Starting phenix.real_space_refine on Sat Dec 9 02:58:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/12_2023/6xlc_22239_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/12_2023/6xlc_22239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/12_2023/6xlc_22239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/12_2023/6xlc_22239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/12_2023/6xlc_22239_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/12_2023/6xlc_22239_updated.pdb" } resolution = 3.66 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= 0.005 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 18 5.16 5 C 6286 2.51 5 N 1620 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 7": "OE1" <-> "OE2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 11": "OE1" <-> "OE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A ASP 455": "OD1" <-> "OD2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 644": "OE1" <-> "OE2" Residue "A GLU 656": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 502": "OD1" <-> "OD2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 523": "OD1" <-> "OD2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ASP 530": "OD1" <-> "OD2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ASP 552": "OD1" <-> "OD2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B ARG 595": "NH1" <-> "NH2" Residue "B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 656": "OE1" <-> "OE2" Residue "B PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9858 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "B" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.41, per 1000 atoms: 0.55 Number of scatterers: 9858 At special positions: 0 Unit cell: (98.487, 92.133, 131.316, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 18 16.00 P 6 15.00 Mg 2 11.99 O 1926 8.00 N 1620 7.00 C 6286 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: 3.57 Conformation dependent library (CDL) restraints added in 1.7 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2324 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 9 sheets defined 37.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 removed outlier: 4.074A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 51 removed outlier: 3.626A pdb=" N LEU A 31 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 48 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 56 Processing helix chain 'A' and resid 88 through 91 No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.566A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 385 through 405 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.834A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 502 through 509 removed outlier: 4.033A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.892A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.899A pdb=" N ARG A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.712A pdb=" N LYS A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.946A pdb=" N ASP A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 638 " --> pdb=" O THR A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 671 Processing helix chain 'B' and resid 12 through 21 removed outlier: 4.447A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 51 removed outlier: 4.072A pdb=" N SER B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 Processing helix chain 'B' and resid 88 through 91 No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.521A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 128 " --> pdb=" O TYR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 384 through 405 Processing helix chain 'B' and resid 408 through 416 Processing helix chain 'B' and resid 418 through 426 Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.790A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.603A pdb=" N THR B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'B' and resid 502 through 509 removed outlier: 4.009A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 540 Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.823A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.573A pdb=" N LYS B 623 " --> pdb=" O LYS B 619 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.858A pdb=" N ASP B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 671 Processing sheet with id= A, first strand: chain 'A' and resid 156 through 160 removed outlier: 7.567A pdb=" N PHE A 176 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 134 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG A 174 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 136 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 172 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER A 138 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY A 170 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 76 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 67 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE A 66 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN A 206 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU A 208 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.512A pdb=" N TYR A 301 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 516 through 519 Processing sheet with id= D, first strand: chain 'A' and resid 561 through 563 removed outlier: 6.446A pdb=" N PHE A 609 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 157 through 160 removed outlier: 3.750A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE B 66 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN B 206 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 208 " --> pdb=" O PRO B 68 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 301 through 307 removed outlier: 3.515A pdb=" N VAL B 364 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 347 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL B 341 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 516 through 519 Processing sheet with id= H, first strand: chain 'B' and resid 561 through 564 removed outlier: 8.947A pdb=" N VAL B 562 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE B 609 " --> pdb=" O VAL B 562 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER B 564 " --> pdb=" O PHE B 609 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 611 " --> pdb=" O SER B 564 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 131 through 134 removed outlier: 7.235A pdb=" N PHE B 176 " --> pdb=" O ASP B 132 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 945 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: 2.89 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3212 1.34 - 1.46: 1542 1.46 - 1.57: 5220 1.57 - 1.69: 10 1.69 - 1.80: 38 Bond restraints: 10022 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O5' ANP B 801 " pdb=" PA ANP B 801 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 10017 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.01: 217 107.01 - 113.75: 5595 113.75 - 120.49: 4035 120.49 - 127.23: 3610 127.23 - 133.97: 69 Bond angle restraints: 13526 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.63 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.73 17.22 3.00e+00 1.11e-01 3.30e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.60 10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.69 10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N ILE A 20 " pdb=" CA ILE A 20 " pdb=" C ILE A 20 " ideal model delta sigma weight residual 113.71 110.65 3.06 9.50e-01 1.11e+00 1.04e+01 ... (remaining 13521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5759 17.80 - 35.60: 330 35.60 - 53.39: 67 53.39 - 71.19: 21 71.19 - 88.99: 15 Dihedral angle restraints: 6192 sinusoidal: 2628 harmonic: 3564 Sorted by residual: dihedral pdb=" CB GLU B 76 " pdb=" CG GLU B 76 " pdb=" CD GLU B 76 " pdb=" OE1 GLU B 76 " ideal model delta sinusoidal sigma weight residual 0.00 -88.99 88.99 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 513 " pdb=" CG GLU B 513 " pdb=" CD GLU B 513 " pdb=" OE1 GLU B 513 " ideal model delta sinusoidal sigma weight residual 0.00 88.90 -88.90 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" O1B ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PB ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sinusoidal sigma weight residual 35.15 -53.13 88.28 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1325 0.055 - 0.109: 188 0.109 - 0.164: 19 0.164 - 0.218: 0 0.218 - 0.273: 2 Chirality restraints: 1534 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1531 not shown) Planarity restraints: 1724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO A 355 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 20 " -0.005 2.00e-02 2.50e+03 9.43e-03 8.90e-01 pdb=" C ILE A 20 " 0.016 2.00e-02 2.50e+03 pdb=" O ILE A 20 " -0.006 2.00e-02 2.50e+03 pdb=" N ASN A 21 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 543 " 0.005 2.00e-02 2.50e+03 6.32e-03 8.00e-01 pdb=" CG TYR B 543 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 543 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 543 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 543 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 543 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 543 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 543 " -0.000 2.00e-02 2.50e+03 ... (remaining 1721 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 133 2.64 - 3.21: 8727 3.21 - 3.77: 15224 3.77 - 4.34: 21757 4.34 - 4.90: 34930 Nonbonded interactions: 80771 Sorted by model distance: nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.079 2.170 nonbonded pdb=" O1B ANP A 801 " pdb="MG MG A 802 " model vdw 2.089 2.170 nonbonded pdb=" O1A ANP B 801 " pdb="MG MG B 802 " model vdw 2.249 2.170 nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.250 2.170 nonbonded pdb=" OH TYR B 456 " pdb=" O GLU B 493 " model vdw 2.255 2.440 ... (remaining 80766 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.910 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: 4.290 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 28.300 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 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 0.144 10022 Z= 0.238 Angle : 0.523 17.324 13526 Z= 0.249 Chirality : 0.039 0.273 1534 Planarity : 0.002 0.029 1724 Dihedral : 12.917 88.987 3868 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.20), residues: 1196 helix: -1.88 (0.19), residues: 492 sheet: -0.99 (0.34), residues: 218 loop : -1.87 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 273 HIS 0.001 0.000 HIS A 197 PHE 0.006 0.001 PHE A 652 TYR 0.016 0.001 TYR B 543 ARG 0.001 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.227 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2808 time to fit residues: 98.2032 Evaluate side-chains 145 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 91 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 431 ASN A 442 ASN A 592 GLN A 673 ASN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 420 ASN B 431 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 10022 Z= 0.279 Angle : 0.635 7.587 13526 Z= 0.326 Chirality : 0.045 0.178 1534 Planarity : 0.004 0.038 1724 Dihedral : 6.551 80.411 1358 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.40 % Allowed : 12.08 % Favored : 85.52 % 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: -1.87 (0.22), residues: 1196 helix: -0.89 (0.22), residues: 498 sheet: -0.83 (0.35), residues: 208 loop : -1.64 (0.23), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 357 HIS 0.003 0.001 HIS B 426 PHE 0.021 0.002 PHE B 652 TYR 0.016 0.002 TYR B 125 ARG 0.005 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 149 average time/residue: 0.2441 time to fit residues: 50.3493 Evaluate side-chains 102 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0956 time to fit residues: 3.9535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10022 Z= 0.154 Angle : 0.486 6.583 13526 Z= 0.248 Chirality : 0.040 0.164 1534 Planarity : 0.003 0.038 1724 Dihedral : 6.144 75.201 1358 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.01 % Allowed : 15.41 % Favored : 83.58 % 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: -1.29 (0.23), residues: 1196 helix: -0.30 (0.24), residues: 496 sheet: -0.76 (0.34), residues: 218 loop : -1.36 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.003 0.001 HIS B 426 PHE 0.011 0.001 PHE B 124 TYR 0.011 0.001 TYR A 441 ARG 0.005 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 108 time to evaluate : 1.138 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 114 average time/residue: 0.2234 time to fit residues: 36.7306 Evaluate side-chains 80 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0924 time to fit residues: 2.4321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.0030 chunk 73 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10022 Z= 0.244 Angle : 0.573 8.989 13526 Z= 0.294 Chirality : 0.043 0.161 1534 Planarity : 0.004 0.042 1724 Dihedral : 6.344 68.827 1358 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.21 % Allowed : 16.61 % Favored : 81.18 % 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: -1.22 (0.23), residues: 1196 helix: -0.23 (0.24), residues: 496 sheet: -0.71 (0.34), residues: 216 loop : -1.34 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 581 HIS 0.005 0.001 HIS B 426 PHE 0.014 0.002 PHE B 609 TYR 0.020 0.002 TYR A 47 ARG 0.006 0.001 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 121 average time/residue: 0.2082 time to fit residues: 37.3395 Evaluate side-chains 98 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0940 time to fit residues: 4.2556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.0060 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10022 Z= 0.147 Angle : 0.479 6.755 13526 Z= 0.244 Chirality : 0.040 0.159 1534 Planarity : 0.003 0.038 1724 Dihedral : 6.094 74.617 1358 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.38 % Allowed : 17.25 % Favored : 81.37 % 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 (0.24), residues: 1196 helix: 0.13 (0.24), residues: 488 sheet: -0.52 (0.36), residues: 216 loop : -1.07 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.001 0.000 HIS A 197 PHE 0.010 0.001 PHE B 313 TYR 0.015 0.001 TYR A 47 ARG 0.005 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.227 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 102 average time/residue: 0.2111 time to fit residues: 32.1544 Evaluate side-chains 84 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0946 time to fit residues: 2.5338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.7627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10022 Z= 0.262 Angle : 0.573 8.295 13526 Z= 0.294 Chirality : 0.043 0.194 1534 Planarity : 0.004 0.044 1724 Dihedral : 6.361 66.687 1358 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.20 % Allowed : 19.37 % Favored : 79.43 % 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 (0.24), residues: 1196 helix: 0.00 (0.24), residues: 480 sheet: -0.58 (0.38), residues: 196 loop : -1.10 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 581 HIS 0.002 0.000 HIS A 426 PHE 0.036 0.002 PHE B 124 TYR 0.013 0.001 TYR A 47 ARG 0.004 0.001 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 1.164 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 100 average time/residue: 0.2689 time to fit residues: 38.3319 Evaluate side-chains 80 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0950 time to fit residues: 2.5525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 84 optimal weight: 0.0060 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.7730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10022 