Starting phenix.real_space_refine on Mon Nov 17 19:27:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5njg_3654/11_2025/5njg_3654.cif Found real_map, /net/cci-nas-00/data/ceres_data/5njg_3654/11_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_3654/11_2025/5njg_3654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5njg_3654/11_2025/5njg_3654.map" model { file = "/net/cci-nas-00/data/ceres_data/5njg_3654/11_2025/5njg_3654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5njg_3654/11_2025/5njg_3654.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 1.99, per 1000 atoms: 0.25 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: 0.66 Conformation dependent library (CDL) restraints added in 407.6 milliseconds 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: 0.19 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: 1.12 Time building geometry restraints manager: 0.89 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.400 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.690 ------------------------------------------------------------------------------- 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 8253 Z= 0.591 Angle : 1.334 13.153 11222 Z= 0.691 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.013 0.002 ARG B 426 TYR 0.044 0.005 TYR B 576 PHE 0.041 0.005 PHE D 98 TRP 0.037 0.004 TRP C 109 HIS 0.004 0.002 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.01388 ( 8242) covalent geometry : angle 1.31222 (11196) SS BOND : bond 0.01072 ( 7) SS BOND : angle 1.68298 ( 14) hydrogen bonds : bond 0.14370 ( 414) hydrogen bonds : angle 9.64209 ( 1170) link_BETA1-4 : bond 0.00456 ( 2) link_BETA1-4 : angle 4.37014 ( 6) link_NAG-ASN : bond 0.01234 ( 2) link_NAG-ASN : angle 9.49000 ( 6) *********************** 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 : 0.247 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: 0.8319 (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: 0.8027 (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: 0.8541 (tttp) outliers start: 6 outliers final: 1 residues processed: 263 average time/residue: 0.0963 time to fit residues: 33.9033 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 : 0.306 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.126447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104140 restraints weight = 13506.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106993 restraints weight = 7714.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108794 restraints weight = 5412.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.109951 restraints weight = 4337.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110713 restraints weight = 3769.420| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8253 Z= 0.155 Angle : 0.783 9.507 11222 Z= 0.392 Chirality : 0.045 0.232 1284 Planarity : 0.006 0.059 1370 Dihedral : 8.114 66.397 1185 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.77 % Favored : 96.03 % Rotamer: Outliers : 1.82 % Allowed : 13.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.25), residues: 1008 helix: -0.39 (0.23), residues: 392 sheet: -1.19 (0.32), residues: 212 loop : -1.72 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 18 TYR 0.028 0.002 TYR B 645 PHE 0.027 0.002 PHE A 511 TRP 0.018 0.002 TRP A 624 HIS 0.003 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8242) covalent geometry : angle 0.76990 (11196) SS BOND : bond 0.00556 ( 7) SS BOND : angle 1.59004 ( 14) hydrogen bonds : bond 0.04242 ( 414) hydrogen bonds : angle 5.75527 ( 1170) link_BETA1-4 : bond 0.00246 ( 2) link_BETA1-4 : angle 2.28746 ( 6) link_NAG-ASN : bond 0.00319 ( 2) link_NAG-ASN : angle 5.41388 ( 6) *********************** 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 233 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 0.300 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: B 373 PHE cc_start: 0.6399 (t80) cc_final: 0.6190 (t80) REVERT: B 479 LEU cc_start: 0.8823 (mt) cc_final: 0.8389 (tp) REVERT: B 512 THR cc_start: 0.9315 (m) cc_final: 0.9086 (p) REVERT: D 81 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7380 (pt0) REVERT: D 82 ASP cc_start: 0.8269 (m-30) cc_final: 0.8009 (m-30) REVERT: D 90 GLN cc_start: 0.9111 (pp30) cc_final: 0.8517 (pp30) REVERT: F 13 VAL cc_start: 0.7898 (m) cc_final: 0.7421 (p) REVERT: F 36 TYR cc_start: 0.8825 (m-80) cc_final: 0.8534 (m-80) outliers start: 16 outliers final: 6 residues processed: 223 average time/residue: 0.0723 time to fit residues: 23.1908 Evaluate side-chains 173 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 67 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 53 optimal weight: 0.0770 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 D 6 GLN F 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105883 restraints weight = 13574.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108583 restraints weight = 7981.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110191 restraints weight = 5717.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111358 restraints weight = 4691.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111983 restraints weight = 4081.783| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8253 Z= 0.137 Angle : 0.707 9.181 11222 Z= 0.356 Chirality : 0.044 0.235 1284 Planarity : 0.005 0.054 1370 Dihedral : 7.354 62.135 1184 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.96 % Favored : 94.84 % Rotamer: Outliers : 2.51 % Allowed : 17.08 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.27), residues: 1008 helix: 0.56 (0.26), residues: 398 sheet: -0.69 (0.34), residues: 212 loop : -1.42 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 18 TYR 0.031 0.002 TYR A 645 PHE 0.018 0.002 PHE F 62 TRP 0.013 0.001 TRP C 35 HIS 0.001 0.000 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8242) covalent geometry : angle 0.69593 (11196) SS BOND : bond 0.00629 ( 7) SS BOND : angle 1.08899 ( 14) hydrogen bonds : bond 0.03698 ( 414) hydrogen bonds : angle 5.30292 ( 1170) link_BETA1-4 : bond 0.00252 ( 2) link_BETA1-4 : angle 2.26270 ( 6) link_NAG-ASN : bond 0.00060 ( 2) link_NAG-ASN : angle 4.85113 ( 6) *********************** 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 226 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 511 PHE cc_start: 0.8776 (t80) cc_final: 0.8425 (t80) REVERT: B 373 PHE cc_start: 0.6539 (t80) cc_final: 0.6318 (t80) REVERT: B 479 LEU cc_start: 0.8960 (mt) cc_final: 0.8550 (tp) REVERT: B 511 PHE cc_start: 0.8742 (t80) cc_final: 0.8273 (t80) REVERT: B 512 THR cc_start: 0.9355 (m) cc_final: 0.9154 (p) REVERT: B 541 MET cc_start: 0.7660 (mmm) cc_final: 0.6979 (mmm) REVERT: B 620 ASP cc_start: 0.8420 (t0) cc_final: 0.8215 (t0) REVERT: C 46 LEU cc_start: 0.8191 (mt) cc_final: 0.7980 (mt) REVERT: C 100 TYR cc_start: 0.7168 (t80) cc_final: 0.6930 (t80) REVERT: D 13 VAL cc_start: 0.7592 (m) cc_final: 0.7184 (p) REVERT: D 18 ARG cc_start: 0.6671 (ttp80) cc_final: 0.6353 (ttp80) REVERT: D 31 ASN cc_start: 0.8888 (m-40) cc_final: 0.8550 (m110) REVERT: D 36 TYR cc_start: 0.8772 (m-80) cc_final: 0.8512 (m-80) REVERT: D 81 GLU cc_start: 0.7790 (pt0) cc_final: 0.7397 (pt0) REVERT: D 82 ASP cc_start: 0.8231 (m-30) cc_final: 0.7965 (m-30) REVERT: D 90 GLN cc_start: 0.9153 (pp30) cc_final: 0.8348 (pp30) REVERT: D 107 ARG cc_start: 0.6193 (OUTLIER) cc_final: 0.5886 (tpt90) REVERT: F 13 VAL cc_start: 0.7972 (m) cc_final: 0.7529 (p) REVERT: F 36 TYR cc_start: 0.8825 (m-80) cc_final: 0.8377 (m-80) outliers start: 22 outliers final: 9 residues processed: 213 average time/residue: 0.0708 time to fit residues: 21.6920 Evaluate side-chains 190 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 A residue 489 PHE Chi-restraints excluded: chain B residue 534 VAL 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 F residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 2 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.127700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105621 restraints weight = 13975.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108331 restraints weight = 8365.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110048 restraints weight = 6077.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111075 restraints weight = 4974.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111787 restraints weight = 4401.537| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8253 Z= 0.163 Angle : 0.692 8.394 11222 Z= 0.350 Chirality : 0.044 0.208 1284 Planarity : 0.005 0.051 1370 Dihedral : 6.919 56.726 1184 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.07 % Favored : 95.73 % Rotamer: Outliers : 3.30 % Allowed : 19.25 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.27), residues: 1008 helix: 0.95 (0.26), residues: 398 sheet: -0.45 (0.36), residues: 212 loop : -1.29 (0.33), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 107 TYR 0.027 0.002 TYR A 645 PHE 0.015 0.002 PHE E 79 TRP 0.012 0.001 TRP C 35 HIS 0.002 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8242) covalent geometry : angle 0.68082 (11196) SS BOND : bond 0.01309 ( 7) SS BOND : angle 1.64314 ( 14) hydrogen bonds : bond 0.03719 ( 414) hydrogen bonds : angle 5.11705 ( 1170) link_BETA1-4 : bond 0.00197 ( 2) link_BETA1-4 : angle 2.07394 ( 6) link_NAG-ASN : bond 0.00065 ( 2) link_NAG-ASN : angle 4.57061 ( 6) *********************** 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 217 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 188 time to evaluate : 0.332 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 482 ARG cc_start: 0.8679 (mmp80) cc_final: 0.7985 (mmt180) REVERT: A 511 PHE cc_start: 0.8818 (t80) cc_final: 0.8428 (t80) REVERT: B 373 PHE cc_start: 0.6623 (t80) cc_final: 0.6410 (t80) REVERT: B 479 LEU cc_start: 0.8979 (mt) cc_final: 0.8534 (tp) REVERT: B 509 MET cc_start: 0.8604 (ttt) cc_final: 0.8257 (ttt) REVERT: B 511 PHE cc_start: 0.8708 (t80) cc_final: 0.8251 (t80) REVERT: B 512 THR cc_start: 0.9359 (m) cc_final: 0.9150 (p) REVERT: D 13 VAL cc_start: 0.7637 (m) cc_final: 0.7279 (p) REVERT: D 18 ARG cc_start: 0.6685 (ttp80) cc_final: 0.6401 (ttp80) REVERT: D 31 ASN cc_start: 0.8745 (m-40) cc_final: 0.8385 (m110) REVERT: D 36 TYR cc_start: 0.8807 (m-80) cc_final: 0.8461 (m-80) REVERT: D 81 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7401 (pt0) REVERT: D 82 ASP cc_start: 0.8176 (m-30) cc_final: 0.7931 (m-30) REVERT: D 90 GLN cc_start: 0.9259 (pp30) cc_final: 0.8431 (pp30) REVERT: D 107 ARG cc_start: 0.6102 (OUTLIER) cc_final: 0.5828 (tpt90) REVERT: F 13 VAL cc_start: 0.7873 (m) cc_final: 0.7553 (p) REVERT: F 36 TYR cc_start: 0.8850 (m-80) cc_final: 0.8359 (m-80) outliers start: 29 outliers final: 21 residues processed: 202 average time/residue: 0.0708 time to fit residues: 21.2056 Evaluate side-chains 193 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 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 C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 81 GLU 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 47 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 56 optimal weight: 0.0170 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107424 restraints weight = 13807.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.109932 restraints weight = 8543.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.111537 restraints weight = 6294.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112483 restraints weight = 5204.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.112727 restraints weight = 4624.186| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8253 Z= 0.130 Angle : 0.673 12.517 11222 Z= 0.338 Chirality : 0.043 0.237 1284 Planarity : 0.005 0.055 1370 Dihedral : 6.527 53.871 1184 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.96 % Favored : 94.84 % Rotamer: Outliers : 3.76 % Allowed : 19.