Starting phenix.real_space_refine on Sat Aug 3 23:39:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snl_40628/08_2024/8snl_40628.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snl_40628/08_2024/8snl_40628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snl_40628/08_2024/8snl_40628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snl_40628/08_2024/8snl_40628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snl_40628/08_2024/8snl_40628.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8snl_40628/08_2024/8snl_40628.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.071 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 Ca 1 9.91 5 Zn 1 6.06 5 S 70 5.16 5 C 5784 2.51 5 N 1550 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 268": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9098 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5167 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 632} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3929 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 467} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1286 SG CYS A 184 23.499 30.046 115.151 1.00 61.20 S Time building chain proxies: 7.28, per 1000 atoms: 0.80 Number of scatterers: 9098 At special positions: 0 Unit cell: (70.21, 112.336, 151.984, 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) Zn 1 29.99 Ca 1 19.99 S 70 16.00 O 1692 8.00 N 1550 7.00 C 5784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 469 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 453 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 502 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 611 " distance=2.03 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 641 " distance=2.03 Simple disulfide: pdb=" SG CYS B 447 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 564 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 606 " distance=2.03 Simple disulfide: pdb=" SG CYS B 579 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.50 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 415 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 409 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 405 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 184 " Number of angles added : 3 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 37.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 32 through 39 removed outlier: 4.071A pdb=" N SER A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.828A pdb=" N ARG A 89 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 153 through 156 removed outlier: 3.757A pdb=" N VAL A 156 " --> pdb=" O TRP A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 243 through 265 Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.508A pdb=" N GLY A 346 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 347 " --> pdb=" O ASP A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 451 through 465 removed outlier: 3.816A pdb=" N SER A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 647 through 658 removed outlier: 3.596A pdb=" N GLN A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 671 through 698 removed outlier: 3.528A pdb=" N SER A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'B' and resid 343 through 349 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 373 through 395 removed outlier: 3.709A pdb=" N TYR B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 451 through 467 removed outlier: 4.049A pdb=" N ASP B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 removed outlier: 3.817A pdb=" N ILE B 537 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 559 through 564 removed outlier: 3.770A pdb=" N CYS B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 590 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 612 removed outlier: 4.062A pdb=" N LYS B 609 " --> pdb=" O HIS B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 