Z= 0.167 Angle : 0.507 7.710 13526 Z= 0.259 Chirality : 0.041 0.160 1534 Planarity : 0.003 0.046 1724 Dihedral : 6.229 69.880 1358 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.65 % Allowed : 20.02 % Favored : 79.34 % 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: -0.74 (0.24), residues: 1196 helix: 0.17 (0.24), residues: 482 sheet: -0.62 (0.38), residues: 196 loop : -0.97 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 148 HIS 0.001 0.000 HIS A 197 PHE 0.028 0.001 PHE B 124 TYR 0.012 0.001 TYR A 47 ARG 0.003 0.000 ARG A 536 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 1.023 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 92 average time/residue: 0.1952 time to fit residues: 27.1028 Evaluate side-chains 74 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.149 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1238 time to fit residues: 1.9669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.7903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10022 Z= 0.161 Angle : 0.504 7.677 13526 Z= 0.258 Chirality : 0.041 0.162 1534 Planarity : 0.004 0.047 1724 Dihedral : 6.139 67.096 1358 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.01 % Allowed : 21.03 % Favored : 77.95 % 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: -0.60 (0.24), residues: 1196 helix: 0.31 (0.25), residues: 482 sheet: -0.67 (0.38), residues: 200 loop : -0.85 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 148 HIS 0.001 0.000 HIS A 197 PHE 0.009 0.001 PHE A 652 TYR 0.007 0.001 TYR B 125 ARG 0.007 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.181 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.2129 time to fit residues: 29.1312 Evaluate side-chains 77 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0939 time to fit residues: 2.9849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.8033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10022 Z= 0.166 Angle : 0.515 7.449 13526 Z= 0.264 Chirality : 0.041 0.154 1534 Planarity : 0.004 0.047 1724 Dihedral : 6.111 68.596 1358 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.46 % Allowed : 21.13 % Favored : 78.41 % 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: -0.46 (0.25), residues: 1196 helix: 0.42 (0.25), residues: 480 sheet: -0.56 (0.38), residues: 200 loop : -0.79 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 148 HIS 0.001 0.000 HIS A 197 PHE 0.009 0.001 PHE A 318 TYR 0.008 0.001 TYR B 125 ARG 0.004 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.066 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.2394 time to fit residues: 27.4771 Evaluate side-chains 68 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0922 time to fit residues: 2.0797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9507 > 50: distance: 40 - 66: 31.654 distance: 47 - 75: 37.040 distance: 58 - 82: 21.444 distance: 62 - 66: 28.573 distance: 63 - 90: 29.538 distance: 66 - 67: 9.038 distance: 67 - 68: 33.094 distance: 67 - 70: 23.543 distance: 68 - 69: 27.409 distance: 68 - 75: 30.985 distance: 69 - 99: 16.064 distance: 70 - 71: 24.031 distance: 72 - 73: 39.830 distance: 72 - 74: 35.216 distance: 75 - 76: 43.924 distance: 76 - 77: 11.955 distance: 76 - 79: 26.568 distance: 77 - 78: 30.195 distance: 77 - 82: 34.722 distance: 78 - 110: 55.765 distance: 79 - 80: 17.470 distance: 79 - 81: 45.017 distance: 82 - 83: 45.748 distance: 83 - 84: 19.648 distance: 83 - 86: 42.003 distance: 84 - 85: 16.798 distance: 84 - 90: 32.897 distance: 86 - 87: 42.222 distance: 87 - 89: 16.847 distance: 90 - 91: 9.429 distance: 91 - 92: 28.822 distance: 91 - 94: 50.572 distance: 92 - 93: 38.236 distance: 92 - 99: 44.282 distance: 94 - 95: 28.803 distance: 95 - 96: 24.689 distance: 96 - 97: 3.463 distance: 99 - 100: 10.702 distance: 100 - 101: 41.041 distance: 100 - 103: 39.913 distance: 101 - 102: 57.738 distance: 101 - 110: 38.793 distance: 103 - 104: 26.127 distance: 104 - 105: 62.154 distance: 105 - 106: 41.882 distance: 106 - 107: 28.903 distance: 107 - 108: 28.159 distance: 107 - 109: 18.632 distance: 110 - 111: 12.766 distance: 111 - 112: 23.113 distance: 111 - 114: 31.213 distance: 112 - 113: 52.793 distance: 112 - 120: 5.964 distance: 114 - 115: 31.304 distance: 115 - 116: 38.772 distance: 115 - 117: 23.054 distance: 116 - 118: 27.517 distance: 117 - 119: 7.256 distance: 118 - 119: 32.803 distance: 120 - 121: 40.894 distance: 121 - 122: 40.509 distance: 121 - 124: 27.159 distance: 122 - 126: 4.531 distance: 124 - 125: 24.929 distance: 126 - 127: 42.951 distance: 127 - 128: 23.481 distance: 127 - 130: 47.427 distance: 128 - 135: 26.286 distance: 130 - 131: 6.158 distance: 131 - 132: 39.336 distance: 132 - 133: 37.719 distance: 132 - 134: 49.738 distance: 135 - 136: 24.190 distance: 136 - 137: 11.262 distance: 136 - 139: 56.944 distance: 137 - 138: 18.797 distance: 137 - 146: 20.820 distance: 139 - 140: 9.217 distance: 140 - 141: 29.520 distance: 140 - 142: 27.588 distance: 141 - 143: 30.113 distance: 142 - 144: 35.288 distance: 143 - 145: 3.654 distance: 144 - 145: 4.607 distance: 146 - 147: 12.602 distance: 147 - 148: 27.711 distance: 147 - 150: 29.764 distance: 148 - 153: 35.210 distance: 150 - 151: 21.561 distance: 150 - 152: 41.518