Starting phenix.real_space_refine on Sun Sep 29 06:06:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgk_36237/09_2024/8jgk_36237_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgk_36237/09_2024/8jgk_36237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgk_36237/09_2024/8jgk_36237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgk_36237/09_2024/8jgk_36237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgk_36237/09_2024/8jgk_36237_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jgk_36237/09_2024/8jgk_36237_trim.cif" } resolution = 4.04 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 72 5.16 5 C 7060 2.51 5 N 1780 2.21 5 O 1884 1.98 5 H 10850 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21650 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 10798 Classifications: {'peptide': 684} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655} Chain breaks: 4 Chain: "B" Number of atoms: 10798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 10798 Classifications: {'peptide': 684} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.25, per 1000 atoms: 0.47 Number of scatterers: 21650 At special positions: 0 Unit cell: (101.37, 101.37, 106.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 4 15.00 O 1884 8.00 N 1780 7.00 C 7060 6.00 H 10850 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 161 " - pdb=" SG CYS A 172 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 161 " - pdb=" SG CYS B 172 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 472 " distance=2.03 Simple disulfide: pdb=" SG CYS B 562 " - pdb=" SG CYS B 568 " distance=2.03 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 Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 1.7 seconds 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 7 sheets defined 68.4% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 92 through 110 removed outlier: 3.653A pdb=" N GLU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 157 removed outlier: 4.160A pdb=" N GLY A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 175 Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 203 through 233 Processing helix chain 'A' and resid 234 through 237 removed outlier: 4.132A pdb=" N CYS A 237 " --> pdb=" O PRO A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 237' Processing helix chain 'A' and resid 240 through 250 removed outlier: 3.589A pdb=" N GLY A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 removed outlier: 4.088A pdb=" N LEU A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 275 removed outlier: 3.576A pdb=" N ILE A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 298 removed outlier: 3.644A pdb=" N VAL A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 Processing helix chain 'A' and resid 306 through 327 Processing helix chain 'A' and resid 328 through 340 removed outlier: 3.530A pdb=" N LEU A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 366 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 389 through 418 removed outlier: 4.400A pdb=" N PHE A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE A 412 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 420 No H-bonds generated for 'chain 'A' and resid 419 through 420' Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 426 through 441 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.987A pdb=" N LEU A 450 " --> pdb=" O PRO A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 494 through 518 removed outlier: 3.872A pdb=" N SER A 498 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 515 " --> pdb=" O ILE A 511 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE A 516 " --> pdb=" O ILE A 512 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 517 " --> pdb=" O MET A 513 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 552 Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.886A pdb=" N GLU A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 588 Processing helix chain 'A' and resid 590 through 600 removed outlier: 3.738A pdb=" N VAL A 594 " --> pdb=" O THR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 605 No H-bonds generated for 'chain 'A' and resid 603 through 605' Processing helix chain 'A' and resid 606 through 623 removed outlier: 3.843A pdb=" N LEU A 610 " --> pdb=" O TYR A 606 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 623 " --> pdb=" O TRP A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 676 through 686 Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 767 through 779 removed outlier: 3.639A pdb=" N VAL A 771 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 805 Processing helix chain 'B' and resid 92 through 110 removed outlier: 3.679A pdb=" N GLU B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 157 removed outlier: 4.119A pdb=" N GLY B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TRP B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 132 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 157 " --> pdb=" O MET B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 203 through 233 Processing helix chain 'B' and resid 234 through 237 removed outlier: 4.087A pdb=" N CYS B 237 " --> pdb=" O PRO B 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 234 through 237' Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.714A pdb=" N GLY B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 removed outlier: 4.096A pdb=" N LEU B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.579A pdb=" N ILE B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 removed outlier: 3.667A pdb=" N VAL B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 306 removed outlier: 3.521A pdb=" N SER B 304 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 327 removed outlier: 3.503A pdb=" N ALA B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 340 Processing helix chain 'B' and resid 348 through 366 Processing helix chain 'B' and resid 389 through 418 removed outlier: 4.268A pdb=" N PHE B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 395 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA B 413 " --> pdb=" O ARG B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 420 No H-bonds generated for 'chain 'B' and resid 419 through 420' Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 426 through 441 Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.918A pdb=" N LEU B 450 " --> pdb=" O PRO B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 494 through 518 removed outlier: 3.998A pdb=" N SER B 498 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 512 " --> pdb=" O ILE B 508 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 515 " --> pdb=" O ILE B 511 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 516 " --> pdb=" O ILE B 512 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 517 " --> pdb=" O MET B 513 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE B 518 " --> pdb=" O THR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 555 through 560 removed outlier: 3.981A pdb=" N GLU B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 588 Processing helix chain 'B' and resid 591 through 601 Processing helix chain 'B' and resid 603 through 605 No H-bonds generated for 'chain 'B' and resid 603 through 605' Processing helix chain 'B' and resid 606 through 623 removed outlier: 3.670A pdb=" N ALA B 623 " --> pdb=" O TRP B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 638 Processing helix chain 'B' and resid 653 through 657 Processing helix chain 'B' and resid 676 through 687 Processing helix chain 'B' and resid 709 through 722 Processing helix chain 'B' and resid 767 through 779 removed outlier: 3.594A pdb=" N VAL B 771 " --> pdb=" O PRO B 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 805 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 380 removed outlier: 7.603A pdb=" N VAL A 379 " --> pdb=" O GLY A 602 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 691 through 695 Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 787 removed outlier: 6.590A pdb=" N CYS A 783 " --> pdb=" O ILE A 794 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE A 794 " --> pdb=" O CYS A 783 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 785 " --> pdb=" O LEU A 792 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA6, first strand: chain 'B' and resid 691 through 695 Processing sheet with id=AA7, first strand: chain 'B' and resid 782 through 787 removed outlier: 6.599A pdb=" N CYS B 783 " --> pdb=" O ILE B 794 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE B 794 " --> pdb=" O CYS B 783 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 785 " --> pdb=" O LEU B 792 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1860 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: 7.22 Time building geometry restraints manager: 6.73 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: 10826 1.03 - 1.23: 25 1.23 - 1.42: 4665 1.42 - 1.62: 6308 1.62 - 1.81: 108 Bond restraints: 21932 Sorted by residual: bond pdb=" CB PRO A 666 " pdb=" CG PRO A 666 " ideal model delta sigma weight residual 1.492 1.583 -0.091 5.00e-02 4.00e+02 3.35e+00 bond pdb=" SD MET B 213 " pdb=" CE MET B 213 " ideal model delta sigma weight residual 1.791 1.754 0.037 2.50e-02 1.60e+03 2.21e+00 bond pdb=" N HIS A 633 " pdb=" CA HIS A 633 " ideal model delta sigma weight residual 1.459 1.476 -0.017 1.23e-02 6.61e+03 1.94e+00 bond pdb=" CA MET B 213 " pdb=" CB MET B 213 " ideal model delta sigma weight residual 1.529 1.511 0.018 1.55e-02 4.16e+03 1.36e+00 bond pdb=" N HIS B 633 " pdb=" CA HIS B 633 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.23e-02 6.61e+03 1.33e+00 ... (remaining 21927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 38767 1.45 - 2.90: 779 2.90 - 4.35: 75 4.35 - 5.80: 16 5.80 - 7.26: 7 Bond angle restraints: 39644 Sorted by residual: angle pdb=" CA PRO A 666 " pdb=" N PRO A 666 " pdb=" CD PRO A 666 " ideal model delta sigma weight residual 112.00 106.09 5.91 1.40e+00 5.10e-01 1.78e+01 angle pdb=" C MET B 213 " pdb=" CA MET B 213 " pdb=" CB MET B 213 " ideal model delta sigma weight residual 110.88 105.76 5.12 1.57e+00 4.06e-01 1.06e+01 angle pdb=" CA ARG B 710 " pdb=" CB ARG B 710 " pdb=" CG ARG B 710 " ideal model delta sigma weight residual 114.10 120.24 -6.14 2.00e+00 2.50e-01 9.42e+00 angle pdb=" C ILE B 716 " pdb=" N GLU B 717 " pdb=" CA GLU B 717 " ideal model delta sigma weight residual 120.72 116.07 4.65 1.67e+00 3.59e-01 7.76e+00 angle pdb=" CA TRP A 152 " pdb=" CB TRP A 152 " pdb=" CG TRP A 152 " ideal model delta sigma weight residual 113.60 118.34 -4.74 1.90e+00 2.77e-01 6.23e+00 ... (remaining 39639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.52: 9858 30.52 - 61.04: 417 61.04 - 91.55: 23 91.55 - 122.07: 4 122.07 - 152.59: 2 Dihedral angle restraints: 10304 sinusoidal: 5472 harmonic: 4832 Sorted by residual: dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 92.59 -152.59 1 2.00e+01 2.50e-03 4.53e+01 dihedral pdb=" C5' ADP B 901 " pdb=" O5' ADP B 901 " pdb=" PA ADP B 901 " pdb=" O2A ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 90.07 -150.07 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 57.15 -117.15 1 2.00e+01 2.50e-03 3.50e+01 ... (remaining 10301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1275 0.036 - 0.073: 301 0.073 - 0.109: 104 0.109 - 0.146: 14 0.146 - 0.182: 4 Chirality restraints: 1698 Sorted by residual: chirality pdb=" CA ARG B 710 " pdb=" N ARG B 710 " pdb=" C ARG B 710 " pdb=" CB ARG B 710 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CA PRO B 392 " pdb=" N PRO B 392 " pdb=" C PRO B 392 " pdb=" CB PRO B 392 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA GLU B 717 " pdb=" N GLU B 717 " pdb=" C GLU B 717 " pdb=" CB GLU B 717 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 1695 not shown) Planarity restraints: 3144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 665 " -0.062 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO A 666 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 666 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 666 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 193 " 0.017 2.00e-02 2.50e+03 1.07e-02 4.61e+00 pdb=" CG TRP B 193 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 193 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 193 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 193 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 193 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 193 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 193 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 193 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 193 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP B 193 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP B 193 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP B 193 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 193 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 193 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 193 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 213 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C MET B 213 " 0.036 2.00e-02 2.50e+03 pdb=" O MET B 213 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR B 214 " -0.012 2.00e-02 2.50e+03 ... (remaining 3141 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1153 2.18 - 2.79: 44020 2.79 - 3.39: 60813 3.39 - 4.00: 74905 4.00 - 4.60: 117230 Nonbonded interactions: 298121 Sorted by model distance: nonbonded pdb=" O PRO B 234 " pdb=" HZ1 LYS B 521 " model vdw 1.580 2.450 nonbonded pdb=" O PRO A 234 " pdb=" HZ1 LYS A 521 " model vdw 1.584 2.450 nonbonded pdb=" O PHE A 251 " pdb="HH21 ARG A 311 " model vdw 1.594 2.450 nonbonded pdb="HH12 ARG B 588 " pdb=" O GLY B 625 " model vdw 1.599 2.450 nonbonded pdb=" O ILE A 684 " pdb="HH22 ARG A 709 " model vdw 1.608 2.450 ... (remaining 298116 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.360 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 44.180 