ASN D 655 ASN C 251 HIS C 259 ASN C 286 GLN C 368 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17656 Z= 0.164 Angle : 0.759 9.980 24012 Z= 0.380 Chirality : 0.040 0.127 2764 Planarity : 0.006 0.055 2984 Dihedral : 7.572 46.549 2392 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.68 % Allowed : 8.79 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 1.50 % 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: -3.51 (0.15), residues: 2196 helix: -1.80 (0.13), residues: 1260 sheet: -2.69 (0.58), residues: 56 loop : -3.01 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 454 HIS 0.002 0.001 HIS C 413 PHE 0.021 0.002 PHE B 519 TYR 0.026 0.002 TYR A 323 ARG 0.005 0.001 ARG D 458 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 200 time to evaluate : 1.891 Fit side-chains revert: symmetry clash REVERT: B 433 MET cc_start: 0.6298 (ttp) cc_final: 0.6090 (mtp) REVERT: D 433 MET cc_start: 0.6296 (ttp) cc_final: 0.6091 (mtp) REVERT: C 433 MET cc_start: 0.6298 (ttp) cc_final: 0.6092 (mtp) outliers start: 64 outliers final: 16 residues processed: 252 average time/residue: 0.3010 time to fit residues: 112.4115 Evaluate side-chains 148 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 0.0020 chunk 166 optimal weight: 0.0570 chunk 136 optimal weight: 0.0070 chunk 55 optimal weight: 50.0000 chunk 200 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.3926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17656 Z= 0.158 Angle : 0.715 10.677 24012 Z= 0.351 Chirality : 0.040 0.163 2764 Planarity : 0.005 0.051 2984 Dihedral : 6.517 39.219 2392 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 2.24 % Allowed : 11.95 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -2.01 (0.17), residues: 2196 helix: -0.52 (0.14), residues: 1280 sheet: None (None), residues: 0 loop : -2.51 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 496 HIS 0.006 0.001 HIS B 293 PHE 0.015 0.001 PHE D 519 TYR 0.022 0.002 TYR C 323 ARG 0.006 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 185 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 16 residues processed: 217 average time/residue: 0.2718 time to fit residues: 90.8474 Evaluate side-chains 140 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 95 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 293 HIS ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 GLN B 293 HIS B 530 GLN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 GLN D 530 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN C 293 HIS C 530 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17656 Z= 0.243 Angle : 0.754 11.894 24012 Z= 0.377 Chirality : 0.042 0.144 2764 Planarity : 0.005 0.044 2984 Dihedral : 6.541 32.984 2392 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.07 % Allowed : 13.33 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -1.67 (0.17), residues: 2196 helix: -0.24 (0.14), residues: 1300 sheet: None (None), residues: 0 loop : -2.42 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 677 HIS 0.007 0.002 HIS B 293 PHE 0.018 0.002 PHE D 207 TYR 0.029 0.002 TYR A 525 ARG 0.005 0.001 ARG C 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 433 MET cc_start: 0.5886 (ttm) cc_final: 0.5521 (ttm) REVERT: A 640 MET cc_start: 0.7594 (tpt) cc_final: 0.6989 (tpt) REVERT: B 640 MET cc_start: 0.7509 (tpt) cc_final: 0.7012 (tpt) REVERT: D 640 MET cc_start: 0.7553 (tpt) cc_final: 0.6959 (tpt) REVERT: C 640 MET cc_start: 0.7555 (tpt) cc_final: 0.6961 (tpt) outliers start: 36 outliers final: 25 residues processed: 174 average time/residue: 0.3020 time to fit residues: 83.4932 Evaluate side-chains 147 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 625 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 158 optimal weight: 40.0000 chunk 87 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 108 optimal weight: 0.2980 chunk 190 optimal weight: 8.9990 chunk 53 optimal weight: 0.4980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17656 