Starting phenix.real_space_refine on Sun Apr 7 03:08:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/04_2024/8fwk_29511.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/04_2024/8fwk_29511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/04_2024/8fwk_29511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/04_2024/8fwk_29511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/04_2024/8fwk_29511.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/04_2024/8fwk_29511.pdb" } resolution = 3.5 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= 0.005 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 6072 2.51 5 N 1640 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ARG 685": "NH1" <-> "NH2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B ARG 763": "NH1" <-> "NH2" Residue "B ARG 805": "NH1" <-> "NH2" Residue "B ARG 807": "NH1" <-> "NH2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 648": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 763": "NH1" <-> "NH2" Residue "A ARG 805": "NH1" <-> "NH2" Residue "A ARG 807": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9462 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4731 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 13, 'TRANS': 583} Chain: "A" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4731 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 13, 'TRANS': 583} Time building chain proxies: 5.20, per 1000 atoms: 0.55 Number of scatterers: 9462 At special positions: 0 Unit cell: (104.76, 87.48, 137.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1716 8.00 N 1640 7.00 C 6072 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: 3.55 Conformation dependent library (CDL) restraints added in 1.9 seconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 59.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 261 through 294 removed outlier: 3.500A pdb=" N VAL B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 326 through 353 removed outlier: 4.770A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 390 Processing helix chain 'B' and resid 391 through 408 Processing helix chain 'B' and resid 412 through 458 removed outlier: 3.969A pdb=" N ILE B 416 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 468 through 510 removed outlier: 3.645A pdb=" N GLU B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 516 removed outlier: 3.844A pdb=" N CYS B 516 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 541 removed outlier: 4.081A pdb=" N VAL B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 533 " --> pdb=" O ASP B 529 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 548 removed outlier: 3.765A pdb=" N PHE B 547 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 548 " --> pdb=" O ASN B 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 544 through 548' Processing helix chain 'B' and resid 550 through 567 removed outlier: 3.504A pdb=" N LEU B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 634 removed outlier: 3.660A pdb=" N ILE B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 665 Processing helix chain 'B' and resid 680 through 685 removed outlier: 3.546A pdb=" N ARG B 685 " --> pdb=" O ALA B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 705 through 710 Processing helix chain 'B' and resid 729 through 742 removed outlier: 4.086A pdb=" N GLN B 733 " --> pdb=" O GLY B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 770 removed outlier: 4.121A pdb=" N GLU B 762 " --> pdb=" O ASP B 758 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA B 767 " --> pdb=" O ARG B 763 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 261 through 294 removed outlier: 3.876A pdb=" N VAL A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 326 through 353 removed outlier: 4.770A pdb=" N ARG A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 390 Processing helix chain 'A' and resid 391 through 408 Processing helix chain 'A' and resid 412 through 458 removed outlier: 3.970A pdb=" N ILE A 416 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 468 through 510 removed outlier: 3.645A pdb=" N GLU A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.845A pdb=" N CYS A 516 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 541 removed outlier: 4.080A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.764A pdb=" N PHE A 547 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 548 " --> pdb=" O ASN A 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 544 through 548' Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.504A pdb=" N LEU A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 637 removed outlier: 4.335A pdb=" N ARG A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 680 through 685 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 705 through 710 Processing helix chain 'A' and resid 729 through 742 removed outlier: 4.086A pdb=" N GLN A 733 " --> pdb=" O GLY A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 770 removed outlier: 4.120A pdb=" N GLU A 762 " --> pdb=" O ASP A 758 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 817 through 829 Processing sheet with id=AA1, first strand: chain 'B' and resid 590 through 591 Processing sheet with id=AA2, first strand: chain 'B' and resid 617 through 620 removed outlier: 5.516A pdb=" N GLN B 617 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 780 " --> pdb=" O GLN B 617 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU B 619 " --> pdb=" O VAL B 780 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 591 Processing sheet with id=AA4, first strand: chain 'A' and resid 617 through 620 removed outlier: 5.517A pdb=" N GLN A 617 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 780 " --> pdb=" O GLN A 617 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 619 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 748 " --> pdb=" O ILE A 779 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N VAL A 781 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU A 750 " --> pdb=" O VAL A 781 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1431 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: 2.56 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1520 1.30 - 1.43: 2556 1.43 - 1.55: 5510 1.55 - 1.68: 6 1.68 - 1.81: 56 Bond restraints: 9648 Sorted by residual: bond pdb=" C TRP B 360 " pdb=" O TRP B 360 " ideal model delta sigma weight residual 1.235 1.170 0.065 1.33e-02 5.65e+03 2.42e+01 bond pdb=" CA TRP B 360 " pdb=" C TRP B 360 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.56e-02 4.11e+03 1.90e+01 bond pdb=" N ARG B 364 " pdb=" CA ARG B 364 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.30e+01 bond pdb=" C HIS B 361 " pdb=" O HIS B 361 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.47e-02 4.63e+03 9.40e+00 bond pdb=" CA HIS B 361 " pdb=" CB HIS B 361 " ideal model delta sigma weight residual 1.531 1.486 0.045 1.62e-02 3.81e+03 7.62e+00 ... (remaining 9643 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.28: 166 106.28 - 113.39: 5100 113.39 - 120.50: 4356 120.50 - 127.61: 3368 127.61 - 134.72: 92 Bond angle restraints: 13082 Sorted by residual: angle pdb=" N ARG B 359 " pdb=" CA ARG B 359 " pdb=" C ARG B 359 " ideal model delta sigma weight residual 111.28 100.04 11.24 1.09e+00 8.42e-01 1.06e+02 angle pdb=" N ILE A 632 " pdb=" CA ILE A 632 " pdb=" C ILE A 632 " ideal model delta sigma weight residual 110.62 119.69 -9.07 1.02e+00 9.61e-01 7.90e+01 angle pdb=" N GLY A 687 " pdb=" CA GLY A 687 " pdb=" C GLY A 687 " ideal model delta sigma weight residual 112.73 120.21 -7.48 1.20e+00 6.94e-01 3.88e+01 angle pdb=" N LEU B 750 " pdb=" CA LEU B 750 " pdb=" C LEU B 750 " ideal model delta sigma weight residual 110.23 101.25 8.98 1.45e+00 4.76e-01 3.84e+01 angle pdb=" N ARG B 688 " pdb=" CA ARG B 688 " pdb=" C ARG B 688 " ideal model delta sigma weight residual 111.14 117.73 -6.59 1.08e+00 8.57e-01 3.72e+01 ... (remaining 13077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 5245 15.16 - 30.32: 312 30.32 - 45.48: 95 45.48 - 60.64: 16 60.64 - 75.81: 20 Dihedral angle restraints: 5688 sinusoidal: 2256 harmonic: 3432 Sorted by residual: dihedral pdb=" C HIS B 361 " pdb=" N HIS B 361 " pdb=" CA HIS B 361 " pdb=" CB HIS B 361 " ideal model delta harmonic sigma weight residual -122.60 -138.34 15.74 0 2.50e+00 1.60e-01 3.96e+01 dihedral pdb=" N HIS B 361 " pdb=" C HIS B 361 " pdb=" CA HIS B 361 " pdb=" CB HIS B 361 " ideal model delta harmonic sigma weight residual 122.80 138.44 -15.64 0 2.50e+00 1.60e-01 3.91e+01 dihedral pdb=" CA ARG B 685 " pdb=" C ARG B 685 " pdb=" N TYR B 686 " pdb=" CA TYR B 686 " ideal model delta harmonic sigma weight residual -180.00 -155.58 -24.42 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 1468 0.159 - 0.319: 30 0.319 - 0.478: 3 0.478 - 0.637: 0 0.637 - 0.797: 1 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA HIS B 361 " pdb=" N HIS B 361 " pdb=" C HIS B 361 " pdb=" CB HIS B 361 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA LEU A 356 " pdb=" N LEU A 356 " pdb=" C LEU A 356 " pdb=" CB LEU A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA SER B 357 " pdb=" N SER B 357 " pdb=" C SER B 357 " pdb=" CB SER B 357 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 1499 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 687 " 0.028 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C GLY B 687 " -0.096 2.00e-02 2.50e+03 pdb=" O GLY B 687 " 0.036 2.00e-02 2.50e+03 pdb=" N ARG B 688 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 356 " 0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C LEU B 356 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU B 356 " 0.030 2.00e-02 2.50e+03 pdb=" N SER B 357 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 360 " 0.022 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C TRP B 360 " -0.073 2.00e-02 2.50e+03 pdb=" O TRP B 360 " 0.027 2.00e-02 2.50e+03 pdb=" N HIS B 361 " 0.024 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2620 2.81 - 3.33: 9011 3.33 - 3.86: 15034 3.86 - 4.38: 16342 4.38 - 4.90: 27933 Nonbonded interactions: 70940 Sorted by model distance: nonbonded pdb=" O THR B 323 " pdb=" OG SER B 327 " model vdw 2.289 2.440 nonbonded pdb=" O THR A 323 " pdb=" OG SER A 327 " model vdw 2.290 2.440 nonbonded pdb=" O GLY B 588 " pdb=" OG1 THR B 777 " model vdw 2.296 2.440 nonbonded pdb=" O GLY A 588 " pdb=" OG1 THR A 777 " model vdw 2.296 2.440 nonbonded pdb=" O GLY A 692 " pdb=" CB ASN A 693 " model vdw 2.305 3.440 ... (remaining 70935 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: 1.000 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: 5.430 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.510 Find NCS groups from input model: 0.510 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9648 Z= 0.309 Angle : 1.070 11.590 13082 Z= 0.619 Chirality : 0.065 0.797 1502 Planarity : 0.007 0.056 1658 Dihedral : 12.403 75.806 3492 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 1.18 % Allowed : 11.60 % Favored : 87.23 % Rotamer: Outliers : 1.29 % Allowed : 2.38 % Favored : 96.34 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.18), residues: 1190 helix: -2.26 (0.15), residues: 696 sheet: -1.84 (1.02), residues: 24 loop : -4.34 (0.20), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 360 HIS 0.009 0.001 HIS B 352 PHE 0.017 0.002 PHE A 611 TYR 0.024 0.002 TYR B 536 ARG 0.004 0.000 ARG A 807 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 209 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 599 TYR cc_start: 0.5351 (m-10) cc_final: 0.4387 (m-10) REVERT: B 614 MET cc_start: 0.7748 (ptp) cc_final: 0.7409 (tmm) REVERT: B 710 MET cc_start: 0.5602 (mmp) cc_final: 0.5383 (mmp) REVERT: B 775 ASN cc_start: 0.7737 (m-40) cc_final: 0.7513 (t0) REVERT: A 274 LEU cc_start: 0.8346 (tp) cc_final: 0.8122 (tp) REVERT: A 530 TYR cc_start: 0.8701 (t80) cc_final: 0.8059 (t80) REVERT: A 553 MET cc_start: 0.8271 (mmp) cc_final: 0.8037 (ttm) REVERT: A 561 MET cc_start: 0.7879 (tmm) cc_final: 0.7626 (tmm) REVERT: A 614 MET cc_start: 0.7702 (ptp) cc_final: 0.7470 (ptt) REVERT: A 775 ASN cc_start: 0.8139 (m-40) cc_final: 0.7824 (t0) outliers start: 13 outliers final: 4 residues processed: 217 average time/residue: 0.2610 time to fit residues: 75.5297 Evaluate side-chains 111 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 92 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 6.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 HIS B 410 ASN B 445 GLN B 484 GLN B 683 ASN B 693 ASN ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 HIS B 823 GLN A 410 ASN A 445 GLN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9648 Z= 0.171 Angle : 0.682 10.166 13082 Z= 0.354 Chirality : 0.042 0.172 1502 Planarity : 0.004 0.034 1658 Dihedral : 5.828 48.715 1330 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.59 % Favored : 88.82 % Rotamer: Outliers : 3.17 % Allowed : 12.48 % Favored : 84.36 % 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: -2.73 (0.22), residues: 1190 helix: -0.44 (0.19), residues: 688 sheet: -2.00 (0.72), residues: 44 loop : -4.05 (0.23), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 822 HIS 0.004 0.001 HIS A 352 PHE 0.018 0.001 PHE A 597 TYR 0.029 0.002 TYR B 716 ARG 0.004 0.000 ARG B 814 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 614 MET cc_start: 0.7639 (ptp) cc_final: 0.7283 (tmm) REVERT: B 775 ASN cc_start: 0.7709 (m-40) cc_final: 0.7476 (t0) REVERT: A 239 TRP cc_start: 0.3718 (p90) cc_final: 0.3407 (p90) REVERT: A 530 TYR cc_start: 0.8457 (t80) cc_final: 0.8228 (t80) REVERT: A 561 MET cc_start: 0.8207 (tmm) cc_final: 0.7883 (tmm) REVERT: A 775 ASN cc_start: 0.8099 (m-40) cc_final: 0.7768 (t0) outliers start: 32 outliers final: 19 residues processed: 128 average time/residue: 0.2097 time to fit residues: 38.5326 Evaluate side-chains 106 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 684 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 106 optimal weight: 0.0270 chunk 36 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 GLN ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9648 Z= 0.175 Angle : 0.654 10.245 13082 Z= 0.341 Chirality : 0.042 0.166 1502 Planarity : 0.004 0.027 1658 Dihedral : 5.190 46.801 1324 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.92 % Favored : 88.57 % Rotamer: Outliers : 3.37 % Allowed : 13.86 % Favored : 82.77 % 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: -1.78 (0.24), residues: 1190 helix: 0.46 (0.20), residues: 688 sheet: -1.47 (0.77), residues: 44 loop : -3.90 (0.24), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 360 HIS 0.003 0.001 HIS A 352 PHE 0.012 0.001 PHE A 409 TYR 0.019 0.001 TYR B 716 ARG 0.013 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 87 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 MET cc_start: 0.8383 (tmm) cc_final: 0.7874 (tmm) REVERT: B 346 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8073 (tm-30) REVERT: B 361 HIS cc_start: 0.8403 (OUTLIER) cc_final: 0.8043 (m-70) REVERT: B 487 GLU cc_start: 0.8680 (pp20) cc_final: 0.7995 (pp20) REVERT: B 775 ASN cc_start: 0.7832 (m-40) cc_final: 0.7519 (t0) REVERT: A 530 TYR cc_start: 0.8558 (t80) cc_final: 0.8334 (t80) REVERT: A 561 MET cc_start: 0.8396 (tmm) cc_final: 0.7990 (tmm) REVERT: A 589 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6117 (tpp-160) REVERT: A 614 MET cc_start: 0.6975 (ptt) cc_final: 0.6761 (ppp) REVERT: A 751 ASP cc_start: 0.7675 (p0) cc_final: 0.7376 (p0) REVERT: A 775 ASN cc_start: 0.8236 (m-40) cc_final: 0.7789 (t0) outliers start: 34 outliers final: 16 residues processed: 113 average time/residue: 0.2116 time to fit residues: 34.6241 Evaluate side-chains 96 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 361 HIS Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 589 ARG Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.3980 chunk 80 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN B 656 GLN B 683 ASN A 354 HIS A 484 GLN A 656 GLN ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9648 Z= 0.317 Angle : 0.752 10.036 13082 Z= 0.392 Chirality : 0.046 0.164 1502 Planarity : 0.004 0.069 1658 Dihedral : 5.697 47.974 1324 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.44 % Favored : 87.14 % Rotamer: Outliers : 4.55 % Allowed : 14.26 % Favored : 81.19 % 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: -1.59 (0.24), residues: 1190 helix: 0.72 (0.20), residues: 676 sheet: -1.72 (0.98), residues: 24 loop : -3.79 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 488 HIS 0.005 0.001 HIS A 352 PHE 0.019 0.002 PHE A 409 TYR 0.014 0.002 TYR B 716 ARG 0.006 0.001 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 74 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 272 MET cc_start: 0.8448 (tmm) cc_final: 0.7976 (tmm) REVERT: B 346 GLU cc_start: 0.8644 (tm-30) cc_final: 0.7975 (tm-30) REVERT: B 474 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: B 584 ARG cc_start: 0.7816 (tpt90) cc_final: 0.7369 (mtm-85) REVERT: B 751 ASP cc_start: 0.7130 (t0) cc_final: 0.6898 (t0) REVERT: B 775 ASN cc_start: 0.8209 (m-40) cc_final: 0.7837 (t0) REVERT: A 239 TRP cc_start: 0.3969 (p90) cc_final: 0.3591 (p90) REVERT: A 561 MET cc_start: 0.8482 (tmm) cc_final: 0.8060 (tmm) REVERT: A 585 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6214 (m-80) outliers start: 46 outliers final: 25 residues processed: 111 average time/residue: 0.2007 time to fit residues: 32.1910 Evaluate side-chains 88 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 61 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 1 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9648 Z= 0.192 Angle : 0.654 9.413 13082 Z= 0.340 Chirality : 0.042 0.156 1502 Planarity : 0.003 0.029 1658 Dihedral : 5.193 35.341 1322 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.34 % Favored : 88.24 % Rotamer: Outliers : 4.16 % Allowed : 16.24 % Favored : 79.60 % 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: -1.30 (0.24), residues: 1190 helix: 0.99 (0.20), residues: 678 sheet: -1.51 (0.96), residues: 24 loop : -3.74 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 488 HIS 0.010 0.001 HIS A 354 PHE 0.016 0.001 PHE B 597 TYR 0.014 0.001 TYR B 530 ARG 0.006 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 77 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 272 MET cc_start: 0.8406 (tmm) cc_final: 0.7854 (tmm) REVERT: B 275 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8229 (tm-30) REVERT: B 346 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8158 (tm-30) REVERT: B 474 GLU cc_start: 0.8185 (pp20) cc_final: 0.7910 (tp30) REVERT: B 487 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8101 (pp20) REVERT: B 584 ARG cc_start: 0.7794 (tpt90) cc_final: 0.7363 (mtm-85) REVERT: B 751 ASP cc_start: 0.7051 (t0) cc_final: 0.6845 (t0) REVERT: B 775 ASN cc_start: 0.8277 (m-40) cc_final: 0.7834 (t0) REVERT: A 561 MET cc_start: 0.8520 (tmm) cc_final: 0.8160 (tmm) REVERT: A 751 ASP cc_start: 0.7524 (p0) cc_final: 0.7266 (p0) outliers start: 42 outliers final: 25 residues processed: 109 average time/residue: 0.2459 time to fit residues: 37.7873 Evaluate side-chains 94 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 68 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 406 SER Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.0370 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 66 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9648 Z= 0.150 Angle : 0.630 10.085 13082 Z= 0.323 Chirality : 0.041 0.149 1502 Planarity : 0.003 0.032 1658 Dihedral : 4.866 34.295 1322 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.68 % Favored : 87.90 % Rotamer: Outliers : 2.97 % Allowed : 18.32 % Favored : 78.71 % 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: -1.08 (0.25), residues: 1190 helix: 1.04 (0.20), residues: 694 sheet: -1.21 (0.78), residues: 44 loop : -3.68 (0.24), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 360 HIS 0.003 0.001 HIS A 352 PHE 0.014 0.001 PHE B 597 TYR 0.016 0.001 TYR A 716 ARG 0.004 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 84 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 239 TRP cc_start: 0.4196 (p90) cc_final: 0.3926 (p90) REVERT: B 272 MET cc_start: 0.8407 (tmm) cc_final: 0.7790 (tmm) REVERT: B 275 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8166 (tm-30) REVERT: B 346 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 487 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7951 (pp20) REVERT: B 751 ASP cc_start: 0.7061 (t0) cc_final: 0.6853 (t0) REVERT: B 775 ASN cc_start: 0.8191 (m-40) cc_final: 0.7699 (t0) REVERT: A 239 TRP cc_start: 0.3826 (p90) cc_final: 0.3548 (p90) REVERT: A 487 GLU cc_start: 0.8714 (pp20) cc_final: 0.8202 (pp20) REVERT: A 541 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.6989 (t80) REVERT: A 561 MET cc_start: 0.8554 (tmm) cc_final: 0.8128 (tmm) REVERT: A 751 ASP cc_start: 0.7463 (p0) cc_final: 0.7172 (p0) outliers start: 30 outliers final: 17 residues processed: 106 average time/residue: 0.2009 time to fit residues: 31.0668 Evaluate side-chains 88 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 69 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 783 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9648 Z= 0.161 Angle : 0.631 10.471 13082 Z= 0.323 Chirality : 0.041 0.150 1502 Planarity : 0.003 0.049 1658 Dihedral : 4.785 32.720 1322 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.67 % Favored : 88.91 % Rotamer: Outliers : 2.97 % Allowed : 18.42 % Favored : 78.61 % 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: -1.00 (0.25), residues: 1190 helix: 1.12 (0.20), residues: 694 sheet: -0.49 (1.11), residues: 20 loop : -3.62 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 360 HIS 0.003 0.001 HIS A 352 PHE 0.013 0.001 PHE A 592 TYR 0.018 0.001 TYR B 530 ARG 0.006 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 73 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 239 TRP cc_start: 0.4223 (p90) cc_final: 0.3941 (p90) REVERT: B 272 MET cc_start: 0.8416 (tmm) cc_final: 0.7803 (tmm) REVERT: B 275 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 346 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 487 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7967 (pp20) REVERT: B 751 ASP cc_start: 0.7060 (t0) cc_final: 0.6851 (t0) REVERT: B 763 ARG cc_start: 0.7550 (mmm160) cc_final: 0.7217 (ptp-170) REVERT: B 775 ASN cc_start: 0.8250 (m-40) cc_final: 0.7751 (t0) REVERT: A 239 TRP cc_start: 0.3878 (p90) cc_final: 0.3597 (p90) REVERT: A 272 MET cc_start: 0.8156 (tmm) cc_final: 0.7683 (tmm) REVERT: A 487 GLU cc_start: 0.8730 (pp20) cc_final: 0.8112 (pp20) REVERT: A 561 MET cc_start: 0.8617 (tmm) cc_final: 0.8131 (tmm) REVERT: A 592 PHE cc_start: 0.5220 (OUTLIER) cc_final: 0.5012 (t80) REVERT: A 751 ASP cc_start: 0.7484 (p0) cc_final: 0.7218 (p0) outliers start: 30 outliers final: 19 residues processed: 97 average time/residue: 0.2033 time to fit residues: 29.0371 Evaluate side-chains 91 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 360 TRP Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 640 TYR Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 823 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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: 67.8067 > 50: distance: 56 - 60: 3.306 distance: 94 - 119: 30.607 distance: 98 - 123: 32.239 distance: 102 - 108: 28.357 distance: 103 - 130: 26.342 distance: 108 - 109: 21.762 distance: 109 - 110: 27.958 distance: 109 - 112: 34.815 distance: 110 - 111: 25.818 distance: 110 - 119: 25.786 distance: 111 - 142: 37.951 distance: 112 - 113: 15.788 distance: 113 - 114: 7.048 distance: 113 - 115: 15.254 distance: 114 - 116: 44.873 distance: 115 - 117: 35.828 distance: 116 - 118: 16.528 distance: 117 - 118: 8.893 distance: 119 - 120: 30.671 distance: 120 - 121: 26.832 distance: 121 - 122: 29.929 distance: 121 - 123: 38.561 distance: 123 - 124: 5.366 distance: 124 - 125: 33.976 distance: 124 - 127: 35.013 distance: 125 - 126: 32.725 distance: 125 - 130: 32.431 distance: 126 - 158: 43.471 distance: 127 - 128: 23.184 distance: 127 - 129: 38.840 distance: 130 - 131: 22.764 distance: 131 - 132: 20.873 distance: 131 - 134: 12.149 distance: 132 - 133: 12.415 distance: 132 - 142: 16.576 distance: 133 - 167: 67.807 distance: 134 - 135: 8.083 distance: 135 - 136: 13.064 distance: 135 - 137: 13.875 distance: 136 - 138: 17.547 distance: 137 - 139: 10.832 distance: 138 - 140: 9.159 distance: 139 - 140: 4.506 distance: 140 - 141: 13.137 distance: 142 - 143: 21.811 distance: 143 - 144: 9.354 distance: 143 - 146: 15.410 distance: 144 - 145: 30.882 distance: 144 - 150: 20.051 distance: 145 - 175: 40.722 distance: 146 - 147: 15.292 distance: 146 - 148: 36.799 distance: 147 - 149: 20.583 distance: 150 - 151: 11.626 distance: 151 - 152: 15.053 distance: 151 - 154: 14.704 distance: 152 - 153: 10.678 distance: 152 - 158: 40.176 distance: 154 - 155: 27.594 distance: 154 - 156: 33.860 distance: 155 - 157: 27.451 distance: 158 - 159: 26.511 distance: 159 - 160: 22.355 distance: 159 - 162: 31.289 distance: 160 - 161: 8.858 distance: 160 - 167: 28.637 distance: 162 - 163: 16.791 distance: 163 - 164: 24.474 distance: 164 - 165: 34.458 distance: 164 - 166: 33.710 distance: 167 - 168: 19.396 distance: 168 - 169: 34.855 distance: 168 - 171: 23.006 distance: 169 - 170: 23.543 distance: 169 - 175: 44.556 distance: 171 - 172: 32.485 distance: 172 - 173: 32.570 distance: 172 - 174: 26.025 distance: 175 - 176: 20.241 distance: 176 - 177: 10.646 distance: 176 - 179: 17.002 distance: 177 - 178: 14.578 distance: 177 - 187: 32.840 distance: 179 - 180: 9.909 distance: 180 - 181: 13.870 distance: 180 - 182: 12.186 distance: 181 - 183: 27.917 distance: 182 - 184: 9.449 distance: 183 - 185: 6.079 distance: 184 - 185: 24.948 distance: 185 - 186: 29.340 distance: 187 - 188: 4.152 distance: 188 - 189: 32.692 distance: 188 - 191: 9.208 distance: 189 - 190: 27.772 distance: 189 - 195: 17.434 distance: 191 - 192: 45.085 distance: 192 - 193: 16.427 distance: 193 - 194: 47.313