631 removed outlier: 3.524A pdb=" N SER B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 660 removed outlier: 4.455A pdb=" N ARG B 653 " --> pdb=" O MET B 649 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP B 654 " --> pdb=" O THR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 683 Processing helix chain 'B' and resid 691 through 709 Processing helix chain 'B' and resid 715 through 735 removed outlier: 4.211A pdb=" N ALA B 719 " --> pdb=" O ARG B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 756 removed outlier: 3.764A pdb=" N HIS B 744 " --> pdb=" O ASP B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 795 Processing helix chain 'B' and resid 801 through 803 No H-bonds generated for 'chain 'B' and resid 801 through 803' Processing helix chain 'B' and resid 804 through 809 removed outlier: 3.879A pdb=" N THR B 808 " --> pdb=" O ILE B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 820 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.829A pdb=" N ARG A 126 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER A 125 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 119 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 removed outlier: 4.355A pdb=" N VAL A 96 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N CYS A 225 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE A 279 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU A 227 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A 281 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU A 334 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS A 226 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS A 336 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 228 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A 338 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 230 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 371 Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA6, first strand: chain 'A' and resid 533 through 535 Processing sheet with id=AA7, first strand: chain 'A' and resid 589 through 590 removed outlier: 4.112A pdb=" N GLU A 589 " --> pdb=" O ARG A 605 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 612 " --> pdb=" O CYS A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 633 through 635 Processing sheet with id=AA9, first strand: chain 'B' and resid 403 through 411 Processing sheet with id=AB1, first strand: chain 'B' and resid 481 through 482 Processing sheet with id=AB2, first strand: chain 'B' and resid 579 through 582 removed outlier: 3.514A pdb=" N TYR B 593 " --> pdb=" O CYS B 572 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 987 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: 2.58 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1669 1.32 - 1.45: 2699 1.45 - 1.59: 4861 1.59 - 1.72: 0 1.72 - 1.85: 84 Bond restraints: 9313 Sorted by residual: bond pdb=" CA HIS A 409 " pdb=" C HIS A 409 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" C GLY A 408 " pdb=" O GLY A 408 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.20e-02 6.94e+03 1.08e+01 bond pdb=" C TRP A 684 " pdb=" O TRP A 684 " ideal model delta sigma weight residual 1.236 1.200 0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" C HIS A 409 " pdb=" O HIS A 409 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.17e-02 7.31e+03 8.26e+00 bond pdb=" C LEU A 407 " pdb=" O LEU A 407 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.26e-02 6.30e+03 7.67e+00 ... (remaining 9308 not shown) Histogram of bond angle deviations from ideal: 96.11 - 103.69: 108 103.69 - 111.26: 3814 111.26 - 118.84: 3626 118.84 - 126.41: 4913 126.41 - 133.99: 157 Bond angle restraints: 12618 Sorted by residual: angle pdb=" N GLY B 517 " pdb=" CA GLY B 517 " pdb=" C GLY B 517 " ideal model delta sigma weight residual 111.09 102.48 8.61 1.33e+00 5.65e-01 4.20e+01 angle