Find NCS groups from input model: 0.480 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 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 0.091 11082 Z= 0.184 Angle : 0.559 7.255 15052 Z= 0.297 Chirality : 0.037 0.182 1698 Planarity : 0.005 0.091 1844 Dihedral : 14.396 152.591 3920 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.73 (0.23), residues: 1348 helix: 1.47 (0.18), residues: 820 sheet: -1.55 (1.07), residues: 20 loop : -1.07 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 193 HIS 0.004 0.001 HIS B 553 PHE 0.016 0.001 PHE B 393 TYR 0.016 0.001 TYR A 211 ARG 0.014 0.001 ARG B 710 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 634 is missing expected H atoms. Skipping. Residue ILE 634 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.596 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: A 298 TYR cc_start: 0.6738 (t80) cc_final: 0.6488 (t80) REVERT: B 298 TYR cc_start: 0.6756 (t80) cc_final: 0.6417 (t80) REVERT: B 350 TRP cc_start: 0.4598 (p-90) cc_final: 0.3523 (m100) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.4633 time to fit residues: 140.2169 Evaluate side-chains 187 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.201 > 50: distance: 14 - 25: 7.842 distance: 25 - 26: 11.474 distance: 25 - 35: 8.239 distance: 26 - 27: 14.672 distance: 26 - 29: 4.221 distance: 26 - 36: 7.023 distance: 27 - 28: 34.916 distance: 27 - 42: 29.384 distance: 29 - 30: 10.597 distance: 29 - 37: 5.652 distance: 29 - 38: 6.017 distance: 30 - 31: 15.893 distance: 30 - 32: 12.847 distance: 31 - 33: 11.198 distance: 31 - 39: 5.415 distance: 32 - 34: 8.936 distance: 32 - 40: 6.719 distance: 33 - 34: 10.848 distance: 33 - 41: 7.599 distance: 42 - 43: 37.139 distance: 42 - 49: 28.178 distance: 43 - 44: 39.455 distance: 43 - 46: 21.717 distance: 43 - 50: 6.341 distance: 44 - 45: 25.589 distance: 44 - 56: 31.619 distance: 46 - 47: 11.029 distance: 46 - 48: 9.725 distance: 46 - 51: 7.952 distance: 47 - 52: 13.275 distance: 48 - 53: 5.054 distance: 48 - 54: 4.581 distance: 48 - 55: 7.356 distance: 56 - 57: 13.062 distance: 56 - 63: 12.052 distance: 57 - 58: 23.728 distance: 57 - 60: 10.805 distance: 57 - 64: 9.202 distance: 58 - 59: 42.222 distance: 58 - 70: 16.413 distance: 62 - 69: 3.276 distance: 70 - 71: 20.154 distance: 70 - 78: 4.883 distance: 71 - 72: 29.143 distance: 71 - 74: 32.688 distance: 71 - 79: 15.552 distance: 72 - 73: 17.227 distance: 72 - 89: 35.874 distance: 73 - 109: 28.762 distance: 74 - 75: 12.917 distance: 74 - 80: 11.464 distance: 74 - 81: 5.938 distance: 75 - 76: 9.807 distance: 75 - 77: 10.266 distance: 75 - 82: 6.909 distance: 89 - 90: 14.228 distance: 89 - 94: 15.179 distance: 90 - 91: 21.892 distance: 90 - 93: 15.627 distance: 90 - 95: 32.056 distance: 91 - 92: 18.179 distance: 91 - 99: 23.964 distance: 92 - 121: 53.011 distance: 93 - 96: 22.623 distance: 93 - 97: 15.988 distance: 93 - 98: 12.856 distance: 99 - 100: 5.275 distance: 99 - 104: 23.685 distance: 100 - 101: 17.888 distance: 100 - 103: 14.335 distance: 100 - 105: 18.911 distance: 101 - 102: 22.378 distance: 101 - 109: 17.754 distance: 103 - 106: 9.919 distance: 103 - 107: 9.647 distance: 103 - 108: 8.690 distance: 109 - 110: 10.639 distance: 109 - 117: 23.503 distance: 110 - 111: 17.329 distance: 110 - 113: 7.168 distance: 110 - 118: 15.329 distance: 111 - 112: 16.521 distance: 111 - 121: 11.409 distance: 113 - 114: 5.470 distance: 113 - 119: 4.837 distance: 113 - 120: 5.692 distance: 114 - 115: 4.197 distance: 114 - 116: 5.529 distance: 121 - 122: 14.120 distance: 121 - 128: 6.462 distance: 122 - 123: 18.348 distance: 122 - 125: 5.980 distance: 122 - 129: 17.812 distance: 123 - 124: 24.120 distance: 123 - 137: 19.722 distance: 125 - 126: 10.603 distance: 125 - 127: 9.543 distance: 125 - 130: 13.099 distance: 126 - 131: 5.088 distance: 126 - 133: 3.247 distance: 127 - 134: 6.254 distance: 127 - 135: 4.014 distance: 127 - 136: 5.282 distance: 137 - 138: 15.845 distance: 137 - 145: 7.443 distance: 138 - 139: 28.663 distance: 138 - 141: 7.275 distance: 138 - 146: 10.549 distance: 139 - 140: 30.652 distance: 139 - 154: 26.558 distance: 141 - 147: 5.578 distance: 141 - 148: 10.052 distance: 142 - 143: 4.148 distance: 142 - 150: 3.291 distance: 143 - 144: 3.146 distance: 154 - 155: 9.590 distance: 154 - 165: 41.002 distance: 155 - 156: 8.093 distance: 155 - 158: 32.829 distance: 155 - 166: 32.561 distance: 156 - 157: 19.104 distance: 156 - 178: 20.551 distance: 158 - 159: 22.649 distance: 158 - 167: 4.837 distance: 158 - 168: 15.730 distance: 159 - 160: 11.500 distance: 159 - 169: 10.489 distance: 159 - 170: 11.029 distance: 160 - 161: 5.195 distance: 161 - 162: 3.925