Z= 0.211 Angle : 0.709 11.466 24012 Z= 0.357 Chirality : 0.041 0.218 2764 Planarity : 0.004 0.047 2984 Dihedral : 6.299 32.075 2392 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.76 % Allowed : 13.79 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -1.44 (0.17), residues: 2196 helix: -0.02 (0.14), residues: 1284 sheet: -2.16 (0.64), residues: 56 loop : -2.30 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 677 HIS 0.003 0.001 HIS C 165 PHE 0.015 0.001 PHE D 207 TYR 0.024 0.002 TYR D 525 ARG 0.004 0.000 ARG D 392 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 136 time to evaluate : 2.011 Fit side-chains REVERT: A 640 MET cc_start: 0.7635 (tpt) cc_final: 0.7381 (tpt) REVERT: B 640 MET cc_start: 0.7685 (tpt) cc_final: 0.7419 (tpt) REVERT: D 640 MET cc_start: 0.7637 (tpt) cc_final: 0.7376 (tpt) REVERT: C 640 MET cc_start: 0.7641 (tpt) cc_final: 0.7382 (tpt) outliers start: 48 outliers final: 33 residues processed: 180 average time/residue: 0.2760 time to fit residues: 76.2551 Evaluate side-chains 148 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 625 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 52 optimal weight: 0.2980 chunk 212 optimal weight: 30.0000 chunk 176 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 GLN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 17656 Z= 0.159 Angle : 0.683 14.774 24012 Z= 0.340 Chirality : 0.041 0.200 2764 Planarity : 0.004 0.045 2984 Dihedral : 5.866 31.017 2392 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.01 % Allowed : 14.37 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.04 (0.18), residues: 2196 helix: 0.25 (0.14), residues: 1284 sheet: None (None), residues: 0 loop : -2.08 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 677 HIS 0.003 0.001 HIS D 293 PHE 0.012 0.001 PHE B 199 TYR 0.023 0.001 TYR A 525 ARG 0.003 0.000 ARG D 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 1.986 Fit side-chains REVERT: A 130 ASP cc_start: 0.7078 (t0) cc_final: 0.6740 (t0) REVERT: A 372 MET cc_start: 0.7095 (mmm) cc_final: 0.6789 (mmp) REVERT: A 433 MET cc_start: 0.5938 (ttm) cc_final: 0.5643 (ttp) REVERT: A 640 MET cc_start: 0.7658 (tpt) cc_final: 0.7374 (tpt) REVERT: B 130 ASP cc_start: 0.7052 (t0) cc_final: 0.6711 (t0) REVERT: B 640 MET cc_start: 0.7634 (tpt) cc_final: 0.7189 (tpt) REVERT: D 130 ASP cc_start: 0.7062 (t0) cc_final: 0.6844 (t0) REVERT: D 640 MET cc_start: 0.7579 (tpt) cc_final: 0.7265 (tpt) REVERT: C 130 ASP cc_start: 0.7049 (t0) cc_final: 0.6710 (t0) REVERT: C 640 MET cc_start: 0.7587 (tpt) cc_final: 0.7270 (tpt) outliers start: 35 outliers final: 33 residues processed: 169 average time/residue: 0.2653 time to fit residues: 70.1900 Evaluate side-chains 157 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 625 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 212 optimal weight: 30.0000 chunk 132 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 97 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17656 Z= 0.243 Angle : 0.733 14.245 24012 Z= 0.374 Chirality : 0.043 0.318 2764 Planarity : 0.005 0.043 2984 Dihedral : 6.165 29.634 2392 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.59 % Allowed : 15.17 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % 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: -1.17 (0.18), residues: 2196 helix: 0.09 (0.14), residues: 1288 sheet: None (None), residues: 0 loop : -2.05 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 677 HIS 0.004 0.001 HIS C 165 PHE 0.018 0.002 PHE C 207 TYR 0.029 0.002 TYR B 525 ARG 0.003 0.000 ARG D 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 126 time to evaluate : 2.024 Fit side-chains REVERT: A 433 MET cc_start: 0.5866 (ttm) cc_final: 0.5540 (ttp) REVERT: A 640 MET cc_start: 0.7682 (tpt) cc_final: 0.7316 (tpt) REVERT: B 640 MET cc_start: 0.7350 (tpt) cc_final: 0.6916 (tpt) REVERT: D 640 MET cc_start: 0.7676 (tpt) cc_final: 0.7343 (tpt) REVERT: D 645 MET cc_start: 0.5200 (mmm) cc_final: 0.4960 (mpp) REVERT: C 640 MET cc_start: 0.7682 (tpt) cc_final: 0.7346 (tpt) outliers start: 45 outliers final: 30 residues processed: 167 average time/residue: 0.2623 time to fit residues: 68.7923 Evaluate side-chains 155 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 659 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 134 optimal weight: 0.0030 chunk 144 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17656 Z= 0.175 Angle : 0.737 15.375 24012 Z= 0.364 Chirality : 0.043 0.244 2764 Planarity : 0.004 0.046 2984 Dihedral : 5.943 30.297 2392 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.72 % Allowed : 16.09 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -1.07 (0.18), residues: 2196 helix: 0.18 (0.14), residues: 1292 sheet: None (None), residues: 0 loop : -2.03 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 677 HIS 0.004 0.001 HIS A 313 PHE 0.013 0.001 PHE B 199 TYR 0.030 0.001 TYR B 525 ARG 0.003 0.000 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 2.017 Fit side-chains REVERT: A 433 MET cc_start: 0.5982 (ttm) cc_final: 0.5680 (ttp) REVERT: A 607 MET cc_start: 0.3684 (pmm) cc_final: 0.0912 (mpp) REVERT: A 640 MET cc_start: 0.7666 (tpt) cc_final: 0.7333 (tpt) REVERT: B 607 MET cc_start: 0.3687 (pmm) cc_final: 0.0910 (mpp) REVERT: B 640 MET cc_start: 0.7591 (tpt) cc_final: 0.7257 (tpt) REVERT: D 130 ASP cc_start: 0.7266 (t0) cc_final: 0.6945 (t0) REVERT: D 607 MET cc_start: 0.3687 (pmm) cc_final: 0.0912 (mpp) REVERT: D 640 MET cc_start: 0.7586 (tpt) cc_final: 0.7240 (tpt) REVERT: C 607 MET cc_start: 0.3697 (pmm) cc_final: 0.0922 (mpp) REVERT: C 640 MET cc_start: 0.7682 (tpt) cc_final: 0.7319 (tpt) outliers start: 30 outliers final: 30 residues processed: 159 average time/residue: 0.2713 time to fit residues: 67.4818 Evaluate side-chains 155 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 625 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 ASN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17656 Z= 0.268 Angle : 0.804 18.224 24012 Z= 0.400 Chirality : 0.045 0.214 2764 Planarity : 0.005 0.042 2984 Dihedral : 6.291 30.749 2392 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 2.13 % Allowed : 16.32 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.35 (0.18), residues: 2196 helix: -0.06 (0.14), residues: 1288 sheet: None (None), residues: 0 loop : -2.11 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 677 HIS 0.004 0.001 HIS A 293 PHE 0.018 0.002 PHE A 207 TYR 0.032 0.002 TYR C 525 ARG 0.003 0.001 ARG A 517 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 1.975 Fit side-chains REVERT: A 433 MET cc_start: 0.5866 (ttm) cc_final: 0.5530 (ttp) REVERT: A 528 MET cc_start: 0.7202 (ppp) cc_final: 0.6842 (pmm) REVERT: A 640 MET cc_start: 0.7362 (tpt) cc_final: 0.6950 (tpt) REVERT: D 528 MET cc_start: 0.7204 (ppp) cc_final: 0.6868 (pmm) REVERT: D 640 MET cc_start: 0.7327 (tpt) cc_final: 0.6890 (tpt) REVERT: D 645 MET cc_start: 0.5347 (mmm) cc_final: 0.5097 (mpp) REVERT: C 528 MET cc_start: 0.7188 (ppp) cc_final: 0.6819 (pmm) REVERT: C 640 MET cc_start: 0.7231 (tpt) cc_final: 0.6810 (tpt) outliers start: 37 outliers final: 32 residues processed: 168 average time/residue: 0.2715 time to fit residues: 70.8108 Evaluate side-chains 160 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 676 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 676 TRP Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 676 TRP Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 676 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 chunk 201 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17656 Z= 0.219 Angle : 0.775 17.295 24012 Z= 0.381 Chirality : 0.044 0.205 2764 Planarity : 0.005 0.046 2984 Dihedral : 6.108 30.465 2392 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 2.13 % Allowed : 16.90 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.25 (0.18), residues: 2196 helix: 0.03 (0.14), residues: 1288 sheet: None (None), residues: 0 loop : -2.09 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 677 HIS 0.003 0.001 HIS A 165 PHE 0.014 0.001 PHE B 199 TYR 0.030 0.002 TYR C 525 ARG 0.003 0.000 ARG C 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4392 Ramachandran restraints generated. 