Starting phenix.real_space_refine on Wed Feb 12 15:02:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5njg_3654/02_2025/5njg_3654.cif Found real_map, /net/cci-nas-00/data/ceres_data/5njg_3654/02_2025/5njg_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/cci-nas-00/data/ceres_data/5njg_3654/02_2025/5njg_3654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5njg_3654/02_2025/5njg_3654.map" model { file = "/net/cci-nas-00/data/ceres_data/5njg_3654/02_2025/5njg_3654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5njg_3654/02_2025/5njg_3654.cif" } 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. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.25, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 2.10 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: 1.07 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: 2.24 Time building geometry restraints manager: 2.42 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: 0.00 - 2.50: 10553 2.50 - 5.00: 523 5.00 - 7.49: 95 7.49 - 9.99: 19 9.99 - 12.49: 6 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 3.040 nonbonded pdb=" O ARG A 575 " pdb=" OG1 THR A 579 " model vdw 2.184 3.040 nonbonded pdb=" O VAL A 508 " pdb=" OG1 THR A 512 " model vdw 2.264 3.040 nonbonded pdb=" O VAL B 508 " pdb=" OG1 THR B 512 " model vdw 2.264 3.040 nonbonded pdb=" O CYS A 438 " pdb=" OG SER A 441 " model vdw 2.273 3.040 ... (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 Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 0.960 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.630 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.030 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 6 poor density : 259 time to evaluate : 0.733 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: 0.2140 time to fit residues: 74.2309 Evaluate side-chains 171 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.781 ------------------------------------------------------------------------------- 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: 2.9990 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 557 ASN A 601 ASN B 424 GLN C 40 GLN C 82 GLN D 38 GLN E 82 GLN F 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.125408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103046 restraints weight = 13369.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105857 restraints weight = 7714.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107635 restraints weight = 5439.762| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8242 Z= 0.245 Angle : 0.782 9.316 11196 Z= 0.396 Chirality : 0.046 0.233 1284 Planarity : 0.006 0.058 1370 Dihedral : 8.187 66.168 1185 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.87 % Favored : 95.93 % Rotamer: Outliers : 1.94 % Allowed : 12.98 % Favored : 85.08 % 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: -1.80 (0.25), residues: 1008 helix: -0.48 (0.23), residues: 392 sheet: -1.23 (0.32), residues: 212 loop : -1.76 (0.31), residues: 404 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 0.022 0.002 PHE D 62 TYR 0.028 0.002 TYR B 645 ARG 0.004 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 222 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 PHE cc_start: 0.6478 (t80) cc_final: 0.6277 (t80) REVERT: A 379 TRP cc_start: 0.7331 (t-100) cc_final: 0.7057 (t60) REVERT: B 373 PHE cc_start: 0.6477 (t80) cc_final: 0.6255 (t80) REVERT: B 479 LEU cc_start: 0.8833 (mt) cc_final: 0.8415 (tp) REVERT: B 512 THR cc_start: 0.9331 (m) cc_final: 0.9100 (p) REVERT: D 36 TYR cc_start: 0.8802 (m-80) cc_final: 0.8577 (m-80) REVERT: D 81 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: D 82 ASP cc_start: 0.8303 (m-30) cc_final: 0.8067 (m-30) REVERT: D 90 GLN cc_start: 0.9143 (pp30) cc_final: 0.8418 (pp30) REVERT: F 13 VAL cc_start: 0.7991 (m) cc_final: 0.7595 (p) REVERT: F 36 TYR cc_start: 0.8843 (m-80) cc_final: 0.8531 (m-80) REVERT: F 82 ASP cc_start: 0.8402 (m-30) cc_final: 0.8102 (m-30) outliers start: 17 outliers final: 6 residues processed: 211 average time/residue: 0.1640 time to fit residues: 49.9299 Evaluate side-chains 176 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 424 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 2 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 71 optimal weight: 0.0010 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 629 ASN B 437 GLN B 557 ASN B 629 ASN C 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.127348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105932 restraints weight = 13659.