Starting phenix.real_space_refine on Mon Mar 11 10:38:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njg_3654/03_2024/5njg_3654.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njg_3654/03_2024/5njg_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_3654/03_2024/5njg_3654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njg_3654/03_2024/5njg_3654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njg_3654/03_2024/5njg_3654.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njg_3654/03_2024/5njg_3654.pdb" } resolution = 3.78 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= 0.001 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.83, per 1000 atoms: 0.60 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: 3.32 Conformation dependent library (CDL) restraints added in 1.4 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: 0.95 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: 2.33 Time building geometry restraints manager: 3.60 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: 4384 14.45 - 28.89: 338 28.89 - 43.34: 79 43.34 - 57.79: 31 57.79 - 72.23: 5 Dihedral angle restraints: 4837 sinusoidal: 1899 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 4834 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: 0.770 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: 3.250 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.140 Find NCS groups from input model: 0.430 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- 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 : 11.637 70.998 2944 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 % Allowed : 3.42 % Favored : 95.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP C 109 HIS 0.004 0.002 HIS A 457 PHE 0.041 0.005 PHE D 98 TYR 0.044 0.005 TYR B 576 ARG 0.013 0.002 ARG B 426 *********************** 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 : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 TRP cc_start: 0.7422 (t-100) cc_final: 0.6817 (t60) REVERT: A 396 ILE cc_start: 0.8793 (mt) cc_final: 0.8500 (mp) REVERT: A 488 ILE cc_start: 0.8833 (mt) cc_final: 0.8591 (mt) REVERT: A 492 ILE cc_start: 0.8281 (pt) cc_final: 0.7780 (pt) REVERT: A 548 MET cc_start: 0.8118 (mtm) cc_final: 0.7614 (mtt) REVERT: A 624 TRP cc_start: 0.8288 (t60) cc_final: 0.7982 (t60) REVERT: B 373 PHE cc_start: 0.6804 (t80) cc_final: 0.6512 (t80) REVERT: B 379 TRP cc_start: 0.7367 (t-100) cc_final: 0.6686 (t60) REVERT: B 479 LEU cc_start: 0.8692 (mt) cc_final: 0.8320 (tp) REVERT: B 488 ILE cc_start: 0.8756 (mt) cc_final: 0.8452 (mt) REVERT: B 617 GLN cc_start: 0.8253 (tp-100) cc_final: 0.8026 (mm-40) REVERT: D 90 GLN cc_start: 0.8991 (pp30) cc_final: 0.8382 (pp30) REVERT: E 103 LYS cc_start: 0.8851 (tttt) cc_final: 0.8349 (tttp) outliers start: 6 outliers final: 1 residues processed: 263 average time/residue: 0.2081 time to fit residues: 72.6390 Evaluate side-chains 171 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 170 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2458 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 : 0.758 9.907 11196 Z= 0.382 Chirality : 0.045 0.204 1284 Planarity : 0.006 0.068 1370 Dihedral : 8.263 66.497 1185 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.27 % Favored : 95.54 % Rotamer: Outliers : 2.28 % Allowed : 12.76 % Favored : 84.97 % 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: -1.91 (0.25), residues: 1008 helix: -0.50 (0.23), residues: 396 sheet: -1.29 (0.32), residues: 212 loop : -1.92 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 624 HIS 0.002 0.001 HIS B 375 PHE 0.023 0.002 PHE D 62 TYR 0.027 0.002 TYR B 645 ARG 0.005 0.001 ARG D 18 *********************** 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 226 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 206 time to evaluate : 0.911 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: A 379 TRP cc_start: 