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.27), residues: 1008 helix: 1.24 (0.26), residues: 402 sheet: -0.37 (0.36), residues: 210 loop : -1.21 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 18 TYR 0.028 0.001 TYR A 645 PHE 0.018 0.002 PHE B 545 TRP 0.013 0.001 TRP E 35 HIS 0.001 0.000 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8242) covalent geometry : angle 0.66479 (11196) SS BOND : bond 0.00476 ( 7) SS BOND : angle 0.92459 ( 14) hydrogen bonds : bond 0.03512 ( 414) hydrogen bonds : angle 4.89768 ( 1170) link_BETA1-4 : bond 0.00111 ( 2) link_BETA1-4 : angle 1.99535 ( 6) link_NAG-ASN : bond 0.00119 ( 2) link_NAG-ASN : angle 4.17884 ( 6) *********************** 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 221 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.331 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: 0.7309 (pt0) cc_final: 0.6851 (pt0) REVERT: A 482 ARG cc_start: 0.8674 (mmp80) cc_final: 0.8008 (mmt180) REVERT: A 511 PHE cc_start: 0.8758 (t80) cc_final: 0.8404 (t80) REVERT: B 373 PHE cc_start: 0.6722 (t80) cc_final: 0.6517 (t80) REVERT: B 479 LEU cc_start: 0.8921 (mt) cc_final: 0.8468 (tp) REVERT: B 509 MET cc_start: 0.8565 (ttt) cc_final: 0.8233 (ttt) REVERT: B 511 PHE cc_start: 0.8718 (t80) cc_final: 0.8307 (t80) REVERT: B 512 THR cc_start: 0.9354 (m) cc_final: 0.9129 (p) REVERT: C 11 LEU cc_start: 0.8409 (tp) cc_final: 0.7737 (mp) REVERT: D 13 VAL cc_start: 0.7787 (m) cc_final: 0.7526 (p) REVERT: D 31 ASN cc_start: 0.8591 (m-40) cc_final: 0.8358 (m-40) REVERT: D 36 TYR cc_start: 0.8809 (m-80) cc_final: 0.8568 (m-10) REVERT: D 81 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: D 90 GLN cc_start: 0.9281 (pp30) cc_final: 0.8451 (pp30) REVERT: F 13 VAL cc_start: 0.7862 (m) cc_final: 0.6866 (p) REVERT: F 36 TYR cc_start: 0.8810 (m-80) cc_final: 0.8236 (m-80) outliers start: 33 outliers final: 20 residues processed: 200 average time/residue: 0.0743 time to fit residues: 21.4414 Evaluate side-chains 194 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 479 LEU 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 489 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 81 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN D 38 GLN E 40 GLN F 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103118 restraints weight = 13824.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105489 restraints weight = 8625.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107033 restraints weight = 6450.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107980 restraints weight = 5369.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108482 restraints weight = 4796.808| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8253 Z= 0.208 Angle : 0.729 10.538 11222 Z= 0.368 Chirality : 0.045 0.217 1284 Planarity : 0.005 0.051 1370 Dihedral : 6.477 51.222 1184 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.86 % Favored : 94.94 % Rotamer: Outliers : 3.42 % Allowed : 20.05 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.28), residues: 1008 helix: 1.33 (0.26), residues: 406 sheet: -0.30 (0.35), residues: 224 loop : -1.21 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 18 TYR 0.028 0.002 TYR B 645 PHE 0.016 0.002 PHE A 455 TRP 0.011 0.001 TRP E 109 HIS 0.003 0.001 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 8242) covalent geometry : angle 0.71904 (11196) SS BOND : bond 0.00802 ( 7) SS BOND : angle 1.69990 ( 14) hydrogen bonds : bond 0.03742 ( 414) hydrogen bonds : angle 4.92568 ( 1170) link_BETA1-4 : bond 0.00223 ( 2) link_BETA1-4 : angle 1.93113 ( 6) link_NAG-ASN : bond 0.00150 ( 2) link_NAG-ASN : angle 4.28759 ( 6) *********************** 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 201 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 GLU cc_start: 0.7334 (pt0) cc_final: 0.6942 (pt0) REVERT: A 482 ARG cc_start: 0.8691 (mmp80) cc_final: 0.8026 (mmt180) REVERT: A 511 PHE cc_start: 0.8819 (t80) cc_final: 0.8536 (t80) REVERT: B 373 PHE cc_start: 0.6810 (t80) cc_final: 0.6602 (t80) REVERT: B 479 LEU cc_start: 0.8919 (mt) cc_final: 0.8588 (tp) REVERT: B 511 PHE cc_start: 0.8780 (t80) cc_final: 0.8365 (t80) REVERT: D 31 ASN cc_start: 0.8600 (m-40) cc_final: 0.8364 (m-40) REVERT: D 36 TYR cc_start: 0.8865 (m-80) cc_final: 0.8602 (m-10) REVERT: F 36 TYR cc_start: 0.8852 (m-80) cc_final: 0.8328 (m-80) outliers start: 30 outliers final: 23 residues processed: 187 average time/residue: 0.0771 time to fit residues: 20.5530 Evaluate side-chains 188 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 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 440 SER Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 59 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 63 SER Chi-restraints excluded: chain F residue 65 THR 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 80 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 0.0570 chunk 96 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 72 optimal weight: 0.0570 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.127873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107137 restraints weight = 13800.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109584 restraints weight = 8559.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111150 restraints weight = 6347.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112147 restraints weight = 5260.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112658 restraints weight = 4660.057| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8253 Z= 0.129 Angle : 0.675 10.537 11222 Z= 0.339 Chirality : 0.043 0.203 1284 Planarity : 0.005 0.053 1370 Dihedral : 6.160 48.914 1184 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.08 % Allowed : 21.87 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.28), residues: 1008 helix: 1.48 (0.26), residues: 406 sheet: -0.26 (0.34), residues: 224 loop : -1.15 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 18 TYR 0.027 0.001 TYR A 645 PHE 0.012 0.001 PHE C 79 TRP 0.015 0.001 TRP E 35 HIS 0.002 0.000 HIS A 583 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8242) covalent geometry : angle 0.66583 (11196) SS BOND : bond 0.00587 ( 7) SS BOND : angle 1.51108 ( 14) hydrogen bonds : bond 0.03409 ( 414) hydrogen bonds : angle 4.78903 ( 1170) link_BETA1-4 : bond 0.00136 ( 2) link_BETA1-4 : angle 1.84266 ( 6) link_NAG-ASN : bond 0.00182 ( 2) link_NAG-ASN : angle 3.97139 ( 6) *********************** 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 208 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.320 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: 0.7213 (pt0) cc_final: 0.6825 (pt0) REVERT: A 482 ARG cc_start: 0.8670 (mmp80) cc_final: 0.8027 (mmt180) REVERT: A 511 PHE cc_start: 0.8774 (t80) cc_final: 0.8528 (t80) REVERT: B 479 LEU cc_start: 0.8963 (mt) cc_final: 0.8551 (tp) REVERT: B 511 PHE cc_start: 0.8741 (t80) cc_final: 0.8355 (t80) REVERT: C 11 LEU cc_start: 0.8318 (tp) cc_final: 0.7730 (mp) REVERT: C 80 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8157 (m-10) REVERT: D 31 ASN cc_start: 0.8539 (m-40) cc_final: 0.8334 (m-40) REVERT: D 36 TYR cc_start: 0.8873 (m-80) cc_final: 0.8629 (m-10) REVERT: D 90 GLN cc_start: 0.9304 (pp30) cc_final: 0.8529 (pp30) outliers start: 27 outliers final: 21 residues processed: 195 average time/residue: 0.0697 time to fit residues: 19.8088 Evaluate side-chains 190 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 479 LEU 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 489 PHE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 111 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 17 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107430 restraints weight = 13750.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109871 restraints weight = 8624.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111454 restraints weight = 6440.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112437 restraints weight = 5345.