Starting phenix.real_space_refine on Sun Jun 30 04:31:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3l_41005/06_2024/8t3l_41005_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3l_41005/06_2024/8t3l_41005.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3l_41005/06_2024/8t3l_41005_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3l_41005/06_2024/8t3l_41005_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3l_41005/06_2024/8t3l_41005_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3l_41005/06_2024/8t3l_41005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3l_41005/06_2024/8t3l_41005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3l_41005/06_2024/8t3l_41005_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3l_41005/06_2024/8t3l_41005_trim_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 70 5.16 5 Na 2 4.78 5 C 6715 2.51 5 N 1522 2.21 5 O 1753 1.98 5 H 10056 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 684": "OE1" <-> "OE2" Residue "D GLU 684": "OE1" <-> "OE2" Residue "B ARG 409": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 20122 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 5059 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 296} Chain breaks: 1 Chain: "D" Number of atoms: 5078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 5078 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 298} Chain: "B" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 4899 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 287} Chain breaks: 3 Chain: "C" Number of atoms: 4944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4944 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 288} Chain breaks: 1 Chain: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {' NA': 1, '8IJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'8IJ': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {' NA': 1, 'NKN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'NKN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.81, per 1000 atoms: 0.49 Number of scatterers: 20122 At special positions: 0 Unit cell: (112.725, 112.725, 81.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 70 16.00 P 4 15.00 Na 2 11.00 O 1753 8.00 N 1522 7.00 C 6715 6.00 H 10056 1.00 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: 16.27 Conformation dependent library (CDL) restraints added in 2.0 seconds 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 0 sheets defined 73.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.95 Creating SS restraints... Processing helix chain 'A' and resid 395 through 401 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 453 removed outlier: 5.500A pdb=" N LYS A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ARG A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 537 through 556 removed outlier: 3.892A pdb=" N MET A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.873A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 640 removed outlier: 3.942A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 688 Processing helix chain 'A' and resid 690 through 710 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 453 removed outlier: 5.133A pdb=" N LYS D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ARG D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 537 through 556 removed outlier: 3.631A pdb=" N MET D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU D 553 " --> pdb=" O TRP D 549 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR D 555 " --> pdb=" O ASN D 551 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR D 556 " --> pdb=" O MET D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 4.062A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 638 Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 688 Processing helix chain 'D' and resid 690 through 711 Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 453 removed outlier: 5.850A pdb=" N LYS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 511 through 532 Processing helix chain 'B' and resid 537 through 555 removed outlier: 3.794A pdb=" N MET B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU B 553 " --> pdb=" O TRP B 549 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TYR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR B 555 " --> pdb=" O ASN B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 574 Processing helix chain 'B' and resid 578 through 598 removed outlier: 3.803A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR B 584 " --> pdb=" O PHE B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 removed outlier: 4.021A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 681 Processing helix chain 'B' and resid 691 through 711 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.654A pdb=" N LEU C 413 " --> pdb=" O ARG C 409 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 409 through 414' Processing helix chain 'C' and resid 416 through 453 removed outlier: 5.394A pdb=" N LYS C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ARG C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 498 Processing helix chain 'C' and resid 511 through 532 Processing helix chain 'C' and resid 537 through 556 removed outlier: 4.546A pdb=" N LEU C 553 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR C 555 " --> pdb=" O ASN C 551 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR C 556 " --> pdb=" O MET C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 4.949A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 640 removed outlier: 4.030A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 685 removed outlier: 4.766A pdb=" N MET C 682 " --> pdb=" O LEU C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 710 removed outlier: 3.746A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 2004 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: 7.24 Time building geometry restraints manager: 17.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10038 1.03 - 1.23: 80 1.23 - 1.42: 4413 1.42 - 1.62: 5706 1.62 - 1.82: 128 Bond restraints: 20365 Sorted by residual: bond pdb=" C GLU A 397 " pdb=" O GLU A 397 " ideal model delta sigma weight residual 1.237 1.196 0.040 1.17e-02 7.31e+03 1.19e+01 bond pdb=" C MET A 677 " pdb=" O MET A 677 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N ILE D 479 " pdb=" CA ILE D 479 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.80e+00 bond pdb=" N ASP B 576 " pdb=" H ASP B 576 " ideal model delta sigma weight residual 0.860 0.919 -0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" CA SER A 520 " pdb=" CB SER A 520 " ideal model delta sigma weight residual 1.528 1.483 0.046 1.56e-02 4.11e+03 8.67e+00 ... (remaining 20360 not shown) Histogram of bond angle deviations from ideal: 77.61 - 94.19: 2 94.19 - 110.77: 20862 110.77 - 127.36: 15673 127.36 - 143.94: 47 143.94 - 160.53: 1 Bond angle restraints: 36585 Sorted by residual: angle pdb=" O20 8IJ A 801 " pdb=" C21 8IJ A 801 " pdb=" O22 8IJ A 801 " ideal model delta sigma weight residual 120.00 77.61 42.39 3.00e+00 1.11e-01 2.00e+02 angle pdb=" C23 8IJ A 801 " pdb=" C21 8IJ A 801 " pdb=" O20 8IJ A 801 " ideal model delta sigma weight residual 119.98 160.53 -40.55 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C23 8IJ A 801 " pdb=" C21 8IJ A 801 " pdb=" O22 8IJ A 801 " ideal model delta sigma weight residual 120.00 82.92 37.08 3.00e+00 1.11e-01 1.53e+02 angle pdb=" CA ILE C 679 " pdb=" C ILE C 679 " pdb=" O ILE C 679 " ideal model delta sigma weight residual 120.69 114.81 5.88 1.05e+00 9.07e-01 3.14e+01 angle pdb=" N LEU A 497 " pdb=" CA LEU A 497 " pdb=" C LEU A 497 " ideal model delta sigma weight residual 112.45 105.73 6.72 1.39e+00 5.18e-01 2.34e+01 ... (remaining 36580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 9333 34.41 - 68.83: 273 68.83 - 103.24: 22 103.24 - 137.66: 3 137.66 - 172.07: 2 Dihedral angle restraints: 9633 sinusoidal: 5053 harmonic: 4580 Sorted by residual: dihedral pdb=" CD ARG A 409 " pdb=" NE ARG A 409 " pdb=" CZ ARG A 409 " pdb=" NH1 ARG A 409 " ideal model delta sinusoidal sigma weight residual 0.00 -56.57 56.57 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CD ARG B 409 " pdb=" NE ARG B 409 " pdb=" CZ ARG B 409 " pdb=" NH1 ARG B 409 " ideal model delta sinusoidal sigma weight residual 0.00 -48.08 48.08 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" C18 8IJ A 801 " pdb=" C41 8IJ A 801 " pdb=" O40 8IJ A 801 " pdb=" C43 8IJ A 801 " ideal model delta sinusoidal sigma weight residual -74.44 97.63 -172.07 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 9630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.011: 1556 1.011 - 2.022: 0 2.022 - 3.033: 0 3.033 - 4.044: 0 4.044 - 5.056: 4 Chirality restraints: 1560 Sorted by residual: chirality pdb=" C18 8IJ A 801 " pdb=" C17 8IJ A 801 " pdb=" C19 8IJ A 801 " pdb=" O40 8IJ A 801 " both_signs ideal model delta sigma weight residual False -2.51 2.54 -5.06 2.00e-01 2.50e+01 6.39e+02 chirality pdb=" C5 8IJ A 801 " pdb=" C14 8IJ A 801 " pdb=" C6 8IJ A 801 " pdb=" O4 8IJ A 801 " both_signs ideal model delta sigma weight residual False 2.50 -2.54 5.04 2.00e-01 2.50e+01 6.36e+02 chirality pdb=" CAH NKN C 801 " pdb=" CAG NKN C 801 " pdb=" CAI NKN C 801 " pdb=" OAY NKN C 801 " both_signs ideal model delta sigma weight residual False -2.51 2.51 -5.03 2.00e-01 2.50e+01 6.32e+02 ... (remaining 1557 not shown) Planarity restraints: 2839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 474 " -0.613 9.50e-02 1.11e+02 2.68e-01 7.25e+02 pdb=" NE ARG D 474 " -0.137 2.00e-02 2.50e+03 pdb=" CZ ARG D 474 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG D 474 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 474 " 0.042 2.00e-02 2.50e+03 pdb="HH11 ARG D 474 " 0.362 2.00e-02 2.50e+03 pdb="HH12 ARG D 474 " -0.335 2.00e-02 2.50e+03 pdb="HH21 ARG D 474 " 0.059 2.00e-02 2.50e+03 pdb="HH22 ARG D 474 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 575 " -0.217 9.50e-02 1.11e+02 1.74e-01 5.73e+02 pdb=" NE ARG B 575 " -0.174 2.00e-02 2.50e+03 pdb=" CZ ARG B 575 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG B 575 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 575 " 0.034 2.00e-02 2.50e+03 pdb="HH11 ARG B 575 " 0.325 2.00e-02 2.50e+03 pdb="HH12 ARG B 575 " -0.261 2.00e-02 2.50e+03 pdb="HH21 ARG B 575 " 0.138 2.00e-02 2.50e+03 pdb="HH22 ARG B 575 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 455 " 0.509 9.50e-02 1.11e+02 2.09e-01 3.69e+02 pdb=" NE ARG B 455 " 0.082 2.00e-02 2.50e+03 pdb=" CZ ARG B 455 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG B 455 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 455 " -0.031 2.00e-02 2.50e+03 pdb="HH11 ARG B 455 " -0.250 2.00e-02 2.50e+03 pdb="HH12 ARG B 455 " 0.241 2.00e-02 2.50e+03 pdb="HH21 ARG B 455 " -0.019 2.00e-02 2.50e+03 pdb="HH22 ARG B 455 " -0.079 2.00e-02 2.50e+03 ... (remaining 2836 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 1834 2.23 - 2.82: 43429 2.82 - 3.41: 54550 3.41 - 4.01: 69953 4.01 - 4.60: 108008 Nonbonded interactions: 277774 Sorted by model distance: nonbonded pdb="HD21 ASN B 408 " pdb=" OD2 ASP B 411 " model vdw 1.634 1.850 nonbonded pdb=" HZ3 LYS B 656 " pdb=" OH TYR C 631 " model vdw 1.638 1.850 nonbonded pdb=" OG SER B 402 " pdb=" HG1 THR B 406 " model vdw 1.647 1.850 nonbonded pdb=" OE1 GLN C 561 " pdb=" H GLN C 561 " model vdw 1.647 1.850 nonbonded pdb=" HH TYR D 463 " pdb=" OH TYR D 537 " model vdw 1.666 1.850 ... (remaining 277769 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' and (resid 392 through 456 or resid 461 through 463 or resid 467 thro \ ugh 683 or resid 688 through 712)) selection = (chain 'B' and resid 392 through 712) selection = (chain 'C' and (resid 392 through 456 or resid 461 through 463 or resid 467 thro \ ugh 683 or resid 688 through 712)) selection = (chain 'D' and (resid 392 through 456 or resid 461 through 463 or resid 467 thro \ ugh 683 or resid 688 through 712)) } 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: 4.720 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: 0.270 Extract box with map and model: 12.050 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 66.900 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 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 0.057 10309 Z= 0.310 Angle : 0.968 42.393 13911 Z= 0.545 Chirality : 0.258 5.056 1560 Planarity : 0.016 0.409 1673 Dihedral : 17.148 172.074 3745 