0.7426 (t-100) cc_final: 0.7060 (t60) REVERT: B 373 PHE cc_start: 0.6671 (t80) cc_final: 0.6410 (t80) REVERT: B 379 TRP cc_start: 0.7357 (t-100) cc_final: 0.7097 (t60) REVERT: B 479 LEU cc_start: 0.8667 (mt) cc_final: 0.8366 (tp) REVERT: D 36 TYR cc_start: 0.8474 (m-80) cc_final: 0.8212 (m-80) REVERT: D 81 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: D 90 GLN cc_start: 0.8839 (pp30) cc_final: 0.8259 (pp30) REVERT: F 13 VAL cc_start: 0.7987 (m) cc_final: 0.7547 (p) outliers start: 20 outliers final: 9 residues processed: 213 average time/residue: 0.1559 time to fit residues: 47.8808 Evaluate side-chains 175 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 486 SER Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain F residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN A 569 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8242 Z= 0.195 Angle : 0.683 8.956 11196 Z= 0.345 Chirality : 0.043 0.185 1284 Planarity : 0.005 0.064 1370 Dihedral : 7.516 62.150 1184 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.76 % Favored : 95.04 % Rotamer: Outliers : 2.51 % Allowed : 17.88 % Favored : 79.61 % 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: -0.92 (0.26), residues: 1008 helix: 0.49 (0.25), residues: 398 sheet: -0.83 (0.34), residues: 212 loop : -1.55 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 35 HIS 0.001 0.000 HIS A 630 PHE 0.016 0.002 PHE F 62 TYR 0.030 0.002 TYR A 645 ARG 0.002 0.000 ARG D 18 *********************** 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 220 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 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: A 511 PHE cc_start: 0.8653 (t80) cc_final: 0.8410 (t80) REVERT: B 373 PHE cc_start: 0.6777 (t80) cc_final: 0.6529 (t80) REVERT: B 479 LEU cc_start: 0.8755 (mt) cc_final: 0.8485 (tp) REVERT: B 511 PHE cc_start: 0.8394 (t80) cc_final: 0.8008 (t80) REVERT: B 541 MET cc_start: 0.7315 (mmm) cc_final: 0.6916 (mmm) REVERT: C 100 TYR cc_start: 0.7136 (t80) cc_final: 0.6853 (t80) REVERT: D 13 VAL cc_start: 0.7513 (m) cc_final: 0.7138 (p) REVERT: D 31 ASN cc_start: 0.8542 (m-40) cc_final: 0.8289 (m110) REVERT: D 90 GLN cc_start: 0.8786 (pp30) cc_final: 0.8302 (pp30) REVERT: F 13 VAL cc_start: 0.7987 (m) cc_final: 0.7582 (p) outliers start: 22 outliers final: 11 residues processed: 208 average time/residue: 0.1560 time to fit residues: 47.2952 Evaluate side-chains 180 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 B 424 GLN B 569 GLN C 82 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 8242 Z= 0.392 Angle : 0.741 8.433 11196 Z= 0.378 Chirality : 0.047 0.197 1284 Planarity : 0.005 0.060 1370 Dihedral : 7.334 58.684 1184 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.46 % Favored : 94.35 % Rotamer: Outliers : 4.44 % Allowed : 19.70 % Favored : 75.85 % 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: -0.55 (0.27), residues: 1008 helix: 0.81 (0.25), residues: 400 sheet: -0.66 (0.37), residues: 192 loop : -1.33 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 109 HIS 0.003 0.001 HIS A 583 PHE 0.019 0.002 PHE E 79 TYR 0.030 0.002 TYR A 645 ARG 0.003 0.000 ARG E 39 *********************** 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 213 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 174 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8529 (mmp80) cc_final: 0.7781 (mmt180) REVERT: B 479 LEU cc_start: 0.8785 (mt) cc_final: 0.8514 (tp) REVERT: D 31 ASN cc_start: 0.8456 (m-40) cc_final: 0.8227 (m-40) REVERT: F 13 VAL cc_start: 0.7987 (m) cc_final: 0.7638 (p) outliers start: 39 outliers final: 27 residues processed: 196 average time/residue: 0.1579 time to fit residues: 44.6093 Evaluate side-chains 189 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 424 GLN Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain B residue 424 GLN Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 42 ASN Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.2980 chunk 1 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 0.0370 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 B 424 GLN B 557 ASN B 569 GLN E 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8242 Z= 0.168 Angle : 0.640 8.746 11196 Z= 0.325 Chirality : 0.043 0.221 1284 Planarity : 0.005 0.063 1370 Dihedral : 6.912 59.484 1184 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.56 % Favored : 95.24 % Rotamer: Outliers : 2.85 % Allowed : 21.41 % Favored : 75.74 % 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: -0.11 (0.27), residues: 1008 helix: 1.29 (0.26), residues: 390 sheet: -0.44 (0.36), residues: 210 loop : -1.17 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 35 HIS 0.001 0.000 HIS B 375 PHE 0.022 0.002 PHE B 545 TYR 0.027 0.002 TYR B 645 ARG 0.002 0.000 ARG E 39 *********************** 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 213 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 188 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8513 (mmp80) cc_final: 0.7796 (mmt180) REVERT: A 511 PHE cc_start: 0.8619 (t80) cc_final: 0.8265 (t80) REVERT: B 479 LEU cc_start: 0.8720 (mt) cc_final: 0.8426 (tp) REVERT: B 511 PHE cc_start: 0.8429 (t80) cc_final: 0.8143 (t80) REVERT: C 5 GLN cc_start: 0.7515 (tp40) cc_final: 0.7229 (tp-100) REVERT: C 11 LEU cc_start: 0.8312 (tp) cc_final: 0.7694 (mp) REVERT: D 13 VAL cc_start: 0.7620 (m) cc_final: 0.7320 (p) REVERT: D 31 ASN cc_start: 0.8261 (m-40) cc_final: 0.8043 (m-40) REVERT: F 13 VAL cc_start: 0.7957 (m) cc_final: 0.7085 (p) outliers start: 25 outliers final: 16 residues processed: 198 average time/residue: 0.1555 time to fit residues: 44.2566 Evaluate side-chains 192 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 7 optimal weight: 0.0670 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.0970 chunk 91 optimal weight: 0.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 569 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8242 Z= 0.174 Angle : 0.639 11.699 11196 Z= 0.321 Chirality : 0.042 0.177 1284 Planarity : 0.005 0.060 1370 Dihedral : 6.590 57.232 1184 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.16 % Favored : 94.64 % Rotamer: Outliers : 3.76 % Allowed : 21.98 % Favored : 74.26 % 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: 0.05 (0.28), residues: 1008 helix: 1.45 (0.27), residues: 392 sheet: -0.39 (0.35), residues: 210 loop : -1.11 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 35 HIS 0.001 0.000 HIS B 583 PHE 0.024 0.001 PHE A 545 TYR 0.026 0.001 TYR A 645 ARG 0.007 0.000 ARG D 18 *********************** 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 218 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8536 (mmp80) cc_final: 0.7849 (mmt180) REVERT: A 511 PHE cc_start: 0.8618 (t80) cc_final: 0.8403 (t80) REVERT: A 541 MET cc_start: 0.7075 (mmm) cc_final: 0.6822 (mmm) REVERT: B 479 LEU cc_start: 0.8749 (mt) cc_final: 0.8465 (tp) REVERT: B 511 PHE cc_start: 0.8408 (t80) cc_final: 0.8138 (t80) REVERT: C 5 GLN cc_start: 0.7486 (tp40) cc_final: 0.7215 (tp-100) REVERT: C 11 LEU cc_start: 0.8298 (tp) cc_final: 0.7708 (mp) REVERT: D 13 VAL cc_start: 0.7618 (m) cc_final: 0.7335 (p) REVERT: D 31 ASN cc_start: 0.8233 (m-40) cc_final: 0.7995 (m110) outliers start: 33 outliers final: 24 residues processed: 200 average time/residue: 0.1766 time to fit residues: 51.1951 Evaluate side-chains 195 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 85 THR 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: 0.8980 chunk 69 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8242 Z= 0.197 Angle : 0.648 10.549 11196 Z= 0.328 Chirality : 0.043 0.180 1284 Planarity : 0.005 0.059 1370 Dihedral : 6.445 56.728 1184 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.26 % Favored : 94.54 % Rotamer: Outliers : 3.64 % Allowed : 23.35 % Favored : 73.01 % 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: 0.16 (0.28), residues: 1008 helix: 1.51 (0.27), residues: 392 sheet: -0.26 (0.35), residues: 222 loop : -1.08 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 35 HIS 0.001 0.000 HIS A 583 PHE 0.020 0.002 PHE A 545 TYR 0.026 0.002 TYR A 645 ARG 0.008 0.000 ARG D 18 *********************** 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 211 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8517 (mmp80) cc_final: 0.7848 (mmt180) REVERT: A 511 PHE cc_start: 0.8605 (t80) cc_final: 0.8377 (t80) REVERT: B 479 LEU cc_start: 0.8703 (mt) cc_final: 0.8370 (tp) REVERT: B 511 PHE cc_start: 0.8408 (t80) cc_final: 0.8147 (t80) REVERT: C 5 GLN cc_start: 0.7460 (tp40) cc_final: 0.7213 (tp-100) REVERT: C 11 LEU cc_start: 0.8288 (tp) cc_final: 0.7719 (mp) REVERT: D 31 ASN cc_start: 0.8269 (m-40) cc_final: 0.7984 (m110) REVERT: E 11 LEU cc_start: 0.8301 (tp) cc_final: 0.7666 (mp) REVERT: F 17 ASP cc_start: 0.7559 (p0) cc_final: 0.7256 (p0) outliers start: 32 outliers final: 23 residues processed: 195 average time/residue: 0.1924 time to fit residues: 53.3351 Evaluate side-chains 196 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 85 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 617 GLN B 424 GLN B 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4361 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= 0.258 Angle : 0.663 9.508 11196 Z= 0.340 Chirality : 0.044 0.225 1284 Planarity : 0.005 0.056 1370 Dihedral : 6.430 58.025 1184 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.16 % Favored : 94.64 % Rotamer: Outliers : 3.64 % Allowed : 23.46 % Favored : 72.89 % 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: 0.21 (0.28), residues: 1008 helix: 1.52 (0.27), residues: 400 sheet: -0.32 (0.34), residues: 224 loop : -1.01 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 35 HIS 0.002 0.000 HIS B 583 PHE 0.021 0.002 PHE B 373 TYR 0.026 0.002 TYR B 645 ARG 0.010 0.000 ARG D 18 *********************** 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 208 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.7251 (pt0) cc_final: 0.6979 (pt0) REVERT: A 482 ARG cc_start: 0.8522 (mmp80) cc_final: 0.7901 (mmt180) REVERT: A 511 PHE cc_start: 0.8597 (t80) cc_final: 0.8352 (t80) REVERT: B 441 SER cc_start: 0.8969 (t) cc_final: 0.8743 (t) REVERT: B 479 LEU cc_start: 0.8731 (mt) cc_final: 0.8524 (tp) REVERT: B 511 PHE cc_start: 0.8474 (t80) cc_final: 0.8209 (t80) REVERT: C 11 LEU cc_start: 0.8265 (tp) cc_final: 0.7696 (mp) REVERT: C 80 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8179 (m-10) REVERT: D 31 ASN cc_start: 0.8269 (m-40) cc_final: 0.8038 (m-40) REVERT: E 11 LEU cc_start: 0.8305 (tp) cc_final: 0.7693 (mp) REVERT: F 17 ASP cc_start: 0.7766 (p0) cc_final: 0.7456 (p0) outliers start: 32 outliers final: 28 residues processed: 191 average time/residue: 0.1541 time to fit residues: 42.8212 Evaluate side-chains 202 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN B 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4472 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= 0.241 Angle : 0.659 8.673 11196 Z= 0.337 Chirality : 0.044 0.214 1284 Planarity : 0.005 0.053 1370 Dihedral : 6.375 58.636 1184 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.26 % Favored : 94.54 % Rotamer: Outliers : 4.33 % Allowed : 23.69 % Favored : 71.98 % 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: 0.28 (0.28), residues: 1008 helix: 1.54 (0.27), residues: 400 sheet: -0.27 (0.34), residues: 224 loop : -0.93 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 35 HIS 0.002 0.001 HIS A 583 PHE 0.020 0.002 PHE B 373 TYR 0.024 0.002 TYR A 645 ARG 0.010 0.000 ARG D 18 *********************** 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 213 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8561 (mmp80) cc_final: 0.7954 (mmt180) REVERT: A 511 PHE cc_start: 0.8617 (t80) cc_final: 0.8354 (t80) REVERT: B 492 ILE cc_start: 0.8756 (pt) cc_final: 0.8494 (pt) REVERT: B 511 PHE cc_start: 0.8497 (t80) cc_final: 0.8257 (t80) REVERT: C 11 LEU cc_start: 0.8273 (tp) cc_final: 0.7724 (mp) REVERT: C 80 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: D 13 VAL cc_start: 0.7440 (m) cc_final: 0.7195 (p) REVERT: D 31 ASN cc_start: 0.8245 (m-40) cc_final: 0.7986 (m110) REVERT: E 11 LEU cc_start: 0.8360 (tp) cc_final: 0.7741 (mp) REVERT: F 17 ASP cc_start: 0.7779 (p0) cc_final: 0.7431 (p0) REVERT: F 105 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7751 (pt0) outliers start: 38 outliers final: 32 residues processed: 192 average time/residue: 0.1419 time to fit residues: 40.1674 Evaluate side-chains 204 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 504 ASP Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.0770 chunk 61 optimal weight: 0.0980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN B 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4640 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= 0.162 Angle : 0.637 10.334 11196 Z= 0.323 Chirality : 0.042 0.203 1284 Planarity : 0.004 0.050 1370 Dihedral : 6.187 56.436 1184 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.96 % Favored : 94.84 % Rotamer: Outliers : 3.08 % Allowed : 24.72 % Favored : 72.21 % 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: 0.41 (0.28), residues: 1008 helix: 1.61 (0.27), residues: 398 sheet: -0.22 (0.34), residues: 222 loop : -0.79 (0.35), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 35 HIS 0.001 0.000 HIS A 583 PHE 0.020 0.001 PHE B 373 TYR 0.024 0.002 TYR A 645 ARG 0.010 0.000 ARG D 18 ********************** 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 208 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 ARG cc_start: 0.8566 (mmp80) cc_final: 0.7968 (mmt180) REVERT: A 511 PHE cc_start: 0.8552 (t80) cc_final: 0.8329 (t80) REVERT: B 492 ILE cc_start: 0.8706 (pt) cc_final: 0.8462 (pt) REVERT: B 511 PHE cc_start: 0.8452 (t80) cc_final: 0.8209 (t80) REVERT: C 11 LEU cc_start: 0.8259 (tp) cc_final: 0.7750 (mp) REVERT: C 80 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8056 (m-80) REVERT: D 13 VAL cc_start: 0.7377 (m) cc_final: 0.7132 (p) REVERT: D 31 ASN cc_start: 0.8167 (m-40) cc_final: 0.7832 (m110) REVERT: E 11 LEU cc_start: 0.8296 (tp) cc_final: 0.7722 (mp) REVERT: F 17 ASP cc_start: 0.7660 (p0) cc_final: 0.7340 (p0) outliers start: 27 outliers final: 22 residues processed: 192 average time/residue: 0.1594 time to fit residues: 44.0751 Evaluate side-chains 197 residues out of total 878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 TRP Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 521 SER Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 496 MET Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN B 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107799 restraints weight = 13588.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110224 restraints weight = 8647.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111769 restraints weight = 6509.457| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8242 Z= 0.204 Angle : 0.645 11.389 11196 Z= 0.326 Chirality : 0.043 0.190 1284 Planarity : 0.004 0.048 1370 Dihedral : 6.102 55.707 1184 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.26 % Favored : 94.54 % Rotamer: Outliers : 3.42 % Allowed : 24.03 % Favored : 72.55 % 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 (0.28), residues: 1008 helix: 1.57 (0.27), residues: 402 sheet: -0.19 (0.34), residues: 222 loop : -0.86 (0.36), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 92 HIS 0.002 0.000 HIS A 583 PHE 0.017 0.001 PHE B 373 TYR 0.024 0.001 TYR A 645 ARG 0.008 0.000 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1863.46 seconds wall clock time: 34 minutes 37.88 seconds (2077.88 seconds total)