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108710 restraints weight = 7922.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110512 restraints weight = 5604.328| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3197 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= 0.184 Angle : 0.698 9.132 11196 Z= 0.353 Chirality : 0.044 0.226 1284 Planarity : 0.005 0.053 1370 Dihedral : 7.359 62.226 1184 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.86 % Favored : 94.94 % Rotamer: Outliers : 2.62 % Allowed : 16.40 % Favored : 80.98 % 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: -0.74 (0.27), residues: 1008 helix: 0.58 (0.25), residues: 396 sheet: -0.69 (0.34), residues: 212 loop : -1.38 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 35 HIS 0.001 0.000 HIS B 583 PHE 0.015 0.002 PHE D 62 TYR 0.031 0.002 TYR A 645 ARG 0.003 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 232 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.925 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 511 PHE cc_start: 0.8794 (t80) cc_final: 0.8416 (t80) REVERT: B 373 PHE cc_start: 0.6571 (t80) cc_final: 0.6329 (t80) REVERT: B 479 LEU cc_start: 0.8960 (mt) cc_final: 0.8530 (tp) REVERT: B 511 PHE cc_start: 0.8628 (t80) cc_final: 0.7990 (t80) REVERT: B 512 THR cc_start: 0.9343 (m) cc_final: 0.9140 (p) REVERT: B 620 ASP cc_start: 0.8404 (t0) cc_final: 0.8191 (t0) REVERT: C 46 LEU cc_start: 0.8208 (mt) cc_final: 0.8008 (mt) REVERT: C 100 TYR cc_start: 0.7177 (t80) cc_final: 0.6944 (t80) REVERT: D 13 VAL cc_start: 0.7610 (m) cc_final: 0.7198 (p) REVERT: D 18 ARG cc_start: 0.6681 (ttp80) cc_final: 0.6362 (ttp80) REVERT: D 31 ASN cc_start: 0.8836 (m-40) cc_final: 0.8513 (m110) REVERT: D 36 TYR cc_start: 0.8716 (m-80) cc_final: 0.8490 (m-80) REVERT: D 81 GLU cc_start: 0.7851 (pt0) cc_final: 0.7466 (pt0) REVERT: D 82 ASP cc_start: 0.8223 (m-30) cc_final: 0.7982 (m-30) REVERT: D 90 GLN cc_start: 0.9166 (pp30) cc_final: 0.8502 (pp30) REVERT: D 107 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5887 (tpt90) REVERT: F 13 VAL cc_start: 0.7890 (m) cc_final: 0.7550 (p) REVERT: F 36 TYR cc_start: 0.8820 (m-80) cc_final: 0.8330 (m-80) REVERT: F 82 ASP cc_start: 0.8295 (m-30) cc_final: 0.8028 (m-30) outliers start: 23 outliers final: 8 residues processed: 220 average time/residue: 0.1709 time to fit residues: 53.3532 Evaluate side-chains 183 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 419 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain D residue 107 ARG 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 3 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 36 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN B 437 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.129912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109128 restraints weight = 13743.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111684 restraints weight = 8444.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113272 restraints weight = 6197.288| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 8242 Z= 0.179 Angle : 0.654 8.451 11196 Z= 0.332 Chirality : 0.042 0.225 1284 Planarity : 0.005 0.055 1370 Dihedral : 6.762 57.099 1184 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.46 % Favored : 95.34 % Rotamer: Outliers : 3.42 % Allowed : 18.11 % Favored : 78.47 % 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: -0.27 (0.27), residues: 1008 helix: 1.01 (0.26), residues: 396 sheet: -0.35 (0.36), residues: 212 loop : -1.25 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 35 HIS 0.001 0.000 HIS A 630 PHE 0.013 0.001 PHE E 79 TYR 0.028 0.002 TYR A 645 ARG 0.003 0.000 ARG A 378 *********************** 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 234 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.719 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 451 GLU cc_start: 0.7293 (pt0) cc_final: 0.6865 (pt0) REVERT: A 482 ARG cc_start: 0.8654 (mmp80) cc_final: 0.7839 (mmt180) REVERT: A 511 PHE cc_start: 0.8752 (t80) cc_final: 0.8358 (t80) REVERT: B 373 PHE cc_start: 0.6700 (t80) cc_final: 0.6488 (t80) REVERT: B 479 LEU cc_start: 0.8988 (mt) cc_final: 0.8569 (tp) REVERT: B 509 MET cc_start: 0.8612 (ttt) cc_final: 0.8264 (ttt) REVERT: B 511 PHE cc_start: 0.8573 (t80) cc_final: 0.8080 (t80) REVERT: C 11 LEU cc_start: 0.8355 (tp) cc_final: 0.7653 (mp) REVERT: D 13 VAL cc_start: 0.7573 (m) cc_final: 0.7234 (p) REVERT: D 18 ARG cc_start: 0.6665 (ttp80) cc_final: 0.6390 (ttp80) REVERT: D 31 ASN cc_start: 0.8709 (m-40) cc_final: 0.8406 (m110) REVERT: D 36 TYR cc_start: 0.8686 (m-80) cc_final: 0.8450 (m-10) REVERT: D 81 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7404 (pt0) REVERT: D 82 ASP cc_start: 0.8160 (m-30) cc_final: 0.7903 (m-30) REVERT: D 90 GLN cc_start: 0.9171 (pp30) cc_final: 0.8527 (pp30) REVERT: D 107 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.5856 (tpt90) REVERT: F 13 VAL cc_start: 0.7859 (m) cc_final: 0.7584 (p) REVERT: F 36 TYR cc_start: 0.8743 (m-80) cc_final: 0.8311 (m-80) outliers start: 30 outliers final: 18 residues processed: 218 average time/residue: 0.1680 time to fit residues: 52.5591 Evaluate side-chains 205 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 489 PHE 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 B residue 539 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 107 ARG 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 85 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.105980 restraints weight = 13685.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108483 restraints weight = 8541.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110036 restraints weight = 6313.988| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8242 Z= 0.239 Angle : 0.691 12.111 11196 Z= 0.351 Chirality : 0.044 0.246 1284 Planarity : 0.005 0.053 1370 Dihedral : 6.536 53.155 1184 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.86 % Favored : 94.94 % Rotamer: Outliers : 3.87 % Allowed : 19.02 % Favored : 77.11 % 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: -0.26 (0.27), residues: 1008 helix: 1.09 (0.26), residues: 408 sheet: -0.57 (0.37), residues: 200 loop : -1.23 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 35 HIS 0.003 0.001 HIS B 630 PHE 0.014 0.002 PHE E 79 TYR 0.028 0.002 TYR A 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 215 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.7330 (pt0) cc_final: 0.6855 (pt0) REVERT: A 482 ARG cc_start: 0.8685 (mmp80) cc_final: 0.7989 (mmt180) REVERT: A 511 PHE cc_start: 0.8755 (t80) cc_final: 0.8529 (t80) REVERT: B 479 LEU cc_start: 0.8950 (mt) cc_final: 0.8515 (tp) REVERT: B 511 PHE cc_start: 0.8643 (t80) cc_final: 0.8077 (t80) REVERT: C 11 LEU cc_start: 0.8403 (tp) cc_final: 0.7741 (mp) REVERT: D 13 VAL cc_start: 0.7586 (m) cc_final: 0.7287 (p) REVERT: D 31 ASN cc_start: 0.8580 (m-40) cc_final: 0.8362 (m-40) REVERT: D 36 TYR cc_start: 0.8752 (m-80) cc_final: 0.8482 (m-10) REVERT: D 81 GLU cc_start: 0.7822 (pt0) cc_final: 0.7428 (pt0) REVERT: D 90 GLN cc_start: 0.9305 (pp30) cc_final: 0.8526 (pp30) REVERT: D 107 ARG cc_start: 0.6087 (OUTLIER) cc_final: 0.5876 (tpt90) REVERT: F 13 VAL cc_start: 0.7733 (m) cc_final: 0.7481 (p) REVERT: F 36 TYR cc_start: 0.8813 (m-80) cc_final: 0.8340 (m-80) outliers start: 34 outliers final: 27 residues processed: 197 average time/residue: 0.1728 time to fit residues: 48.3597 Evaluate side-chains 197 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 549 MET 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 440 SER Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 107 ARG 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 17 ASP Chi-restraints excluded: chain F residue 53 SER 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 93 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107518 restraints weight = 13691.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109972 restraints weight = 8475.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111547 restraints weight = 6279.799| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8242 Z= 0.208 Angle : 0.669 9.930 11196 Z= 0.339 Chirality : 0.043 0.202 1284 Planarity : 0.005 0.053 1370 Dihedral : 6.303 52.434 1184 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.63 % Rotamer: Outliers : 3.42 % Allowed : 20.27 % Favored : 76.31 % 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: -0.07 (0.27), residues: 1008 helix: 1.33 (0.26), residues: 408 sheet: -0.55 (0.36), residues: 200 loop : -1.18 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 35 HIS 0.002 0.001 HIS B 630 PHE 0.014 0.002 PHE B 545 TYR 0.027 0.002 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 211 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.7295 (pt0) cc_final: 0.6853 (pt0) REVERT: A 482 ARG cc_start: 0.8692 (mmp80) cc_final: 0.7982 (mmt180) REVERT: A 511 PHE cc_start: 0.8768 (t80) cc_final: 0.8562 (t80) REVERT: B 479 LEU cc_start: 0.8984 (mt) cc_final: 0.8512 (tp) REVERT: B 511 PHE cc_start: 0.8632 (t80) cc_final: 0.8213 (t80) REVERT: C 11 LEU cc_start: 0.8343 (tp) cc_final: 0.7722 (mp) REVERT: D 13 VAL cc_start: 0.7644 (m) cc_final: 0.7437 (p) REVERT: D 36 TYR cc_start: 0.8750 (m-80) cc_final: 0.8421 (m-80) REVERT: D 90 GLN cc_start: 0.9280 (pp30) cc_final: 0.8538 (pp30) REVERT: F 13 VAL cc_start: 0.7708 (m) cc_final: 0.7466 (p) REVERT: F 36 TYR cc_start: 0.8799 (m-80) cc_final: 0.8249 (m-80) outliers start: 30 outliers final: 25 residues processed: 195 average time/residue: 0.1672 time to fit residues: 47.1433 Evaluate side-chains 200 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 549 MET 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 440 SER Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 85 THR 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 53 SER 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 52 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.127942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106187 restraints weight = 13676.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.108779 restraints weight = 8427.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110437 restraints weight = 6218.835| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4414 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= 0.196 Angle : 0.677 11.978 11196 Z= 0.340 Chirality : 0.043 0.210 1284 Planarity : 0.005 0.052 1370 Dihedral : 6.075 47.424 1184 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.53 % Allowed : 21.18 % Favored : 75.28 % 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: 1.47 (0.27), residues: 406 sheet: -0.45 (0.35), residues: 200 loop : -1.06 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 35 HIS 0.003 0.001 HIS B 630 PHE 0.023 0.002 PHE A 545 TYR 0.026 0.002 TYR A 645 ARG 0.005 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 213 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.7353 (pt0) cc_final: 0.6923 (pt0) REVERT: A 482 ARG cc_start: 0.8737 (mmp80) cc_final: 0.8029 (mmt180) REVERT: A 511 PHE cc_start: 0.8773 (t80) cc_final: 0.8555 (t80) REVERT: B 479 LEU cc_start: 0.9020 (mt) cc_final: 0.8601 (tp) REVERT: B 511 PHE cc_start: 0.8685 (t80) cc_final: 0.8273 (t80) REVERT: C 11 LEU cc_start: 0.8394 (tp) cc_final: 0.7783 (mp) REVERT: C 80 PHE cc_start: 0.8647 (OUTLIER) cc_final: 0.8197 (m-10) REVERT: D 36 TYR cc_start: 0.8822 (m-80) cc_final: 0.8446 (m-80) REVERT: D 90 GLN cc_start: 0.9285 (pp30) cc_final: 0.8508 (pp30) REVERT: F 13 VAL cc_start: 0.7634 (m) cc_final: 0.7386 (p) REVERT: F 36 TYR cc_start: 0.8834 (m-80) cc_final: 0.8243 (m-80) outliers start: 31 outliers final: 25 residues processed: 197 average time/residue: 0.1594 time to fit residues: 45.5667 Evaluate side-chains 195 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 549 MET Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 85 THR 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 F residue 3 VAL Chi-restraints excluded: chain F residue 53 SER 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 90 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 5 optimal weight: 0.1980 chunk 91 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107464 restraints weight = 13706.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109958 restraints weight = 8660.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111517 restraints weight = 6459.266| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8242 Z= 0.189 Angle : 0.675 11.026 11196 Z= 0.342 Chirality : 0.043 0.209 1284 Planarity : 0.004 0.050 1370 Dihedral : 5.901 45.513 1184 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.76 % Allowed : 21.75 % Favored : 74.49 % 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: 1.49 (0.27), residues: 408 sheet: -0.39 (0.35), residues: 200 loop : -1.07 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 35 HIS 0.003 0.001 HIS B 630 PHE 0.019 0.001 PHE A 545 TYR 0.026 0.001 TYR B 645 ARG 0.005 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 218 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 185 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.7277 (pt0) cc_final: 0.6848 (pt0) REVERT: A 482 ARG cc_start: 0.8738 (mmp80) cc_final: 0.8058 (mmt180) REVERT: A 511 PHE cc_start: 0.8735 (t80) cc_final: 0.8501 (t80) REVERT: B 479 LEU cc_start: 0.8962 (mt) cc_final: 0.8451 (tp) REVERT: B 511 PHE cc_start: 0.8641 (t80) cc_final: 0.8281 (t80) REVERT: C 11 LEU cc_start: 0.8256 (tp) cc_final: 0.7711 (mp) REVERT: C 80 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: D 36 TYR cc_start: 0.8775 (m-80) cc_final: 0.8412 (m-80) REVERT: D 90 GLN cc_start: 0.9267 (pp30) cc_final: 0.8567 (pp30) REVERT: E 11 LEU cc_start: 0.8324 (tp) cc_final: 0.7673 (mp) REVERT: F 13 VAL cc_start: 0.7438 (m) cc_final: 0.6645 (p) REVERT: F 36 TYR cc_start: 0.8775 (m-80) cc_final: 0.8201 (m-80) outliers start: 33 outliers final: 23 residues processed: 202 average time/residue: 0.1738 time to fit residues: 51.4021 Evaluate side-chains 198 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 B residue 379 TRP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 440 SER 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 C residue 80 PHE Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 85 THR 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 96 CYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 53 SER 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 38 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN D 38 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.129159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107338 restraints weight = 13826.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.109963 restraints weight = 8459.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111667 restraints weight = 6216.053| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8242 Z= 0.192 Angle : 0.673 10.513 11196 Z= 0.341 Chirality : 0.043 0.219 1284 Planarity : 0.004 0.047 1370 Dihedral : 5.799 45.525 1184 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.30 % Allowed : 21.98 % Favored : 74.72 % 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: 0.22 (0.28), residues: 1008 helix: 1.52 (0.27), residues: 408 sheet: -0.33 (0.35), residues: 200 loop : -1.01 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 48 HIS 0.002 0.001 HIS B 630 PHE 0.023 0.001 PHE B 373 TYR 0.025 0.001 TYR A 645 ARG 0.004 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 210 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.7307 (pt0) cc_final: 0.6907 (pt0) REVERT: A 482 ARG cc_start: 0.8767 (mmp80) cc_final: 0.8109 (mmt180) REVERT: A 511 PHE cc_start: 0.8719 (t80) cc_final: 0.8452 (t80) REVERT: B 479 LEU cc_start: 0.8997 (mt) cc_final: 0.8468 (tp) REVERT: B 511 PHE cc_start: 0.8675 (t80) cc_final: 0.8302 (t80) REVERT: C 11 LEU cc_start: 0.8297 (tp) cc_final: 0.7757 (mp) REVERT: C 80 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: D 36 TYR cc_start: 0.8819 (m-80) cc_final: 0.8389 (m-80) REVERT: E 11 LEU cc_start: 0.8356 (tp) cc_final: 0.7722 (mp) REVERT: F 36 TYR cc_start: 0.8796 (m-80) cc_final: 0.8252 (m-80) outliers start: 29 outliers final: 24 residues processed: 193 average time/residue: 0.1606 time to fit residues: 44.9363 Evaluate side-chains 203 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 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 549 MET Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 496 MET 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 D residue 65 THR Chi-restraints excluded: chain D residue 85 THR 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 E residue 96 CYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 53 SER 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 17 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106957 restraints weight = 13636.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109399 restraints weight = 8620.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110906 restraints weight = 6461.255| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8242 Z= 0.246 Angle : 0.693 10.154 11196 Z= 0.352 Chirality : 0.045 0.225 1284 Planarity : 0.004 0.045 1370 Dihedral : 5.826 46.788 1184 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.42 % Allowed : 22.21 % Favored : 74.37 % 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: 0.23 (0.28), residues: 1008 helix: 1.52 (0.27), residues: 408 sheet: -0.36 (0.35), residues: 200 loop : -0.97 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 48 HIS 0.003 0.001 HIS B 630 PHE 0.025 0.002 PHE B 373 TYR 0.025 0.002 TYR A 645 ARG 0.005 0.000 ARG F 107 ********************** 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 to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.7353 (pt0) cc_final: 0.6934 (pt0) REVERT: A 482 ARG cc_start: 0.8737 (mmp80) cc_final: 0.8118 (mmt180) REVERT: A 511 PHE cc_start: 0.8761 (t80) cc_final: 0.8428 (t80) REVERT: B 479 LEU cc_start: 0.8968 (mt) cc_final: 0.8651 (tp) REVERT: B 511 PHE cc_start: 0.8734 (t80) cc_final: 0.8389 (t80) REVERT: C 11 LEU cc_start: 0.8330 (tp) cc_final: 0.7796 (mp) REVERT: C 80 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: C 103 LYS cc_start: 0.8734 (tttp) cc_final: 0.8330 (mtpp) REVERT: D 36 TYR cc_start: 0.8857 (m-80) cc_final: 0.8392 (m-80) REVERT: E 11 LEU cc_start: 0.8365 (tp) cc_final: 0.7735 (mp) REVERT: F 36 TYR cc_start: 0.8799 (m-80) cc_final: 0.8244 (m-80) outliers start: 30 outliers final: 24 residues processed: 194 average time/residue: 0.1600 time to fit residues: 45.1107 Evaluate side-chains 198 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 549 MET Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 496 MET 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 D residue 65 THR Chi-restraints excluded: chain D residue 85 THR 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 96 CYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 65 THR 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 79 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107324 restraints weight = 13724.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109720 restraints weight = 8570.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111249 restraints weight = 6437.181| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8242 Z= 0.225 Angle : 0.687 10.872 11196 Z= 0.349 Chirality : 0.044 0.213 1284 Planarity : 0.004 0.046 1370 Dihedral : 5.803 46.926 1184 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.08 % Allowed : 22.89 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 1008 helix: 1.58 (0.27), residues: 408 sheet: -0.34 (0.35), residues: 200 loop : -0.96 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 48 HIS 0.002 0.001 HIS B 630 PHE 0.029 0.002 PHE B 373 TYR 0.025 0.002 TYR A 645 ARG 0.004 0.000 ARG D 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2488.07 seconds wall clock time: 45 minutes 32.79 seconds (2732.79 seconds total)