Starting phenix.real_space_refine on Sun Oct 13 10:37:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/10_2024/8hya_35085.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/10_2024/8hya_35085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/10_2024/8hya_35085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/10_2024/8hya_35085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/10_2024/8hya_35085.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hya_35085/10_2024/8hya_35085.cif" } resolution = 3.4 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= -0.003 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 9536 2.51 5 N 2364 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 14586 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7254 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 894} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'R16': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'R16': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 8.95, per 1000 atoms: 0.61 Number of scatterers: 14586 At special positions: 0 Unit cell: (115.44, 107.12, 127.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2626 8.00 N 2364 7.00 C 9536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.9 seconds 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 8 sheets defined 69.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 32 through 54 Processing helix chain 'A' and resid 60 through 77 removed outlier: 3.911A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 97 through 114 Proline residue: A 107 - end of helix removed outlier: 4.659A pdb=" N GLU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 125 through 151 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 172 through 183 Processing helix chain 'A' and resid 187 through 213 removed outlier: 3.599A pdb=" N THR A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 254 removed outlier: 4.086A pdb=" N ALA A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 279 removed outlier: 4.014A pdb=" N GLU A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 306 through 339 removed outlier: 4.258A pdb=" N SER A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 349 through 377 removed outlier: 3.669A pdb=" N PHE A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 419 through 450 removed outlier: 4.009A pdb=" N PHE A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 482 removed outlier: 3.678A pdb=" N ILE A 463 " --> pdb=" O PRO A 459 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.717A pdb=" N VAL A 496 " --> pdb=" O ASP A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 550 Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 576 through 582 removed outlier: 3.883A pdb=" N GLY A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 585 No H-bonds generated for 'chain 'A' and resid 583 through 585' Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 602 through 638 removed outlier: 5.885A pdb=" N SER A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALA A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 654 Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 670 through 699 Processing helix chain 'A' and resid 704 through 723 Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 740 through 744 removed outlier: 3.534A pdb=" N VAL A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 817 Processing helix chain 'A' and resid 837 through 844 Processing helix chain 'A' and resid 846 through 866 Processing helix chain 'A' and resid 866 through 871 Processing helix chain 'A' and resid 874 through 884 removed outlier: 4.087A pdb=" N LEU A 878 " --> pdb=" O ALA A 874 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 879 " --> pdb=" O MET A 875 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1042 Processing helix chain 'B' and resid 33 through 54 Processing helix chain 'B' and resid 60 through 77 removed outlier: 3.911A pdb=" N ALA B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 97 through 114 Proline residue: B 107 - end of helix removed outlier: 4.659A pdb=" N GLU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 125 through 151 Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 187 through 213 removed outlier: 3.599A pdb=" N THR B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 254 removed outlier: 4.086A pdb=" N ALA B 236 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 279 removed outlier: 4.015A pdb=" N GLU B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 299 Processing helix chain 'B' and resid 306 through 339 removed outlier: 4.258A pdb=" N SER B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 349 through 377 removed outlier: 3.669A pdb=" N PHE B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 419 through 450 removed outlier: 4.009A pdb=" N PHE