pdb=" C ALA A 270 " pdb=" CA ALA A 270 " pdb=" CB ALA A 270 " ideal model delta sigma weight residual 116.54 110.59 5.95 1.15e+00 7.56e-01 2.68e+01 angle pdb=" C ASN A 269 " pdb=" CA ASN A 269 " pdb=" CB ASN A 269 " ideal model delta sigma weight residual 115.79 110.56 5.23 1.19e+00 7.06e-01 1.93e+01 angle pdb=" CA CYS B 564 " pdb=" CB CYS B 564 " pdb=" SG CYS B 564 " ideal model delta sigma weight residual 114.40 124.36 -9.96 2.30e+00 1.89e-01 1.87e+01 angle pdb=" N SER B 516 " pdb=" CA SER B 516 " pdb=" C SER B 516 " ideal model delta sigma weight residual 110.97 115.37 -4.40 1.09e+00 8.42e-01 1.63e+01 ... (remaining 12613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5109 17.72 - 35.44: 408 35.44 - 53.16: 63 53.16 - 70.89: 22 70.89 - 88.61: 9 Dihedral angle restraints: 5611 sinusoidal: 2280 harmonic: 3331 Sorted by residual: dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 604 " pdb=" CB CYS A 604 " ideal model delta sinusoidal sigma weight residual -86.00 -174.61 88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS A 423 " pdb=" SG CYS A 423 " pdb=" SG CYS A 453 " pdb=" CB CYS A 453 " ideal model delta sinusoidal sigma weight residual -86.00 -170.83 84.83 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS A 591 " pdb=" SG CYS A 591 " pdb=" SG CYS A 611 " pdb=" CB CYS A 611 " ideal model delta sinusoidal sigma weight residual -86.00 -150.84 64.84 1 1.00e+01 1.00e-02 5.52e+01 ... (remaining 5608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 995 0.044 - 0.088: 285 0.088 - 0.132: 91 0.132 - 0.176: 7 0.176 - 0.219: 3 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA VAL B 430 " pdb=" N VAL B 430 " pdb=" C VAL B 430 " pdb=" CB VAL B 430 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA SER A 608 " pdb=" N SER A 608 " pdb=" C SER A 608 " pdb=" CB SER A 608 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CG LEU B 491 " pdb=" CB LEU B 491 " pdb=" CD1 LEU B 491 " pdb=" CD2 LEU B 491 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 1378 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 612 " -0.089 5.00e-02 4.00e+02 1.32e-01 2.81e+01 pdb=" N PRO A 613 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO A 613 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 613 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 312 " 0.014 2.00e-02 2.50e+03 1.95e-02 9.53e+00 pdb=" CG TRP A 312 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 312 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 312 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 312 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 312 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 312 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 312 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 312 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 685 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO A 686 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 686 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 686 " -0.042 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 528 2.73 - 3.27: 9418 3.27 - 3.81: 15144 3.81 - 4.36: 19041 4.36 - 4.90: 31856 Nonbonded interactions: 75987 Sorted by model distance: nonbonded pdb=" OE1 GLN B 624 " pdb=" OH TYR B 626 " model vdw 2.183 3.040 nonbonded pdb=" OG1 THR A 62 " pdb=" OD2 ASP B 475 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR A 340 " pdb=" OG1 THR A 393 " model vdw 2.207 3.040 nonbonded pdb=" NH1 ARG A 89 " pdb=" OG1 THR A 116 " model vdw 2.207 3.120 nonbonded pdb=" OG1 THR B 376 " pdb=" OE1 GLU B 656 " model vdw 2.208 3.040 ... (remaining 75982 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.630 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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 : 0.004 0.080 9313 Z= 0.279 Angle : 0.729 9.957 12618 Z= 0.430 Chirality : 0.045 0.219 1381 Planarity : 0.006 