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.64 % Allowed : 2.56 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.43 (0.25), residues: 1179 helix: 1.83 (0.17), residues: 890 sheet: None (None), residues: 0 loop : -1.93 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 697 HIS 0.002 0.001 HIS B 410 PHE 0.021 0.001 PHE A 490 TYR 0.012 0.001 TYR B 627 ARG 0.005 0.000 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 301 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7420 (tm-30) REVERT: A 669 LEU cc_start: 0.8573 (mm) cc_final: 0.8263 (mm) REVERT: D 439 PHE cc_start: 0.7782 (t80) cc_final: 0.7204 (t80) REVERT: D 681 LEU cc_start: 0.8448 (mm) cc_final: 0.8220 (mm) REVERT: B 579 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7045 (ptt180) REVERT: B 631 TYR cc_start: 0.7656 (t80) cc_final: 0.7210 (t80) outliers start: 7 outliers final: 3 residues processed: 306 average time/residue: 0.4897 time to fit residues: 206.4714 Evaluate side-chains 279 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 276 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 679 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10309 Z= 0.200 Angle : 0.538 6.977 13911 Z= 0.287 Chirality : 0.034 0.254 1560 Planarity : 0.005 0.127 1673 Dihedral : 13.070 157.370 1427 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.01 % Allowed : 9.07 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.94 (0.25), residues: 1179 helix: 2.20 (0.17), residues: 894 sheet: None (None), residues: 0 loop : -1.84 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 697 HIS 0.001 0.001 HIS B 410 PHE 0.012 0.001 PHE A 490 TYR 0.007 0.001 TYR A 555 ARG 0.005 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 278 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 669 LEU cc_start: 0.8524 (mm) cc_final: 0.8194 (mm) REVERT: A 707 ASP cc_start: 0.7488 (m-30) cc_final: 0.7145 (t0) REVERT: D 439 PHE cc_start: 0.7745 (t80) cc_final: 0.7169 (t80) REVERT: D 681 LEU cc_start: 0.8521 (mm) cc_final: 0.8315 (mm) REVERT: B 579 ARG cc_start: 0.7581 (ptm160) cc_final: 0.7026 (ptt180) REVERT: C 498 GLN cc_start: 0.6315 (mt0) cc_final: 0.6075 (mt0) outliers start: 11 outliers final: 10 residues processed: 284 average time/residue: 0.5133 time to fit residues: 201.6405 Evaluate side-chains 279 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 269 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain D residue 519 GLN Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 679 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10309 Z= 0.264 Angle : 0.546 6.269 13911 Z= 0.299 Chirality : 0.035 0.172 1560 Planarity : 0.004 0.062 1673 Dihedral : 12.361 156.089 1427 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.56 % Allowed : 11.63 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.74 (0.25), residues: 1179 helix: 2.09 (0.17), residues: 893 sheet: None (None), residues: 0 loop : -1.99 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 549 HIS 0.002 0.001 HIS C 410 PHE 0.013 0.001 PHE C 439 TYR 0.010 0.001 TYR A 555 ARG 0.004 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 265 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7576 (tm-30) REVERT: A 669 LEU cc_start: 0.8516 (mm) cc_final: 0.8136 (mm) REVERT: A 707 ASP cc_start: 0.7450 (m-30) cc_final: 0.7148 (t0) REVERT: D 439 PHE cc_start: 0.7784 (t80) cc_final: 0.7183 (t80) REVERT: B 455 ARG cc_start: 0.7517 (ptt90) cc_final: 0.7279 (ptt90) REVERT: B 579 ARG cc_start: 0.7738 (ptm160) cc_final: 0.7447 (ptm160) REVERT: B 677 MET cc_start: 0.6877 (OUTLIER) cc_final: 0.6551 (ttp) REVERT: C 677 MET cc_start: 0.7210 (tmm) cc_final: 0.7003 (tmm) outliers start: 17 outliers final: 14 residues processed: 272 average time/residue: 0.4818 time to fit residues: 181.8526 Evaluate side-chains 277 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 262 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 679 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.2980 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 114 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 519 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10309 Z= 0.153 Angle : 0.475 5.809 13911 Z= 0.260 Chirality : 0.032 0.115 1560 Planarity : 0.003 0.048 1673 Dihedral : 11.713 162.102 1427 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.28 % Allowed : 13.19 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.26 (0.26), residues: 1179 helix: 2.45 (0.17), residues: 895 sheet: None (None), residues: 0 loop : -1.81 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 697 HIS 0.001 0.000 HIS B 410 PHE 0.009 0.001 PHE B 659 TYR 0.009 0.001 TYR B 401 ARG 0.002 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 267 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7475 (tm-30) REVERT: A 707 ASP cc_start: 0.7457 (m-30) cc_final: 0.7176 (t0) REVERT: D 439 PHE cc_start: 0.7732 (t80) cc_final: 0.7126 (t80) REVERT: B 455 ARG cc_start: 0.7559 (ptt90) cc_final: 0.7346 (ptt90) REVERT: B 579 ARG cc_start: 0.7716 (ptm160) cc_final: 0.7422 (ptm160) REVERT: B 677 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6607 (ttp) REVERT: C 709 GLU cc_start: 0.4996 (tm-30) cc_final: 0.4771 (tp30) outliers start: 14 outliers final: 11 residues processed: 274 average time/residue: 0.4976 time to fit residues: 189.4299 Evaluate side-chains 273 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 261 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 679 ILE 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: 0.9980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10309 Z= 0.291 Angle : 0.559 6.665 13911 Z= 0.308 Chirality : 0.035 0.159 1560 Planarity : 0.004 0.055 1673 Dihedral : 11.559 172.515 1426 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.75 % Allowed : 13.55 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.52 (0.25), residues: 1179 helix: 1.95 (0.17), residues: 903 sheet: None (None), residues: 0 loop : -2.33 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 697 HIS 0.002 0.001 HIS C 410 PHE 0.015 0.002 PHE C 439 TYR 0.013 0.002 TYR C 554 ARG 0.003 0.000 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 267 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7614 (tm-30) REVERT: A 707 ASP cc_start: 0.7444 (m-30) cc_final: 0.7168 (t0) REVERT: D 439 PHE cc_start: 0.7823 (t80) cc_final: 0.7260 (t80) REVERT: B 579 ARG cc_start: 0.7662 (ptm160) cc_final: 0.7286 (ptm160) REVERT: B 677 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6603 (ttp) REVERT: C 677 MET cc_start: 0.7213 (tmm) cc_final: 0.6998 (tmm) outliers start: 30 outliers final: 23 residues processed: 284 average time/residue: 0.4656 time to fit residues: 185.1624 Evaluate side-chains 287 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 263 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 676 ASN Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 679 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10309 Z= 0.198 Angle : 0.507 6.251 13911 Z= 0.276 Chirality : 0.034 0.155 1560 Planarity : 0.003 0.044 1673 Dihedral : 11.342 178.654 1426 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.47 % Allowed : 15.48 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.80 (0.25), residues: 1179 helix: 2.18 (0.17), residues: 898 sheet: None (None), residues: 0 loop : -2.26 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 697 HIS 0.001 0.000 HIS B 410 PHE 0.011 0.001 PHE C 439 TYR 0.010 0.001 TYR B 401 ARG 0.003 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 263 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 ASP cc_start: 0.7436 (m-30) cc_final: 0.7203 (t0) REVERT: D 439 PHE cc_start: 0.7757 (t80) cc_final: 0.7154 (t80) REVERT: B 579 ARG cc_start: 0.7662 (ptm160) cc_final: 0.7420 (ptm160) REVERT: C 412 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.6078 (mtt) REVERT: C 709 GLU cc_start: 0.5062 (tm-30) cc_final: 0.4857 (tp30) outliers start: 27 outliers final: 23 residues processed: 277 average time/residue: 0.4730 time to fit residues: 182.7522 Evaluate side-chains 286 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 262 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 0.0870 chunk 63 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 71 optimal weight: 0.4980 