B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN B 440 " --> pdb=" O THR B 436 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 450 " --> pdb=" O PHE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 482 removed outlier: 3.679A pdb=" N ILE B 463 " --> pdb=" O PRO B 459 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 500 removed outlier: 3.717A pdb=" N VAL B 496 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 550 Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.883A pdb=" N GLY B 580 " --> pdb=" O CYS B 576 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 581 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 602 through 638 removed outlier: 5.886A pdb=" N SER B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ALA B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 654 Processing helix chain 'B' and resid 655 through 668 Processing helix chain 'B' and resid 670 through 699 Processing helix chain 'B' and resid 704 through 723 Processing helix chain 'B' and resid 731 through 739 Processing helix chain 'B' and resid 740 through 744 removed outlier: 3.533A pdb=" N VAL B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 817 Processing helix chain 'B' and resid 837 through 844 Processing helix chain 'B' and resid 846 through 866 Processing helix chain 'B' and resid 866 through 871 Processing helix chain 'B' and resid 874 through 884 removed outlier: 4.086A pdb=" N LEU B 878 " --> pdb=" O ALA B 874 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 879 " --> pdb=" O MET B 875 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 880 " --> pdb=" O GLN B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1042 Processing sheet with id=AA1, first strand: chain 'A' and resid 761 through 762 removed outlier: 3.687A pdb=" N ASP A 783 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE A 833 " --> pdb=" O ILE A 781 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ILE A 781 " --> pdb=" O PHE A 833 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 835 " --> pdb=" O TRP A 779 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TRP A 779 " --> pdb=" O ILE A 835 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 807 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 802 through 803 removed outlier: 3.936A pdb=" N VAL A 786 " --> pdb=" O PHE A 803 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 889 through 892 removed outlier: 6.972A pdb=" N ARG A 966 " --> pdb=" O LEU A 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 913 through 914 Processing sheet with id=AA5, first strand: chain 'B' and resid 761 through 762 removed outlier: 3.686A pdb=" N ASP B 783 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE B 833 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE B 781 " --> pdb=" O PHE B 833 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 835 " --> pdb=" O TRP B 779 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TRP B 779 " --> pdb=" O ILE B 835 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 807 " --> pdb=" O ILE B 781 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 802 through 803 removed outlier: 3.936A pdb=" N VAL B 786 " --> pdb=" O PHE B 803 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 889 through 892 removed outlier: 6.972A pdb=" N ARG B 966 " --> pdb=" O LEU B 909 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 913 through 914 949 hydrogen bonds defined for protein. 2787 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: 5.76 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2314 1.32 - 1.44: 3852 1.44 - 1.56: 8616 1.56 - 1.69: 2 1.69 - 1.81: 102 Bond restraints: 14886 Sorted by residual: bond pdb=" C THR B 423 " pdb=" O THR B 423 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" C THR A 423 " pdb=" O THR A 423 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" N SER A 418 " pdb=" CA SER A 418 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" N SER B 418 " pdb=" CA SER B 418 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.07e+01 bond pdb=" CA SER A 418 " pdb=" CB SER A 418 " ideal model delta sigma weight residual 1.530 1.477 0.054 1.69e-02 3.50e+03 1.01e+01 ... (remaining 14881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 19702 2.10 - 4.19: 382 4.19 - 6.29: 50 6.29 - 8.39: 16 8.39 - 10.49: 6 Bond angle restraints: 20156 Sorted by residual: angle pdb=" N LEU B 424 " pdb=" CA LEU B 424 " pdb=" C LEU B 424 " ideal model delta sigma weight residual 111.33 104.16 7.17 1.21e+00 6.83e-01 3.51e+01 angle pdb=" N LEU A 424 " pdb=" CA LEU A 424 " pdb=" C LEU A 424 " ideal model delta sigma weight residual 111.33 104.17 7.16 1.21e+00 6.83e-01 3.50e+01 angle pdb=" C LEU B 424 " pdb=" N PHE B 425 " pdb=" CA PHE B 425 " ideal model delta sigma weight residual 120.28 112.63 7.65 1.34e+00 5.57e-01 3.26e+01 angle pdb=" C LEU A 424 " pdb=" N