0.132 1626 Dihedral : 13.026 83.473 3396 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.70 (0.24), residues: 1141 helix: 0.89 (0.27), residues: 364 sheet: -0.42 (0.46), residues: 121 loop : -1.31 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 312 HIS 0.009 0.001 HIS A 405 PHE 0.015 0.002 PHE A 323 TYR 0.012 0.001 TYR B 797 ARG 0.008 0.001 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8025 (tt0) cc_final: 0.7571 (tt0) REVERT: A 237 ARG cc_start: 0.7258 (ttt180) cc_final: 0.7037 (ttm170) REVERT: A 355 SER cc_start: 0.6951 (m) cc_final: 0.6740 (t) REVERT: A 367 LYS cc_start: 0.6984 (tptp) cc_final: 0.6610 (tmtt) REVERT: A 459 TYR cc_start: 0.7502 (t80) cc_final: 0.7176 (t80) REVERT: A 572 LYS cc_start: 0.6614 (mttm) cc_final: 0.6107 (mtpm) REVERT: A 574 LYS cc_start: 0.6001 (mptt) cc_final: 0.4488 (mtmt) REVERT: A 640 LYS cc_start: 0.6148 (mmtt) cc_final: 0.5537 (ttpt) REVERT: A 643 LYS cc_start: 0.7208 (ptpt) cc_final: 0.6845 (tptp) REVERT: A 653 TRP cc_start: 0.7990 (m100) cc_final: 0.7577 (m100) REVERT: A 666 LYS cc_start: 0.7819 (tttp) cc_final: 0.7573 (tttm) REVERT: B 354 ARG cc_start: 0.4412 (ptp-110) cc_final: 0.4118 (ptt-90) REVERT: B 372 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.6540 (tmt170) REVERT: B 688 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7189 (mm-30) REVERT: B 715 ARG cc_start: 0.6945 (mpt180) cc_final: 0.6466 (mmm160) REVERT: B 773 ARG cc_start: 0.6681 (mtt180) cc_final: 0.5786 (mmt180) REVERT: B 777 LEU cc_start: 0.7075 (tp) cc_final: 0.6558 (mm) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 1.1874 time to fit residues: 283.9672 Evaluate side-chains 132 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 646 GLN B 403 GLN B 425 GLN B 427 ASN B 512 GLN B 556 HIS B 648 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9313 Z= 0.205 Angle : 0.568 9.349 12618 Z= 0.297 Chirality : 0.043 0.141 1381 Planarity : 0.005 0.063 1626 Dihedral : 4.657 24.316 1236 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.48 % Allowed : 9.64 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.40 (0.24), residues: 1141 helix: 1.45 (0.27), residues: 362 sheet: -0.61 (0.44), residues: 128 loop : -1.24 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 312 HIS 0.006 0.001 HIS B 595 PHE 0.013 0.001 PHE A 679 TYR 0.014 0.001 TYR B 797 ARG 0.005 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 147 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7309 (ttt180) cc_final: 0.7089 (ttm170) REVERT: A 367 LYS cc_start: 0.6864 (tptp) cc_final: 0.6481 (tmtt) REVERT: A 406 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 422 GLU cc_start: 0.5768 (OUTLIER) cc_final: 0.5160 (mt-10) REVERT: A 459 TYR cc_start: 0.7547 (t80) cc_final: 0.6337 (t80) REVERT: A 554 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.6008 (pm20) REVERT: A 572 LYS cc_start: 0.6440 (mttm) cc_final: 0.6169 (mtpm) REVERT: A 574 LYS cc_start: 0.5655 (mptt) cc_final: 0.4348 (mttt) REVERT: A 636 ASP cc_start: 0.6298 (t0) cc_final: 0.5931 (t0) REVERT: A 640 LYS cc_start: 0.6690 (mmtt) cc_final: 0.6245 (ttpt) REVERT: A 653 TRP cc_start: 0.7967 (m100) cc_final: 0.7653 (m100) REVERT: A 666 LYS cc_start: 0.7992 (tttp) cc_final: 0.7522 (tttm) REVERT: B 354 ARG cc_start: 0.5073 (ptp-110) cc_final: 0.4484 (ptt90) REVERT: B 372 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.6712 (tmt170) REVERT: B 505 MET cc_start: 0.8327 (ttm) cc_final: 0.8113 (mtp) REVERT: B 566 ILE cc_start: 0.6124 (pt) cc_final: 0.5768 (pt) REVERT: B 654 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.6515 (t0) REVERT: B 688 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7263 (mm-30) REVERT: B 715 ARG cc_start: 0.6776 (mpt180) cc_final: 0.6318 (tpp-160) REVERT: B 726 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7809 (mp) REVERT: B 773 ARG cc_start: 0.6670 (mtt180) cc_final: 0.5822 (mmt180) REVERT: B 777 LEU cc_start: 0.7135 (tp) cc_final: 0.6594 (mm) outliers start: 35 outliers final: 13 residues processed: 174 average time/residue: 1.0497 time to fit residues: 197.6001 Evaluate side-chains 134 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 556 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9313 Z= 0.259 Angle : 0.568 9.398 12618 Z= 0.297 Chirality : 0.044 0.151 1381 Planarity : 0.005 0.052 1626 Dihedral : 4.699 25.077 1236 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.78 % Allowed : 13.32 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.38 (0.24), residues: 1141 helix: 1.49 (0.27), residues: 362 sheet: -0.87 (0.43), residues: 134 loop : -1.17 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 629 HIS 0.005 0.001 HIS B 595 PHE 0.012 0.001 PHE B 668 TYR 0.011 0.001 TYR B 761 ARG 0.004 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: A 302 LYS cc_start: 0.6989 (mmtt) cc_final: 0.6500 (ptpp) REVERT: A 367 LYS cc_start: 0.6903 (tptp) cc_final: 0.6523 (tmtt) REVERT: A 422 GLU cc_start: 0.5694 (OUTLIER) cc_final: 0.5080 (mt-10) REVERT: A 459 TYR cc_start: 0.7382 (t80) cc_final: 0.7101 (t80) REVERT: A 574 LYS cc_start: 0.5613 (mptt) cc_final: 0.4050 (mttt) REVERT: A 640 LYS cc_start: 0.7102 (mmtt) cc_final: 0.6433 (ttpt) REVERT: A 642 GLU cc_start: 0.6625 (pp20) cc_final: 0.6354 (pp20) REVERT: A 653 TRP cc_start: 0.8010 (m100) cc_final: 0.7699 (m100) REVERT: A 666 LYS cc_start: 0.8068 (tttp) cc_final: 0.7578 (ttpp) REVERT: A 682 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.6989 (mp) REVERT: B 354 ARG cc_start: 0.5212 (ptp-110) cc_final: 0.4504 (ptt-90) REVERT: B 372 ARG cc_start: 0.8209 (ttm-80) cc_final: 0.6808 (tmt170) REVERT: B 485 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8044 (ptmm) REVERT: B 566 ILE cc_start: 0.6401 (pt) cc_final: 0.5927 (pt) REVERT: B 666 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7807 (mt) REVERT: B 688 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7388 (mm-30) REVERT: B 715 ARG cc_start: 0.6835 (mpt180) cc_final: 0.6283 (tpp-160) REVERT: B 736 LEU cc_start: 0.7751 (tt) cc_final: 0.7520 (pp) REVERT: B 773 ARG cc_start: 0.6713 (mtt180) cc_final: 0.5853 (mmt180) REVERT: B 777 LEU cc_start: 0.7105 (tp) cc_final: 0.6515 (mm) REVERT: B 821 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7277 (tt0) outliers start: 38 outliers final: 15 residues processed: 164 average time/residue: 1.0573 time to fit residues: 188.1070 Evaluate side-chains 138 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9313 Z= 0.237 Angle : 0.557 8.526 12618 Z= 0.293 Chirality : 0.043 0.152 1381 Planarity : 0.004 0.052 1626 Dihedral : 4.667 25.699 1236 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.47 % Allowed : 15.01 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.38 (0.24), residues: 1141 helix: 1.48 (0.27), residues: 363 sheet: -0.88 (0.44), residues: 128 loop : -1.17 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 629 HIS 0.004 0.001 HIS B 595 PHE 0.013 0.001 PHE B 668 TYR 0.010 0.001 TYR B 761 ARG 0.003 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 121 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7438 (pp20) REVERT: A 106 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: A 190 ASP cc_start: 0.6017 (OUTLIER) cc_final: 0.5751 (t0) REVERT: A 256 ASP cc_start: 0.6845 (m-30) cc_final: 0.6594 (m-30) REVERT: A 302 LYS cc_start: 0.7083 (mmtt) cc_final: 0.6656 (ptpp) REVERT: A 367 LYS cc_start: 0.6919 (tptp) cc_final: 0.6534 (tmtt) REVERT: A 422 GLU cc_start: 0.5728 (OUTLIER) cc_final: 0.5050 (mt-10) REVERT: A 500 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7830 (m) REVERT: A 501 CYS cc_start: 0.6281 (OUTLIER) cc_final: 0.6013 (p) REVERT: A 574 LYS cc_start: 0.5611 (mptt) cc_final: 0.4007 (mttt) REVERT: A 640 LYS cc_start: 0.7129 (mmtt) cc_final: 0.6445 (ttpt) REVERT: A 642 GLU cc_start: 0.6738 (pp20) cc_final: 0.6336 (pp20) REVERT: A 653 TRP cc_start: 0.8042 (m100) cc_final: 0.7679 (m100) REVERT: A 666 LYS cc_start: 0.8082 (tttp) cc_final: 0.7598 (ttpp) REVERT: A 682 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7027 (mp) REVERT: B 354 ARG cc_start: 0.5271 (ptp-110) cc_final: 0.4538 (ptt90) REVERT: B 372 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.6606 (tmt170) REVERT: B 436 ASP cc_start: 0.7941 (m-30) cc_final: 0.7703 (m-30) REVERT: B 620 GLU cc_start: 0.6933 (mm-30) cc_final: 0.6653 (mm-30) REVERT: B 666 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7802 (mt) REVERT: B 688 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7348 (mm-30) REVERT: B 715 ARG cc_start: 0.6796 (mpt180) cc_final: 0.6266 (tpp-160) REVERT: B 736 LEU cc_start: 0.7812 (tt) cc_final: 0.7460 (pp) REVERT: B 773 ARG cc_start: 0.6695 (mtt180) cc_final: 0.5879 (mmt180) REVERT: B 777 LEU cc_start: 0.7066 (tp) cc_final: 0.6568 (mm) outliers start: 45 outliers final: 16 residues processed: 153 average time/residue: 0.8971 time to fit residues: 149.8638 Evaluate side-chains 139 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.0060 chunk 94 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 427 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9313 Z= 0.193 Angle : 0.533 7.648 12618 Z= 0.278 Chirality : 0.043 0.188 1381 Planarity : 0.004 0.051 1626 Dihedral : 4.531 25.759 1236 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.97 % Allowed : 15.21 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.29 (0.24), residues: 1141 helix: 1.53 (0.27), residues: 364 sheet: -0.60 (0.45), residues: 125 loop : -1.15 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.004 0.001 HIS B 595 PHE 0.012 0.001 PHE B 668 TYR 0.022 0.001 TYR B 797 ARG 0.003 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 128 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7307 (tt0) REVERT: A 190 ASP cc_start: 0.6012 (OUTLIER) cc_final: 0.5715 (t0) REVERT: A 256 ASP cc_start: 0.6873 (m-30) cc_final: 0.6575 (m-30) REVERT: A 302 LYS cc_start: 0.7098 (mmtt) cc_final: 0.6600 (ptpp) REVERT: A 367 LYS cc_start: 0.6884 (tptp) cc_final: 0.6540 (tmtt) REVERT: A 422 GLU cc_start: 0.5618 (OUTLIER) cc_final: 0.4943 (mt-10) REVERT: A 524 ASN cc_start: 0.7933 (m110) cc_final: 0.7722 (m-40) REVERT: A 574 LYS cc_start: 0.5466 (mptt) cc_final: 0.3844 (mttt) REVERT: A 640 LYS cc_start: 0.7129 (mmtt) cc_final: 0.6593 (ttpt) REVERT: A 642 GLU cc_start: 0.6778 (pp20) cc_final: 0.6394 (pp20) REVERT: A 653 TRP cc_start: 0.8036 (m100) cc_final: 0.7697 (m100) REVERT: A 666 LYS cc_start: 0.8076 (tttp) cc_final: 0.7589 (ttpp) REVERT: A 682 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7010 (mp) REVERT: B 354 ARG cc_start: 0.5525 (ptp-110) cc_final: 0.4670 (ptt-90) REVERT: B 372 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.6544 (tmt170) REVERT: B 436 ASP cc_start: 0.7957 (m-30) cc_final: 0.7708 (m-30) REVERT: B 666 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7783 (mt) REVERT: B 715 ARG cc_start: 0.6819 (mpt180) cc_final: 0.6264 (tpp-160) REVERT: B 736 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7480 (pp) REVERT: B 773 ARG cc_start: 0.6738 (mtt180) cc_final: 0.5946 (mmt180) REVERT: B 777 LEU cc_start: 0.7052 (tp) cc_final: 0.6551 (mm) outliers start: 50 outliers final: 20 residues processed: 162 average time/residue: 0.9187 time to fit residues: 162.0264 Evaluate side-chains 140 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.0980 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 427 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9313 Z= 0.209 Angle : 0.557 8.036 12618 Z= 0.291 Chirality : 0.044 0.208 1381 Planarity : 0.004 0.050 1626 Dihedral : 4.616 26.557 1236 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.88 % Allowed : 17.59 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.32 (0.24), residues: 1141 helix: 1.48 (0.27), residues: 364 sheet: -0.63 (0.45), residues: 125 loop : -1.15 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.004 0.001 HIS B 561 PHE 0.013 0.001 PHE B 668 TYR 0.010 0.001 TYR A 436 ARG 0.002 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: A 190 ASP cc_start: 0.5963 (OUTLIER) cc_final: 0.5713 (t0) REVERT: A 256 ASP cc_start: 0.6889 (m-30) cc_final: 0.6606 (m-30) REVERT: A 302 LYS cc_start: 0.7186 (mmtt) cc_final: 0.6613 (ptpp) REVERT: A 531 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6725 (mm110) REVERT: A 574 LYS cc_start: 0.5395 (mptt) cc_final: 0.3801 (mttt) REVERT: A 640 LYS cc_start: 0.7163 (mmtt) cc_final: 0.6495 (ttpt) REVERT: A 642 GLU cc_start: 0.6807 (pp20) cc_final: 0.6409 (pp20) REVERT: A 653 TRP cc_start: 0.8010 (m100) cc_final: 0.7646 (m100) REVERT: A 666 LYS cc_start: 0.8077 (tttp) cc_final: 0.7594 (ttpp) REVERT: A 682 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7200 (mp) REVERT: B 354 ARG cc_start: 0.5552 (ptp-110) cc_final: 0.4696 (ptt-90) REVERT: B 372 ARG cc_start: 0.7784 (ttm-80) cc_final: 0.6542 (tmt170) REVERT: B 436 ASP cc_start: 0.7960 (m-30) cc_final: 0.7713 (m-30) REVERT: B 666 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7620 (mp) REVERT: B 715 ARG cc_start: 0.6829 (mpt180) cc_final: 0.6264 (tpp-160) REVERT: B 736 LEU cc_start: 0.7889 (tt) cc_final: 0.7472 (pp) REVERT: B 773 ARG cc_start: 0.6730 (mtt180) cc_final: 0.5948 (mmt180) REVERT: B 777 LEU cc_start: 0.7074 (tp) cc_final: 0.6568 (mm) outliers start: 39 outliers final: 19 residues processed: 150 average time/residue: 0.9485 time to fit residues: 154.7423 Evaluate side-chains 137 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 683 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0538 > 50: distance: 80 - 98: 5.484 distance: 86 - 109: 9.248 distance: 90 - 113: 11.747 distance: 93 - 98: 3.931 distance: 94 - 124: 12.895 distance: 98 - 99: 5.889 distance: 99 - 100: 6.291 distance: 99 - 102: 15.783 distance: 100 - 101: 4.172 distance: 100 - 109: 5.608 distance: 101 - 132: 11.334 distance: 102 - 103: 13.203 distance: 103 - 104: 4.620 distance: 104 - 106: 5.714 distance: 105 - 107: 5.701 distance: 107 - 108: 3.827 distance: 109 - 110: 6.132 distance: 110 - 111: 5.018 distance: 111 - 112: 21.526 distance: 112 - 138: 39.515 distance: 113 - 114: 3.675 distance: 114 - 117: 4.445 distance: 115 - 116: 10.329 distance: 115 - 124: 3.260 distance: 116 - 142: 30.873 distance: 117 - 118: 10.923 distance: 118 - 119: 14.565 distance: 118 - 120: 24.073 distance: 119 - 121: 12.342 distance: 120 - 122: 16.308 distance: 121 - 123: 10.290 distance: 122 - 123: 27.173 distance: 124 - 125: 10.732 distance: 125 - 126: 12.400 distance: 125 - 128: 13.154 distance: 126 - 127: 10.605 distance: 126 - 132: 10.715 distance: 127 - 150: 7.453 distance: 128 - 129: 5.480 distance: 132 - 133: 19.416 distance: 133 - 134: 22.507 distance: 133 - 136: 14.778 distance: 134 - 135: 12.841 distance: 135 - 158: 44.025 distance: 136 - 137: 18.833 distance: 138 - 139: 7.485 distance: 139 - 140: 8.620 distance: 140 - 141: 14.817 distance: 140 - 142: 8.901 distance: 141 - 166: 24.992 distance: 142 - 143: 11.774 distance: 143 - 144: 18.336 distance: 144 - 145: 13.506 distance: 144 - 150: 15.529 distance: 145 - 171: 29.829 distance: 146 - 147: 13.111 distance: 147 - 148: 37.590 distance: 147 - 149: 19.003 distance: 150 - 151: 10.497 distance: 151 - 152: 17.444 distance: 151 - 154: 24.891 distance: 152 - 153: 18.749 distance: 152 - 158: 9.797 distance: 154 - 155: 40.218 distance: 155 - 156: 30.886 distance: 155 - 157: 9.492 distance: 158 - 159: 15.987 distance: 159 - 160: 37.396 distance: 159 - 162: 20.564 distance: 160 - 161: 26.717 distance: 160 - 166: 15.383 distance: 162 - 163: 17.419 distance: 163 - 164: 17.148 distance: 163 - 165: 23.119 distance: 166 - 167: 55.720 distance: 167 - 168: 22.395 distance: 168 - 169: 30.761 distance: 168 - 171: 15.940