2196 Oldfield, 0 Emsley, 2196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.993 Fit side-chains REVERT: A 433 MET cc_start: 0.5941 (ttm) cc_final: 0.5578 (ttp) REVERT: A 528 MET cc_start: 0.7205 (ppp) cc_final: 0.6809 (pmm) REVERT: A 645 MET cc_start: 0.5231 (mmm) cc_final: 0.4989 (mpp) REVERT: D 528 MET cc_start: 0.7209 (ppp) cc_final: 0.6820 (pmm) REVERT: D 640 MET cc_start: 0.7267 (tpt) cc_final: 0.6834 (mmm) REVERT: C 640 MET cc_start: 0.7254 (tpt) cc_final: 0.6931 (mmm) outliers start: 37 outliers final: 33 residues processed: 158 average time/residue: 0.2863 time to fit residues: 69.3321 Evaluate side-chains 157 residues out of total 1972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 676 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 619 ARG Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 676 TRP Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain D residue 676 TRP Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 489 LEU Chi-restraints excluded: chain C residue 619 ARG Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 676 TRP 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: 59.611 > 50: distance: 19 - 42: 26.898 distance: 23 - 26: 17.078 distance: 24 - 50: 13.155 distance: 26 - 27: 32.033 distance: 27 - 28: 33.804 distance: 27 - 30: 19.903 distance: 28 - 29: 23.336 distance: 28 - 34: 42.062 distance: 29 - 55: 24.143 distance: 30 - 31: 4.696 distance: 31 - 32: 17.608 distance: 34 - 35: 39.118 distance: 35 - 36: 23.038 distance: 35 - 38: 31.231 distance: 36 - 37: 23.316 distance: 36 - 42: 44.002 distance: 37 - 67: 17.470 distance: 38 - 39: 35.607 distance: 39 - 40: 11.213 distance: 39 - 41: 15.319 distance: 42 - 43: 16.458 distance: 43 - 44: 13.850 distance: 43 - 46: 28.188 distance: 44 - 45: 15.402 distance: 44 - 50: 9.471 distance: 45 - 74: 33.210 distance: 46 - 47: 41.453 distance: 47 - 48: 8.855 distance: 47 - 49: 42.633 distance: 50 - 51: 11.614 distance: 51 - 52: 3.406 distance: 51 - 54: 16.912 distance: 52 - 53: 16.751 distance: 52 - 55: 14.812 distance: 53 - 82: 20.843 distance: 55 - 56: 3.442 distance: 56 - 57: 17.705 distance: 56 - 59: 14.560 distance: 57 - 58: 6.026 distance: 57 - 67: 6.264 distance: 58 - 90: 4.431 distance: 59 - 60: 7.308 distance: 60 - 61: 14.466 distance: 61 - 63: 12.119 distance: 62 - 64: 10.925 distance: 63 - 65: 7.871 distance: 64 - 65: 9.663 distance: 65 - 66: 17.915 distance: 67 - 68: 14.145 distance: 68 - 69: 10.832 distance: 68 - 71: 8.876 distance: 69 - 70: 15.563 distance: 69 - 74: 8.665 distance: 70 - 97: 34.416 distance: 71 - 72: 12.532 distance: 71 - 73: 18.136 distance: 74 - 75: 8.808 distance: 75 - 76: 9.919 distance: 75 - 78: 11.529 distance: 76 - 77: 5.297 distance: 76 - 82: 16.272 distance: 78 - 79: 4.090 distance: 79 - 81: 4.754 distance: 82 - 83: 27.139 distance: 83 - 84: 29.543 distance: 83 - 86: 33.211 distance: 84 - 85: 33.276 distance: 84 - 90: 15.722 distance: 85 - 116: 26.194 distance: 86 - 87: 24.521 distance: 87 - 88: 8.190 distance: 87 - 89: 9.060 distance: 90 - 91: 27.826 distance: 91 - 92: 12.638 distance: 91 - 94: 28.867 distance: 92 - 93: 46.175 distance: 92 - 97: 8.962 distance: 93 - 123: 29.034 distance: 94 - 95: 16.446 distance: 94 - 96: 19.430 distance: 97 - 98: 19.070 distance: 98 - 99: 11.179 distance: 98 - 101: 33.802 distance: 99 - 100: 8.146 distance: 99 - 109: 20.595 distance: 100 - 131: 23.452 distance: 101 - 102: 13.925 distance: 102 - 103: 11.470 distance: 102 - 104: 11.983 distance: 103 - 105: 19.818 distance: 104 - 106: 3.420 distance: 105 - 107: 28.044 distance: 106 - 107: 15.595 distance: 107 - 108: 16.957