PHE A 425 " pdb=" CA PHE A 425 " ideal model delta sigma weight residual 120.28 112.63 7.65 1.34e+00 5.57e-01 3.26e+01 angle pdb=" N GLU A 420 " pdb=" CA GLU A 420 " pdb=" C GLU A 420 " ideal model delta sigma weight residual 111.07 105.65 5.42 1.07e+00 8.73e-01 2.57e+01 ... (remaining 20151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 7965 17.76 - 35.52: 765 35.52 - 53.28: 110 53.28 - 71.03: 12 71.03 - 88.79: 14 Dihedral angle restraints: 8866 sinusoidal: 3506 harmonic: 5360 Sorted by residual: dihedral pdb=" CA PHE A 152 " pdb=" C PHE A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta harmonic sigma weight residual -180.00 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PHE B 152 " pdb=" C PHE B 152 " pdb=" N PRO B 153 " pdb=" CA PRO B 153 " ideal model delta harmonic sigma weight residual 180.00 -159.82 -20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU B 168 " pdb=" C LEU B 168 " pdb=" N SER B 169 " pdb=" CA SER B 169 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 8863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2089 0.064 - 0.129: 263 0.129 - 0.193: 14 0.193 - 0.258: 2 0.258 - 0.322: 4 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CB THR B 421 " pdb=" CA THR B 421 " pdb=" OG1 THR B 421 " pdb=" CG2 THR B 421 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB THR A 421 " pdb=" CA THR A 421 " pdb=" OG1 THR A 421 " pdb=" CG2 THR A 421 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA GLU B 420 " pdb=" N GLU B 420 " pdb=" C GLU B 420 " pdb=" CB GLU B 420 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2369 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 489 " 0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO B 490 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 489 " -0.075 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO A 490 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 156 " 0.020 2.00e-02 2.50e+03 1.90e-02 9.03e+00 pdb=" CG TRP B 156 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 156 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 156 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 156 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 156 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 156 " 0.002 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2821 2.77 - 3.31: 15207 3.31 - 3.84: 24700 3.84 - 4.37: 27883 4.37 - 4.90: 48491 Nonbonded interactions: 119102 Sorted by model distance: nonbonded pdb=" OG SER A 897 " pdb=" O GLN A 958 " model vdw 2.242 3.040 nonbonded pdb=" OG SER B 897 " pdb=" O GLN B 958 " model vdw 2.243 3.040 nonbonded pdb=" NE2 GLN A 128 " pdb=" O TYR A 381 " model vdw 2.252 3.120 nonbonded pdb=" NE2 GLN B 128 " pdb=" O TYR B 381 " model vdw 2.252 3.120 nonbonded pdb=" NZ LYS A 386 " pdb=" O LEU A 451 " model vdw 2.276 3.120 ... (remaining 119097 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.060 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14886 Z= 0.250 Angle : 0.712 10.486 20156 Z= 0.400 Chirality : 0.044 0.322 2372 Planarity : 0.005 0.112 2472 Dihedral : 13.946 88.793 5410 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1836 helix: 1.41 (0.15), residues: 1212 sheet: 1.66 (0.57), residues: 80 loop : -1.47 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 156 HIS 0.003 0.001 HIS B 626 PHE 0.029 0.001 PHE B 425 TYR 0.041 0.002 TYR A 617 ARG 0.008 0.001 ARG B 551 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3672 Ramachandran restraints generated. 1836 Oldfield, 0 Emsley, 1836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 1.798 Fit side-chains REVERT: A 94 ASN cc_start: 0.8857 (t0) cc_final: 0.8613 (t0) REVERT: A 172 ASP cc_start: 0.8508 (t0) cc_final: 0.8222 (t70) REVERT: A 355 PHE cc_start: 0.8176 (m-10) cc_final: 0.7946 (m-80) REVERT: A 492 ASP cc_start: 0.7556 (t70) cc_final: 0.7344 (t70) REVERT: A 533 MET cc_start: 0.7611 (tmm) cc_final: 0.6994 (tmm) REVERT: A 613 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 755 HIS cc_start: 0.6008 (m-70) cc_final: 0.5565 (m-70) REVERT: A 914 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8413 (mmmt) REVERT: B 94 ASN cc_start: 0.8886 (t0) cc_final: 0.8608 (t0) REVERT: B 172 ASP cc_start: 0.8472 (t0) cc_final: 0.8222 (t0) REVERT: B 533 MET cc_start: 0.7573 (tmm) cc_final: 0.6928 (tmm) REVERT: B 613 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7206 (tm-30) REVERT: B 755 HIS cc_start: 0.5964 (m-70) cc_final: 0.5569 (m-70) REVERT: B 865 LEU cc_start: 0.8822 (mm) cc_final: 0.8477 (mt) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2639 time to fit residues: 129.6454 Evaluate side-chains 247 residues out of total 1606 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 0.0470 chunk 55 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 0.0170 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: