Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 13:19:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njg_3654/07_2023/5njg_3654.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njg_3654/07_2023/5njg_3654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njg_3654/07_2023/5njg_3654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njg_3654/07_2023/5njg_3654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njg_3654/07_2023/5njg_3654.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njg_3654/07_2023/5njg_3654.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.008 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 50 5.16 5 C 5234 2.51 5 N 1288 2.21 5 O 1466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 426": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 65": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 8038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2249 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 277} Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2249 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 277} Chain: "C" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "F" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 100} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.53, per 1000 atoms: 0.56 Number of scatterers: 8038 At special positions: 0 Unit cell: (82.081, 94.549, 107.017, 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 50 16.00 O 1466 8.00 N 1288 7.00 C 5234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.05 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG G 1 " - " ASN A 596 " " NAG H 1 " - " ASN B 596 " Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1872 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 47.1% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 373 through 391 removed outlier: 3.616A pdb=" N LEU A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 413 removed outlier: 4.023A pdb=" N SER A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 422 through 441 removed outlier: 3.526A pdb=" N GLY A 428 " --> pdb=" O GLN A 424 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 435 " --> pdb=" O PHE A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 removed outlier: 3.739A pdb=" N LEU A 447 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 448 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL A 450 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 502 through 529 Processing helix chain 'A' and resid 533 through 550 removed outlier: 4.282A pdb=" N ALA A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 removed outlier: 4.324A pdb=" N VAL A 556 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN A 557 " --> pdb=" O GLY A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 552 through 557' Processing helix chain 'A' and resid 558 through 561 removed outlier: 3.777A pdb=" N ILE A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 558 through 561' Processing helix chain 'A' and resid 565 through 571 removed outlier: 3.507A pdb=" N LEU A 568 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN A 569 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR A 570 " --> pdb=" O TRP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 582 removed outlier: 3.899A pdb=" N TYR A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 587 removed outlier: 3.582A pdb=" N PHE A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 587 " --> pdb=" O HIS A 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 582 through 587' Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 623 through 652 removed outlier: 3.773A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 391 removed outlier: 3.615A pdb=" N LEU B 377 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 413 removed outlier: 4.023A pdb=" N SER B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing helix chain 'B' and resid 422 through 441 removed outlier: 3.525A pdb=" N GLY B 428 " --> pdb=" O GLN B 424 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 435 " --> pdb=" O PHE B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.739A pdb=" N LEU B 447 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE B 448 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL B 450 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 502 through 529 Processing helix chain 'B' and resid 533 through 550 removed outlier: 4.281A pdb=" N ALA B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 4.323A pdb=" N VAL B 556 " --> pdb=" O SER B 552 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN B 557 " --> pdb=" O GLY B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 552 through 557' Processing helix chain 'B' and resid 558 through 561 removed outlier: 3.777A pdb=" N ILE B 561 " --> pdb=" O LEU B 558 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 558 through 561' Processing helix chain 'B' and resid 565 through 571 removed outlier: 3.507A pdb=" N LEU B 568 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 582 removed outlier: 3.899A pdb=" N TYR B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 587 removed outlier: 3.582A pdb=" N PHE B 586 " --> pdb=" O GLN B 582 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 587 " --> pdb=" O HIS B 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 582 through 587' Processing helix chain 'B' and resid 610 through 618 Processing helix chain 'B' and resid 623 through 652 removed outlier: 3.774A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.608A pdb=" N THR C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 79 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.222A pdb=" N ARG C 39 " --> pdb=" O TRP C 48 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP C 48 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.501A pdb=" N TYR C 108 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.140A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG D 45 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.608A pdb=" N THR E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.222A pdb=" N ARG E 39 " --> pdb=" O TRP E 48 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N TRP E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.501A pdb=" N TYR E 108 " --> pdb=" O THR E 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.140A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG F 45 " --> pdb=" O GLN F 37 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1170 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 3.65 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: 1319 1.32 - 1.44: 2395 1.44 - 1.57: 4452 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8242 Sorted by residual: bond pdb=" CB GLN A 569 " pdb=" CG GLN A 569 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 7.94e+00 bond pdb=" CB GLN B 569 " pdb=" CG GLN B 569 " ideal model delta sigma weight residual 1.520 1.437 0.083 3.00e-02 1.11e+03 7.71e+00 bond pdb=" C ASN A 601 " pdb=" N PRO A 602 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 7.02e+00 bond pdb=" C ASN B 601 " pdb=" N PRO B 602 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.83e+00 bond pdb=" C ASN F 42 " pdb=" N ALA F 43 " ideal model delta sigma weight residual 1.340 1.195 0.146 5.87e-02 2.90e+02 6.15e+00 ... (remaining 8237 not shown) Histogram of bond angle deviations from ideal: 98.17 - 105.71: 189 105.71 - 113.25: 4435 113.25 - 120.79: 4007 120.79 - 128.33: 2491 128.33 - 135.87: 74 Bond angle restraints: 11196 Sorted by residual: angle pdb=" C PRO A 602 " pdb=" N CYS A 603 " pdb=" CA CYS A 603 " ideal model delta sigma weight residual 122.17 113.86 8.31 1.62e+00 3.81e-01 2.63e+01 angle pdb=" C PRO B 602 " pdb=" N CYS B 603 " pdb=" CA CYS B 603 " ideal model delta sigma weight residual 122.17 113.88 8.29 1.62e+00 3.81e-01 2.62e+01 angle pdb=" N PRO A 602 " pdb=" CA PRO A 602 " pdb=" C PRO A 602 " ideal model delta sigma weight residual 112.47 122.52 -10.05 2.06e+00 2.36e-01 2.38e+01 angle pdb=" N PRO B 602 " pdb=" CA PRO B 602 " pdb=" C PRO B 602 " ideal model delta sigma weight residual 112.47 122.48 -10.01 2.06e+00 2.36e-01 2.36e+01 angle pdb=" C TYR B 605 " pdb=" CA TYR B 605 " pdb=" CB TYR B 605 " ideal model delta sigma weight residual 111.48 103.98 7.50 1.59e+00 3.96e-01 2.23e+01 ... (remaining 11191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.45: 4319 14.45 - 28.89: 327 28.89 - 43.34: 79 43.34 - 57.79: 23 57.79 - 72.23: 5 Dihedral angle restraints: 4753 sinusoidal: 1815 harmonic: 2938 Sorted by residual: dihedral pdb=" CA ASN A 601 " pdb=" C ASN A 601 " pdb=" N PRO A 602 " pdb=" CA PRO A 602 " ideal model delta harmonic sigma weight residual 180.00 -124.15 -55.85 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA ASN B 601 " pdb=" C ASN B 601 " pdb=" N PRO B 602 " pdb=" CA PRO B 602 " ideal model delta harmonic sigma weight residual -180.00 -124.17 -55.83 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA PRO A 602 " pdb=" C PRO A 602 " pdb=" N CYS A 603 " pdb=" CA CYS A 603 " ideal model delta harmonic sigma weight residual 180.00 137.89 42.11 0 5.00e+00 4.00e-02 7.09e+01 ... (remaining 4750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1084 0.094 - 0.188: 186 0.188 - 0.282: 6 0.282 - 0.376: 4 0.376 - 0.470: 4 Chirality restraints: 1284 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 596 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B 596 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CB ILE A 573 " pdb=" CA ILE A 573 " pdb=" CG1 ILE A 573 " pdb=" CG2 ILE A 573 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 1281 not shown) Planarity restraints: 1372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 601 " -0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO A 602 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 602 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 602 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 601 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.80e+00 pdb=" N PRO B 602 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 602 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 602 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 576 " 0.019 2.00e-02 2.50e+03 1.82e-02 6.62e+00 pdb=" CG TYR B 576 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR B 576 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 576 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 576 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 576 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 576 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 576 " 0.001 2.00e-02 2.50e+03 ... (remaining 1369 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 848 2.73 - 3.27: 7957 3.27 - 3.81: 13432 3.81 - 4.36: 16003 4.36 - 4.90: 27840 Nonbonded interactions: 66080 Sorted by model distance: nonbonded pdb=" O ARG B 575 " pdb=" OG1 THR B 579 " model vdw 2.183 2.440 nonbonded pdb=" O ARG A 575 " pdb=" OG1 THR A 579 " model vdw 2.184 2.440 nonbonded pdb=" O VAL A 508 " pdb=" OG1 THR A 512 " model vdw 2.264 2.440 nonbonded pdb=" O VAL B 508 " pdb=" OG1 THR B 512 " model vdw 2.264 2.440 nonbonded pdb=" O CYS A 438 " pdb=" OG SER A 441 " model vdw 2.273 2.440 ... (remaining 66075 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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: 0.010 Extract box with map and model: 3.550 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.640 Find NCS groups from input model: 0.460 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.014 0.146 8242 Z= 0.880 Angle : 1.312 12.489 11196 Z= 0.687 Chirality : 0.071 0.470 1284 Planarity : 0.009 0.070 1370 Dihedral : 11.426 70.998 2860 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.94 % Favored : 92.86 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.61 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.21), residues: 1008 helix: -3.07 (0.15), residues: 382 sheet: -1.95 (0.28), residues: 226 loop : -2.70 (0.28), residues: 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 0.977 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 outliers start: 6 outliers final: 1 residues processed: 263 average time/residue: 0.2129 time to fit residues: 74.3379 Evaluate side-chains 165 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0777 time to fit residues: 1.4268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 376 GLN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN B 424 GLN B 629 ASN C 40 GLN C 82 GLN D 38 GLN E 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 8242 Z= 0.225 Angle : 0.763 9.459 11196 Z= 0.385 Chirality : 0.044 0.201 1284 Planarity : 0.006 0.070 1370 Dihedral : 7.165 66.497 1100 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.37 % Favored : 95.44 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -1.87 (0.25), residues: 1008 helix: -0.48 (0.23), residues: 394 sheet: -1.28 (0.32), residues: 212 loop : -1.87 (0.31), residues: 402 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 208 average time/residue: 0.1592 time to fit residues: 47.9398 Evaluate side-chains 166 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 159 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0913 time to fit residues: 2.3488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 96 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 569 GLN A 617 GLN B 424 GLN B 437 GLN B 569 GLN C 82 GLN D 38 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 8242 Z= 0.195 Angle : 0.679 9.084 11196 Z= 0.343 Chirality : 0.043 0.182 1284 Planarity : 0.005 0.064 1370 Dihedral : 6.481 61.376 1100 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.06 % Favored : 94.74 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -0.78 (0.26), residues: 1008 helix: 0.55 (0.25), residues: 396 sheet: -0.73 (0.36), residues: 192 loop : -1.38 (0.31), residues: 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 208 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 217 average time/residue: 0.1587 time to fit residues: 49.8202 Evaluate side-chains 180 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0797 time to fit residues: 2.4852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 0.0000 chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN B 437 GLN B 569 GLN C 82 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 8242 Z= 0.279 Angle : 0.683 8.073 11196 Z= 0.349 Chirality : 0.044 0.194 1284 Planarity : 0.005 0.060 1370 Dihedral : 6.084 52.915 1100 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.06 % Favored : 94.74 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -0.37 (0.27), residues: 1008 helix: 1.02 (0.26), residues: 390 sheet: -0.51 (0.37), residues: 192 loop : -1.29 (0.32), residues: 426 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 202 average time/residue: 0.1744 time to fit residues: 50.8588 Evaluate side-chains 186 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0797 time to fit residues: 3.8249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.0570 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN A 557 ASN A 569 GLN B 557 ASN B 569 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8242 Z= 0.177 Angle : 0.661 11.922 11196 Z= 0.329 Chirality : 0.043 0.226 1284 Planarity : 0.005 0.060 1370 Dihedral : 5.726 46.100 1100 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.06 % Favored : 94.74 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -0.15 (0.27), residues: 1008 helix: 1.24 (0.26), residues: 394 sheet: -0.44 (0.35), residues: 210 loop : -1.22 (0.33), residues: 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 185 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 190 average time/residue: 0.1549 time to fit residues: 42.8650 Evaluate side-chains 180 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0717 time to fit residues: 2.2963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 8242 Z= 0.245 Angle : 0.686 10.308 11196 Z= 0.342 Chirality : 0.044 0.197 1284 Planarity : 0.005 0.058 1370 Dihedral : 5.569 42.310 1100 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.26 % Favored : 94.54 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: -0.04 (0.28), residues: 1008 helix: 1.27 (0.26), residues: 402 sheet: -0.38 (0.37), residues: 190 loop : -1.11 (0.33), residues: 416 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 181 average time/residue: 0.1659 time to fit residues: 43.2396 Evaluate side-chains 173 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1406 time to fit residues: 2.9412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8144 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 8242 Z= 0.184 Angle : 0.643 8.412 11196 Z= 0.325 Chirality : 0.042 0.182 1284 Planarity : 0.005 0.054 1370 Dihedral : 5.373 41.143 1100 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.96 % Favored : 94.84 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: 0.04 (0.28), residues: 1008 helix: 1.36 (0.26), residues: 402 sheet: -0.45 (0.35), residues: 208 loop : -1.05 (0.34), residues: 398 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 180 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 184 average time/residue: 0.1623 time to fit residues: 43.1076 Evaluate side-chains 172 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0827 time to fit residues: 2.0040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.0770 chunk 74 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 overall best weight: 0.8342 ------------------------------------------------------------------------------- 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: 0.8142 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8242 Z= 0.191 Angle : 0.663 10.424 11196 Z= 0.332 Chirality : 0.042 0.195 1284 Planarity : 0.005 0.051 1370 Dihedral : 5.278 41.805 1100 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.36 % Favored : 94.44 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: 0.14 (0.28), residues: 1008 helix: 1.43 (0.26), residues: 402 sheet: -0.43 (0.34), residues: 210 loop : -0.95 (0.34), residues: 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 177 average time/residue: 0.1650 time to fit residues: 42.3206 Evaluate side-chains 173 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0802 time to fit residues: 2.1567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 8242 Z= 0.247 Angle : 0.680 8.817 11196 Z= 0.342 Chirality : 0.044 0.190 1284 Planarity : 0.005 0.050 1370 Dihedral : 5.283 37.082 1100 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.56 % Favored : 94.25 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: 0.13 (0.28), residues: 1008 helix: 1.41 (0.26), residues: 408 sheet: -0.37 (0.35), residues: 208 loop : -1.03 (0.34), residues: 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 169 average time/residue: 0.1537 time to fit residues: 38.0868 Evaluate side-chains 169 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1605 time to fit residues: 2.5004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.0470 chunk 61 optimal weight: 3.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8242 Z= 0.220 Angle : 0.681 10.043 11196 Z= 0.340 Chirality : 0.043 0.195 1284 Planarity : 0.004 0.048 1370 Dihedral : 5.217 35.822 1100 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.36 % Favored : 94.44 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: 0.24 (0.28), residues: 1008 helix: 1.55 (0.26), residues: 404 sheet: -0.49 (0.35), residues: 200 loop : -0.88 (0.34), residues: 404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 169 average time/residue: 0.1706 time to fit residues: 41.1717 Evaluate side-chains 166 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0693 time to fit residues: 1.2749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 23 optimal weight: 0.0870 chunk 71 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 79 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN ** A 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN C 40 GLN D 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.129865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108623 restraints weight = 13467.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111310 restraints weight = 8210.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.112965 restraints weight = 5986.789| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 8242 Z= 0.175 Angle : 0.663 11.603 11196 Z= 0.330 Chirality : 0.042 0.196 1284 Planarity : 0.004 0.048 1370 Dihedral : 5.083 34.215 1100 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.36 % Favored : 94.44 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % 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: 0.33 (0.28), residues: 1008 helix: 1.52 (0.26), residues: 406 sheet: -0.35 (0.35), residues: 198 loop : -0.77 (0.34), residues: 404 =============================================================================== Job complete usr+sys time: 1729.08 seconds wall clock time: 32 minutes 27.37 seconds (1947.37 seconds total)