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10309 Z= 0.172 Angle : 0.489 5.947 13911 Z= 0.265 Chirality : 0.033 0.163 1560 Planarity : 0.003 0.041 1673 Dihedral : 11.220 179.744 1426 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.47 % Allowed : 15.84 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 2.02 (0.26), residues: 1179 helix: 2.35 (0.17), residues: 897 sheet: None (None), residues: 0 loop : -2.21 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 697 HIS 0.001 0.000 HIS B 410 PHE 0.016 0.001 PHE D 438 TYR 0.010 0.001 TYR C 671 ARG 0.005 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 261 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 ASP cc_start: 0.7382 (m-30) cc_final: 0.7171 (t0) REVERT: D 439 PHE cc_start: 0.7725 (t80) cc_final: 0.7131 (t80) REVERT: D 560 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6480 (pm20) REVERT: B 579 ARG cc_start: 0.7653 (ptm160) cc_final: 0.7432 (ptm160) REVERT: B 677 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6681 (ttp) REVERT: C 412 MET cc_start: 0.6402 (OUTLIER) cc_final: 0.6047 (mtt) outliers start: 27 outliers final: 22 residues processed: 276 average time/residue: 0.5002 time to fit residues: 192.2942 Evaluate side-chains 285 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 260 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 519 GLN ** D 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10309 Z= 0.221 Angle : 0.516 6.168 13911 Z= 0.280 Chirality : 0.034 0.178 1560 Planarity : 0.003 0.044 1673 Dihedral : 11.213 175.016 1426 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.84 % Allowed : 16.03 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.84 (0.25), residues: 1179 helix: 2.25 (0.17), residues: 896 sheet: None (None), residues: 0 loop : -2.36 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 697 HIS 0.001 0.000 HIS C 410 PHE 0.012 0.001 PHE C 439 TYR 0.014 0.001 TYR C 671 ARG 0.004 0.000 ARG A 534 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2358 Ramachandran restraints generated. 1179 Oldfield, 0 Emsley, 1179 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 267 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 439 PHE cc_start: 0.7732 (t80) cc_final: 0.7116 (t80) REVERT: D 531 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: D 560 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6494 (pm20) REVERT: B 677 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6675 (ttp) REVERT: C 412 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5993 (mtt) outliers start: 31 outliers final: 25 residues processed: 282 average time/residue: 0.4776 time to fit residues: 186.8613 Evaluate side-chains 290 residues out of total 1092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 261 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 531 PHE Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 560 GLN Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 526 SER Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain B residue 710 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 526 SER Chi-restraints excluded: chain C residue 652 ASN Chi-restraints excluded: chain C residue 660 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 681 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.3442 > 50: distance: 76 - 90: 20.953 distance: 90 - 91: 20.623 distance: 90 - 98: 16.143 distance: 91 - 92: 20.468 distance: 91 - 94: 8.990 distance: 91 - 99: 11.595 distance: 92 - 93: 30.296 distance: 92 - 109: 15.227 distance: 94 - 95: 28.451 distance: 94 - 100: 18.460 distance: 94 - 101: 14.088 distance: 95 - 96: 7.280 distance: 95 - 97: 12.993 distance: 95 - 102: 19.144 distance: 96 - 103: 10.597 distance: 96 - 104: 26.326 distance: 96 - 105: 10.971 distance: 97 - 106: 24.211 distance: 97 - 107: 15.772 distance: 97 - 108: 17.648 distance: 109 - 110: 23.339 distance: 109 - 116: 22.309 distance: 110 - 111: 29.213 distance: 110 - 113: 5.021 distance: 110 - 117: 11.250 distance: 111 - 112: 12.231 distance: 111 - 125: 15.534 distance: 113 - 114: 23.788 distance: 113 - 115: 44.105 distance: 113 - 118: 19.575 distance: 114 - 120: 3.587 distance: 114 - 121: 17.683 distance: 115 - 122: 24.568 distance: 115 - 123: 22.970 distance: 115 - 124: 29.633 distance: 125 - 126: 32.557 distance: 125 - 134: 64.344 distance: 126 - 127: 21.031 distance: 126 - 129: 13.713 distance: 126 - 135: 26.476 distance: 127 - 128: 35.215 distance: 127 - 140: 13.977 distance: 128 - 187: 48.177 distance: 129 - 130: 21.617 distance: 129 - 136: 27.495 distance: 129 - 137: 17.609 distance: 130 - 131: 49.262 distance: 130 - 138: 10.207 distance: 130 - 139: 7.381 distance: 131 - 132: 3.384 distance: 131 - 133: 5.221 distance: 140 - 141: 14.236 distance: 140 - 146: 15.883 distance: 141 - 142: 5.082 distance: 141 - 144: 23.146 distance: 141 - 147: 11.257 distance: 142 - 143: 26.964 distance: 142 - 154: 15.846 distance: 143 - 211: 33.353 distance: 144 - 148: 25.926 distance: 144 - 149: 4.520 distance: 145 - 146: 21.354 distance: 145 - 150: 12.209 distance: 145 - 151: 3.236 distance: 146 - 152: 12.743 distance: 146 - 153: 10.625 distance: 154 - 155: 22.391 distance: 154 - 162: 25.689 distance: 155 - 156: 13.823 distance: 155 - 158: 21.108 distance: 155 - 163: 25.571 distance: 156 - 157: 21.990 distance: 156 - 173: 13.876 distance: 157 - 230: 45.661 distance: 158 - 159: 21.433 distance: 158 - 164: 12.899 distance: 158 - 165: 25.674 distance: 159 - 160: 8.457 distance: 159 - 161: 30.508 distance: 159 - 166: 28.338 distance: 160 - 167: 27.802 distance: 160 - 168: 3.853 distance: 160 - 169: 20.842 distance: 161 - 170: 22.665 distance: 161 - 171: 19.834 distance: 161 - 172: 22.212 distance: 173 - 174: 13.727 distance: 173 - 181: 17.246 distance: 174 - 175: 22.579 distance: 174 - 177: 19.214 distance: 174 - 182: 22.851 distance: 175 - 176: 10.477 distance: 175 - 187: 15.364 distance: 176 - 249: 36.260 distance: 177 - 178: 17.810 distance: 177 - 183: 14.291 distance: 177 - 184: 14.536 distance: 178 - 179: 16.444 distance: 178 - 180: 4.013 distance: 180 - 185: 11.343 distance: 180 - 186: 13.567 distance: 187 - 188: 15.298 distance: 187 - 198: 26.754 distance: 188 - 189: 30.160 distance: 188 - 191: 23.410 distance: 188 - 199: 20.620 distance: 189 - 190: 26.161 distance: 189 - 211: 21.583 distance: 190 - 266: 14.676 distance: 191 - 192: 15.007 distance: 191 - 200: 15.992 distance: 191 - 201: 4.783 distance: 192 - 193: 23.223 distance: 192 - 202: 10.145 distance: 192 - 203: 17.801 distance: 193 - 194: 13.656 distance: 193 - 204: 6.934 distance: 193 - 205: 10.720 distance: 194 - 195: 22.554 distance: 194 - 206: 8.490 distance: 195 - 196: 14.838 distance: 195 - 197: 6.376 distance: 196 - 207: 5.505 distance: 196 - 208: 10.359 distance: 197 - 209: 4.481 distance: 197 - 210: 8.230 distance: 211 - 212: 18.378 distance: 211 - 219: 29.330 distance: 212 - 213: 15.804 distance: 212 - 215: 14.426 distance: 212 - 220: 23.057 distance: 213 - 214: 15.116 distance: 213 - 230: 17.507 distance: 214 - 277: 18.069 distance: 215 - 216: 13.967 distance: 215 - 221: 24.126 distance: 215 - 222: 16.673 distance: 216 - 217: 8.187 distance: 216 - 223: 22.574 distance: 217 - 224: 23.331 distance: 217 - 225: 24.424 distance: 217 - 226: 20.379 distance: 218 - 227: 9.600 distance: 218 - 228: 4.814 distance: 230 - 231: 13.439 distance: 230 - 238: 9.666 distance: 231 - 232: 13.611 distance: 231 - 234: 7.217 distance: 231 - 239: 18.101 distance: 232 - 233: 30.397 distance: 232 - 249: 13.662 distance: 233 - 294: 27.522 distance: 234 - 235: 3.691 distance: 234 - 240: 15.089 distance: 234 - 241: 16.559 distance: 235 - 236: 16.778 distance: 235 - 237: 14.035 distance: 236 - 243: 11.220 distance: 236 - 244: 21.362 distance: 236 - 245: 17.329 distance: 237 - 246: 7.838 distance: 237 - 247: 10.295 distance: 237 - 248: 6.778 distance: 249 - 250: 14.385 distance: 249 - 258: 26.378 distance: 250 - 251: 8.450 distance: 250 - 253: 26.188 distance: 250 - 259: 15.339 distance: 251 - 252: 16.920 distance: 251 - 266: 7.961 distance: 252 - 310: 15.839 distance: 253 - 254: 16.868 distance: 253 - 260: 28.043 distance: 253 - 261: 8.809 distance: 254 - 255: 28.171 distance: 254 - 262: 9.602 distance: 254 - 263: 25.289 distance: 255 - 256: 11.964 distance: 255 - 257: 9.888 distance: 257 - 264: 10.500 distance: 257 - 265: 19.714