Starting phenix.real_space_refine on Thu Jun 12 04:51:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ho8_34922/06_2025/8ho8_34922_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ho8_34922/06_2025/8ho8_34922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ho8_34922/06_2025/8ho8_34922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ho8_34922/06_2025/8ho8_34922.map" model { file = "/net/cci-nas-00/data/ceres_data/8ho8_34922/06_2025/8ho8_34922_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ho8_34922/06_2025/8ho8_34922_neut.cif" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 52 5.16 5 C 8418 2.51 5 N 2184 2.21 5 O 2800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13454 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6550 Classifications: {'peptide': 809} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 779} Chain: "B" Number of atoms: 6549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6549 Classifications: {'peptide': 809} Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 779} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'BGC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 158 Classifications: {'water': 158} Link IDs: {None: 157} Chain: "B" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Classifications: {'water': 151} Link IDs: {None: 150} Time building chain proxies: 9.58, per 1000 atoms: 0.71 Number of scatterers: 13454 At special positions: 0 Unit cell: (145.25, 92.13, 97.11, 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 52 16.00 O 2800 8.00 N 2184 7.00 C 8418 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 - 3.00 Amino acid : True - 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 Links applied BETA1-4 " BGC C 1 " - " BGC C 2 " " BGC D 1 " - " BGC D 2 " Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 2.5 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 26 sheets defined 33.7% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 156 through 163 Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.867A pdb=" N PHE A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 313 Processing helix chain 'A' and resid 321 through 330 Processing helix chain 'A' and resid 330 through 343 Processing helix chain 'A' and resid 359 through 370 removed outlier: 3.685A pdb=" N LEU A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 387 removed outlier: 3.721A pdb=" N THR A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.914A pdb=" N TRP A 419 " --> pdb=" O ASP A 415 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 421 " --> pdb=" O PRO A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 removed outlier: 4.012A pdb=" N ILE A 436 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 3.707A pdb=" N VAL A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 532 removed outlier: 3.954A pdb=" N LYS A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 Processing helix chain 'A' and resid 585 through 594 Processing helix chain 'A' and resid 601 through 614 Processing helix chain 'A' and resid 636 through 640 removed outlier: 3.823A pdb=" N TYR A 640 " --> pdb=" O ILE A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 removed outlier: 3.837A pdb=" N ALA A 656 " --> pdb=" O CYS A 652 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP A 657 " --> pdb=" O HIS A 653 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 679 removed outlier: 4.082A pdb=" N ILE A 678 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 719 through 730 Processing helix chain 'B' and resid 156 through 163 Processing helix chain 'B' and resid 163 through 168 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 222 through 228 Processing helix chain 'B' and resid 268 through 271 Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.853A pdb=" N PHE B 291 " --> pdb=" O MET B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 312 Processing helix chain 'B' and resid 321 through 330 Processing helix chain 'B' and resid 330 through 343 Processing helix chain 'B' and resid 359 through 370 removed outlier: 3.760A pdb=" N LEU B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 368 " --> pdb=" O GLN B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 387 removed outlier: 3.730A pdb=" N THR B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.922A pdb=" N TRP B 419 " --> pdb=" O ASP B 415 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU B 420 " --> pdb=" O ASP B 416 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 421 " --> pdb=" O PRO B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 removed outlier: 3.998A pdb=" N ILE B 436 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 removed outlier: 4.033A pdb=" N VAL B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 512 through 532 removed outlier: 3.921A pdb=" N LYS B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP B 524 " --> pdb=" O PHE B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 585 through 594 Processing helix chain 'B' and resid 601 through 614 Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.828A pdb=" N TYR B 640 " --> pdb=" O ILE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 665 removed outlier: 3.733A pdb=" N ALA B 656 " --> pdb=" O CYS B 652 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TRP B 657 " --> pdb=" O HIS B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 677 Processing helix chain 'B' and resid 679 through 684 Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 719 through 730 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.677A pdb=" N SER A 94 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 56 removed outlier: 5.628A pdb=" N ILE A 55 " --> pdb=" O CYS A 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 56 removed outlier: 5.628A pdb=" N ILE A 55 " --> pdb=" O CYS A 153 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS A 244 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER A 207 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N SER A 243 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE A 205 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.856A pdb=" N VAL A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 315 through 318 Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 440 through 443 removed outlier: 5.753A pdb=" N LYS A 449 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 510 through 511 Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 584 Processing sheet with id=AB2, first strand: chain 'A' and resid 615 through 616 Processing sheet with id=AB3, first strand: chain 'A' and resid 650 through 651 removed outlier: 6.442A pdb=" N ALA A 698 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N SER A 715 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 735 through 738 removed outlier: 3.889A pdb=" N LEU A 742 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.636A pdb=" N SER B 94 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 25 through 28 Processing sheet with id=AB7, first strand: chain 'B' and resid 54 through 56 removed outlier: 5.622A pdb=" N ILE B 55 " --> pdb=" O CYS B 153 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 54 through 56 removed outlier: 5.622A pdb=" N ILE B 55 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS B 244 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N SER B 207 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER B 243 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE B 205 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.850A pdb=" N VAL B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 315 through 318 removed outlier: 4.811A pdb=" N ILE B 783 " --> pdb=" O ILE B 790 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 357 through 358 Processing sheet with id=AC3, first strand: chain 'B' and resid 440 through 443 removed outlier: 5.728A pdb=" N LYS B 449 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 510 through 511 Processing sheet with id=AC5, first strand: chain 'B' and resid 583 through 584 Processing sheet with id=AC6, first strand: chain 'B' and resid 615 through 616 Processing sheet with id=AC7, first strand: chain 'B' and resid 650 through 651 removed outlier: 6.446A pdb=" N ALA B 698 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER B 715 " --> pdb=" O ALA B 698 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 735 through 738 removed outlier: 3.949A pdb=" N LEU B 742 " --> pdb=" O LEU B 795 " (cutoff:3.500A) 591 hydrogen bonds defined for protein. 1650 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: 9.99 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: 1.22 - 1.34: 4238 1.34 - 1.46: 3223 1.46 - 1.58: 5948 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 13491 Sorted by residual: bond pdb=" CB THR B 20 " pdb=" CG2 THR B 20 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.44e+00 bond pdb=" C5 BGC D 1 " pdb=" O5 BGC D 1 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C5 BGC D 2 " pdb=" O5 BGC D 2 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C5 BGC C 1 " pdb=" O5 BGC C 1 " ideal model delta sigma weight residual 1.411 1.434 -0.023 2.00e-02 2.50e+03 1.35e+00 bond pdb=" C5 BGC C 2 " pdb=" O5 BGC C 2 " ideal model delta sigma weight residual 1.411 1.433 -0.022 2.00e-02 2.50e+03 1.25e+00 ... (remaining 13486 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 17482 1.28 - 2.56: 606 2.56 - 3.84: 128 3.84 - 5.11: 26 5.11 - 6.39: 10 Bond angle restraints: 18252 Sorted by residual: angle pdb=" N TRP B 716 " pdb=" CA TRP B 716 " pdb=" CB TRP B 716 " ideal model delta sigma weight residual 114.17 109.82 4.35 1.14e+00 7.69e-01 1.46e+01 angle pdb=" N TRP A 716 " pdb=" CA TRP A 716 " pdb=" CB TRP A 716 " ideal model delta sigma weight residual 114.17 109.82 4.35 1.14e+00 7.69e-01 1.45e+01 angle pdb=" N VAL A 686 " pdb=" CA VAL A 686 " pdb=" C VAL A 686 " ideal model delta sigma weight residual 111.88 107.91 3.97 1.06e+00 8.90e-01 1.40e+01 angle pdb=" N VAL B 686 " pdb=" CA VAL B 686 " pdb=" C VAL B 686 " ideal model delta sigma weight residual 111.88 107.96 3.92 1.06e+00 8.90e-01 1.37e+01 angle pdb=" N GLY A 741 " pdb=" CA GLY A 741 " pdb=" C GLY A 741 " ideal model delta sigma weight residual 110.38 114.95 -4.57 1.28e+00 6.10e-01 1.27e+01 ... (remaining 18247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 6947 17.88 - 35.75: 711 35.75 - 53.63: 235 53.63 - 71.50: 48 71.50 - 89.38: 25 Dihedral angle restraints: 7966 sinusoidal: 3270 harmonic: 4696 Sorted by residual: dihedral pdb=" CA PHE B 413 " pdb=" C PHE B 413 " pdb=" N ASN B 414 " pdb=" CA ASN B 414 " ideal model delta harmonic sigma weight residual -180.00 -156.04 -23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PHE A 413 " pdb=" C PHE A 413 " pdb=" N ASN A 414 " pdb=" CA ASN A 414 " ideal model delta harmonic sigma weight residual 180.00 -157.15 -22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ILE A 330 " pdb=" C ILE A 330 " pdb=" N TRP A 331 " pdb=" CA TRP A 331 " ideal model delta harmonic sigma weight residual 180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 7963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 928 0.029 - 0.058: 578 0.058 - 0.087: 220 0.087 - 0.116: 121 0.116 - 0.145: 33 Chirality restraints: 1880 Sorted by residual: chirality pdb=" CA ILE B 262 " pdb=" N ILE B 262 " pdb=" C ILE B 262 " pdb=" CB ILE B 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA VAL B 441 " pdb=" N VAL B 441 " pdb=" C VAL B 441 " pdb=" CB VAL B 441 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1877 not shown) Planarity restraints: 2369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 493 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 494 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 494 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 494 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 480 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.87e+00 pdb=" C ASP B 480 " 0.024 2.00e-02 2.50e+03 pdb=" O ASP B 480 " -0.009 2.00e-02 2.50e+03 pdb=" N TRP B 481 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 480 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ASP A 480 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP A 480 " 0.008 2.00e-02 2.50e+03 pdb=" N TRP A 481 " 0.008 2.00e-02 2.50e+03 ... (remaining 2366 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3618 2.80 - 3.33: 12039 3.33 - 3.85: 26208 3.85 - 4.38: 32487 4.38 - 4.90: 50151 Nonbonded interactions: 124503 Sorted by model distance: nonbonded pdb=" OD2 ASP B 321 " pdb=" OH TYR B 682 " model vdw 2.278 3.040 nonbonded pdb=" O MET A 67 " pdb=" O HOH A 901 " model vdw 2.301 3.040 nonbonded pdb=" O MET B 67 " pdb=" O HOH B 901 " model vdw 2.304 3.040 nonbonded pdb=" OE2 GLU B 247 " pdb=" O HOH B 902 " model vdw 2.305 3.040 nonbonded pdb=" OE2 GLU A 247 " pdb=" O HOH A 902 " model vdw 2.307 3.040 ... (remaining 124498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 461 or (resid 462 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ or name OH )) or resid 463 through 810)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 29.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.920 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 48.590 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.100 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:102.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13493 Z= 0.161 Angle : 0.598 8.510 18258 Z= 0.334 Chirality : 0.046 0.145 1880 Planarity : 0.004 0.036 2369 Dihedral : 17.233 89.378 4990 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.30 % Allowed : 16.98 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.44 (0.21), residues: 1614 helix: 0.99 (0.24), residues: 477 sheet: 1.02 (0.28), residues: 281 loop : -0.31 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 331 HIS 0.005 0.001 HIS B 653 PHE 0.017 0.002 PHE B 119 TYR 0.015 0.002 TYR A 13 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_BETA1-4 : bond 0.01096 ( 2) link_BETA1-4 : angle 5.46067 ( 6) hydrogen bonds : bond 0.12737 ( 589) hydrogen bonds : angle 6.56633 ( 1650) covalent geometry : bond 0.00345 (13491) covalent geometry : angle 0.59001 (18252) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 2.487 Fit side-chains REVERT: A 355 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7902 (mtt90) REVERT: A 605 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8447 (ttpt) REVERT: B 229 LYS cc_start: 0.8332 (ttmt) cc_final: 0.7907 (tttt) outliers start: 18 outliers final: 14 residues processed: 144 average time/residue: 2.1783 time to fit residues: 335.3721 Evaluate side-chains 141 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 605 LYS Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 652 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.097842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.085913 restraints weight = 13953.336| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.03 r_work: 0.2815 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 13493 Z= 0.250 Angle : 0.688 7.141 18258 Z= 0.380 Chirality : 0.052 0.178 1880 Planarity : 0.005 0.048 2369 Dihedral : 7.283 55.791 1894 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.53 % Allowed : 15.32 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.34 (0.21), residues: 1614 helix: 0.87 (0.23), residues: 498 sheet: 1.00 (0.28), residues: 281 loop : -0.40 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 331 HIS 0.007 0.002 HIS B 653 PHE 0.020 0.003 PHE A 369 TYR 0.021 0.002 TYR A 13 ARG 0.003 0.001 ARG B 57 Details of bonding type rmsd link_BETA1-4 : bond 0.00815 ( 2) link_BETA1-4 : angle 4.46836 ( 6) hydrogen bonds : bond 0.06319 ( 589) hydrogen bonds : angle 6.07041 ( 1650) covalent geometry : bond 0.00572 (13491) covalent geometry : angle 0.68309 (18252) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.551 Fit side-chains REVERT: A 376 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8054 (mtp85) REVERT: A 379 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: A 802 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8668 (mtpt) REVERT: A 807 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: B 379 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: B 523 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8495 (ttmm) REVERT: B 599 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8311 (mp0) outliers start: 35 outliers final: 17 residues processed: 148 average time/residue: 1.8954 time to fit residues: 300.0255 Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 143 LYS Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 599 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 39 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.100585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.088761 restraints weight = 14078.552| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.03 r_work: 0.2877 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.0491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13493 Z= 0.171 Angle : 0.607 6.748 18258 Z= 0.335 Chirality : 0.048 0.146 1880 Planarity : 0.004 0.039 2369 Dihedral : 6.707 55.503 1884 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.46 % Allowed : 15.17 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.43 (0.21), residues: 1614 helix: 1.02 (0.23), residues: 498 sheet: 1.02 (0.28), residues: 281 loop : -0.38 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 331 HIS 0.006 0.001 HIS B 653 PHE 0.020 0.002 PHE A 369 TYR 0.017 0.002 TYR A 13 ARG 0.003 0.000 ARG B 190 Details of bonding type rmsd link_BETA1-4 : bond 0.00583 ( 2) link_BETA1-4 : angle 4.32637 ( 6) hydrogen bonds : bond 0.05329 ( 589) hydrogen bonds : angle 5.88933 ( 1650) covalent geometry : bond 0.00379 (13491) covalent geometry : angle 0.60211 (18252) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 1.424 Fit side-chains REVERT: A 379 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: A 802 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8662 (mtpt) REVERT: B 379 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: B 560 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: B 599 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: B 670 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8571 (mtt) outliers start: 34 outliers final: 16 residues processed: 150 average time/residue: 1.8934 time to fit residues: 303.2813 Evaluate side-chains 147 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.099733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.087951 restraints weight = 13916.951| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.02 r_work: 0.2866 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.0531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13493 Z= 0.194 Angle : 0.631 6.921 18258 Z= 0.348 Chirality : 0.049 0.150 1880 Planarity : 0.005 0.039 2369 Dihedral : 6.711 55.712 1883 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.67 % Allowed : 14.60 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.43 (0.21), residues: 1614 helix: 1.01 (0.23), residues: 498 sheet: 1.02 (0.28), residues: 281 loop : -0.38 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 331 HIS 0.006 0.002 HIS B 653 PHE 0.019 0.002 PHE A 369 TYR 0.019 0.002 TYR A 13 ARG 0.003 0.000 ARG A 539 Details of bonding type rmsd link_BETA1-4 : bond 0.00672 ( 2) link_BETA1-4 : angle 4.47530 ( 6) hydrogen bonds : bond 0.05595 ( 589) hydrogen bonds : angle 5.90495 ( 1650) covalent geometry : bond 0.00437 (13491) covalent geometry : angle 0.62591 (18252) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 131 time to evaluate : 1.619 Fit side-chains REVERT: A 355 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.7941 (mtt90) REVERT: A 376 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8006 (mtp85) REVERT: A 379 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: A 802 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8670 (mtpt) REVERT: A 807 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: B 379 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: B 523 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8487 (ttmm) REVERT: B 560 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8030 (mm-30) REVERT: B 599 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: B 605 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8601 (ttpt) outliers start: 37 outliers final: 21 residues processed: 151 average time/residue: 1.8979 time to fit residues: 306.1649 Evaluate side-chains 153 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 100 optimal weight: 0.7980 chunk 6 optimal weight: 0.0040 chunk 74 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.091231 restraints weight = 13923.388| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.02 r_work: 0.2916 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13493 Z= 0.121 Angle : 0.541 6.238 18258 Z= 0.298 Chirality : 0.045 0.143 1880 Planarity : 0.004 0.040 2369 Dihedral : 6.258 53.833 1883 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.38 % Allowed : 14.88 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.59 (0.21), residues: 1614 helix: 1.28 (0.24), residues: 490 sheet: 1.05 (0.29), residues: 280 loop : -0.33 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 331 HIS 0.005 0.001 HIS A 653 PHE 0.020 0.002 PHE B 369 TYR 0.014 0.001 TYR A 462 ARG 0.001 0.000 ARG A 360 Details of bonding type rmsd link_BETA1-4 : bond 0.00385 ( 2) link_BETA1-4 : angle 4.08672 ( 6) hydrogen bonds : bond 0.04416 ( 589) hydrogen bonds : angle 5.68536 ( 1650) covalent geometry : bond 0.00252 (13491) covalent geometry : angle 0.53577 (18252) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 1.519 Fit side-chains REVERT: A 376 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7943 (mtp85) REVERT: A 379 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7893 (tt0) REVERT: A 802 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8663 (mtpt) REVERT: B 379 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: B 599 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8235 (mp0) outliers start: 33 outliers final: 18 residues processed: 149 average time/residue: 1.8029 time to fit residues: 287.4431 Evaluate side-chains 144 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 45 CYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 599 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 157 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 ASN B 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.087565 restraints weight = 14133.816| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.03 r_work: 0.2860 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.0572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 13493 Z= 0.217 Angle : 0.644 6.939 18258 Z= 0.356 Chirality : 0.050 0.158 1880 Planarity : 0.005 0.044 2369 Dihedral : 6.603 55.077 1881 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.53 % Allowed : 14.81 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1614 helix: 1.01 (0.23), residues: 499 sheet: 1.03 (0.28), residues: 282 loop : -0.34 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 331 HIS 0.006 0.002 HIS A 653 PHE 0.018 0.003 PHE B 119 TYR 0.020 0.002 TYR A 13 ARG 0.004 0.000 ARG B 57 Details of bonding type rmsd link_BETA1-4 : bond 0.00757 ( 2) link_BETA1-4 : angle 4.51092 ( 6) hydrogen bonds : bond 0.05744 ( 589) hydrogen bonds : angle 5.89164 ( 1650) covalent geometry : bond 0.00494 (13491) covalent geometry : angle 0.63862 (18252) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.610 Fit side-chains REVERT: A 355 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7961 (mtt90) REVERT: A 376 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8004 (mtp85) REVERT: A 379 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: A 802 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8686 (mtpt) REVERT: B 188 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: B 379 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: B 523 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8488 (ttmm) REVERT: B 560 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: B 599 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: B 605 LYS cc_start: 0.8858 (ttpt) cc_final: 0.8644 (ttpt) outliers start: 35 outliers final: 19 residues processed: 147 average time/residue: 1.8622 time to fit residues: 292.9974 Evaluate side-chains 152 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 376 ARG Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 379 GLU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 652 CYS Chi-restraints excluded: chain B residue 670 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.9816 > 50: distance: 31 - 121: 24.685 distance: 34 - 118: 26.026 distance: 46 - 107: 28.985 distance: 49 - 104: 8.834 distance: 60 - 65: 22.889 distance: 65 - 66: 38.328 distance: 66 - 67: 7.626 distance: 66 - 69: 18.779 distance: 67 - 68: 46.498 distance: 67 - 74: 26.322 distance: 69 - 70: 31.844 distance: 70 - 71: 3.544 distance: 71 - 72: 36.730 distance: 71 - 73: 44.536 distance: 74 - 75: 37.344 distance: 75 - 76: 21.953 distance: 75 - 78: 33.197 distance: 76 - 77: 36.313 distance: 76 - 82: 21.171 distance: 78 - 79: 17.935 distance: 79 - 80: 33.517 distance: 79 - 81: 8.117 distance: 82 - 83: 5.547 distance: 83 - 84: 12.471 distance: 83 - 86: 18.795 distance: 84 - 85: 21.860 distance: 84 - 93: 8.392 distance: 86 - 87: 6.564 distance: 87 - 88: 21.371 distance: 87 - 89: 13.278 distance: 88 - 90: 28.285 distance: 89 - 91: 41.332 distance: 90 - 92: 22.006 distance: 91 - 92: 12.670 distance: 93 - 94: 13.263 distance: 93 - 177: 7.591 distance: 94 - 95: 4.512 distance: 94 - 97: 8.006 distance: 95 - 96: 8.794 distance: 95 - 104: 12.632 distance: 96 - 174: 19.323 distance: 98 - 99: 10.892 distance: 98 - 100: 23.817 distance: 99 - 101: 12.326 distance: 100 - 102: 8.475 distance: 101 - 103: 24.465 distance: 102 - 103: 6.753 distance: 104 - 105: 11.885 distance: 105 - 106: 18.299 distance: 105 - 108: 17.356 distance: 106 - 107: 19.133 distance: 106 - 110: 6.954 distance: 108 - 109: 9.245 distance: 110 - 111: 14.280 distance: 110 - 163: 7.830 distance: 111 - 112: 22.194 distance: 111 - 114: 10.697 distance: 112 - 113: 47.458 distance: 112 - 118: 13.067 distance: 113 - 160: 31.436 distance: 114 - 115: 12.363 distance: 115 - 116: 24.002 distance: 115 - 117: 32.875 distance: 118 - 119: 15.482 distance: 119 - 120: 21.054 distance: 119 - 122: 11.082 distance: 120 - 121: 23.557 distance: 120 - 126: 8.738 distance: 122 - 123: 43.551 distance: 122 - 124: 40.383 distance: 123 - 125: 40.252 distance: 127 - 128: 20.460 distance: 127 - 130: 9.913 distance: 128 - 129: 29.751 distance: 128 - 132: 31.563 distance: 130 - 131: 15.917 distance: 132 - 133: 24.382 distance: 133 - 134: 24.747 distance: 133 - 136: 28.459 distance: 134 - 135: 14.485 distance: 134 - 140: 35.183 distance: 136 - 137: 23.998 distance: 137 - 138: 9.008 distance: 137 - 139: 8.846 distance: 141 - 144: 4.998 distance: 142 - 143: 3.508 distance: 142 - 147: 33.409 distance: 144 - 145: 17.432 distance: 144 - 146: 40.367