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112880 restraints weight = 4756.682| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8253 Z= 0.133 Angle : 0.673 9.046 11222 Z= 0.340 Chirality : 0.043 0.210 1284 Planarity : 0.005 0.051 1370 Dihedral : 5.977 45.797 1184 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.08 % Allowed : 22.78 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 1008 helix: 1.54 (0.27), residues: 406 sheet: -0.28 (0.34), residues: 224 loop : -1.05 (0.34), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 18 TYR 0.027 0.001 TYR B 645 PHE 0.021 0.001 PHE B 373 TRP 0.013 0.001 TRP E 35 HIS 0.001 0.000 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8242) covalent geometry : angle 0.66466 (11196) SS BOND : bond 0.00460 ( 7) SS BOND : angle 1.50444 ( 14) hydrogen bonds : bond 0.03325 ( 414) hydrogen bonds : angle 4.71471 ( 1170) link_BETA1-4 : bond 0.00216 ( 2) link_BETA1-4 : angle 1.87431 ( 6) link_NAG-ASN : bond 0.00211 ( 2) link_NAG-ASN : angle 3.83468 ( 6) *********************** 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 197 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.270 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: 0.7214 (pt0) cc_final: 0.6836 (pt0) REVERT: A 482 ARG cc_start: 0.8615 (mmp80) cc_final: 0.8107 (mmm-85) REVERT: A 511 PHE cc_start: 0.8758 (t80) cc_final: 0.8497 (t80) REVERT: B 479 LEU cc_start: 0.8994 (mt) cc_final: 0.8496 (tp) REVERT: B 511 PHE cc_start: 0.8722 (t80) cc_final: 0.8343 (t80) REVERT: C 11 LEU cc_start: 0.8268 (tp) cc_final: 0.7708 (mp) REVERT: C 80 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: D 31 ASN cc_start: 0.8530 (m-40) cc_final: 0.8306 (m-40) REVERT: D 36 TYR cc_start: 0.8870 (m-80) cc_final: 0.8604 (m-10) REVERT: E 11 LEU cc_start: 0.8355 (tp) cc_final: 0.7712 (mp) outliers start: 27 outliers final: 21 residues processed: 182 average time/residue: 0.0735 time to fit residues: 19.3749 Evaluate side-chains 185 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 479 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain B residue 379 TRP Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 111 GLN 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 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 63 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 25 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN C 40 GLN D 38 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 = 0.3657 r_free = 0.3657 target = 0.129174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108297 restraints weight = 13558.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110731 restraints weight = 8522.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.112303 restraints weight = 6371.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113281 restraints weight = 5302.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.113824 restraints weight = 4719.159| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8253 Z= 0.131 Angle : 0.672 9.099 11222 Z= 0.339 Chirality : 0.043 0.206 1284 Planarity : 0.004 0.048 1370 Dihedral : 5.812 45.987 1184 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.08 % Allowed : 22.78 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.28), residues: 1008 helix: 1.56 (0.27), residues: 406 sheet: -0.16 (0.34), residues: 224 loop : -0.95 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 18 TYR 0.025 0.001 TYR A 645 PHE 0.012 0.001 PHE C 79 TRP 0.014 0.001 TRP E 48 HIS 0.002 0.000 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8242) covalent geometry : angle 0.66354 (11196) SS BOND : bond 0.00400 ( 7) SS BOND : angle 1.55593 ( 14) hydrogen bonds : bond 0.03296 ( 414) hydrogen bonds : angle 4.66587 ( 1170) link_BETA1-4 : bond 0.00176 ( 2) link_BETA1-4 : angle 1.80102 ( 6) link_NAG-ASN : bond 0.00254 ( 2) link_NAG-ASN : angle 3.70542 ( 6) *********************** 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 203 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.313 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: 0.7209 (pt0) cc_final: 0.6836 (pt0) REVERT: A 463 TYR cc_start: 0.8226 (m-10) cc_final: 0.8009 (m-10) REVERT: A 482 ARG cc_start: 0.8637 (mmp80) cc_final: 0.8122 (mmm-85) REVERT: A 511 PHE cc_start: 0.8749 (t80) cc_final: 0.8483 (t80) REVERT: A 540 LEU cc_start: 0.8965 (tp) cc_final: 0.8760 (tt) REVERT: B 479 LEU cc_start: 0.8977 (mt) cc_final: 0.8490 (tp) REVERT: B 511 PHE cc_start: 0.8709 (t80) cc_final: 0.8350 (t80) REVERT: C 11 LEU cc_start: 0.8270 (tp) cc_final: 0.7750 (mp) REVERT: C 80 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: D 31 ASN cc_start: 0.8543 (m-40) cc_final: 0.8264 (m-40) REVERT: D 36 TYR cc_start: 0.8865 (m-80) cc_final: 0.8589 (m-10) REVERT: E 11 LEU cc_start: 0.8313 (tp) cc_final: 0.7705 (mp) outliers start: 27 outliers final: 23 residues processed: 190 average time/residue: 0.0763 time to fit residues: 20.9160 Evaluate side-chains 194 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 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 489 PHE Chi-restraints excluded: chain B residue 491 CYS 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 80 PHE 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 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 63 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 11 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 24 optimal weight: 0.8980 overall best weight: 0.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 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 = 0.3662 r_free = 0.3662 target = 0.129605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108571 restraints weight = 13652.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110978 restraints weight = 8649.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112518 restraints weight = 6504.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.113397 restraints weight = 5422.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.114069 restraints weight = 4865.698| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8253 Z= 0.132 Angle : 0.679 10.598 11222 Z= 0.340 Chirality : 0.043 0.204 1284 Planarity : 0.004 0.047 1370 Dihedral : 5.728 45.544 1184 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.96 % Allowed : 22.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.28), residues: 1008 helix: 1.52 (0.27), residues: 408 sheet: -0.12 (0.34), residues: 224 loop : -0.96 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 18 TYR 0.025 0.001 TYR A 645 PHE 0.024 0.001 PHE B 373 TRP 0.019 0.001 TRP E 48 HIS 0.001 0.000 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8242) covalent geometry : angle 0.67106 (11196) SS BOND : bond 0.00482 ( 7) SS BOND : angle 1.52526 ( 14) hydrogen bonds : bond 0.03290 ( 414) hydrogen bonds : angle 4.64220 ( 1170) link_BETA1-4 : bond 0.00293 ( 2) link_BETA1-4 : angle 1.77415 ( 6) link_NAG-ASN : bond 0.00211 ( 2) link_NAG-ASN : angle 3.66218 ( 6) ********************** 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 205 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.321 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: 0.7225 (pt0) cc_final: 0.6840 (pt0) REVERT: A 463 TYR cc_start: 0.8264 (m-10) cc_final: 0.8027 (m-10) REVERT: A 482 ARG cc_start: 0.8656 (mmp80) cc_final: 0.8142 (mmm-85) REVERT: A 511 PHE cc_start: 0.8748 (t80) cc_final: 0.8487 (t80) REVERT: B 479 LEU cc_start: 0.8915 (mt) cc_final: 0.8611 (tp) REVERT: B 511 PHE cc_start: 0.8703 (t80) cc_final: 0.8323 (t80) REVERT: C 11 LEU cc_start: 0.8269 (tp) cc_final: 0.7753 (mp) REVERT: C 80 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8105 (m-80) REVERT: D 31 ASN cc_start: 0.8574 (m-40) cc_final: 0.8227 (m110) REVERT: E 11 LEU cc_start: 0.8296 (tp) cc_final: 0.7706 (mp) outliers start: 26 outliers final: 24 residues processed: 193 average time/residue: 0.0769 time to fit residues: 21.4805 Evaluate side-chains 194 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 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 489 PHE Chi-restraints excluded: chain B residue 491 CYS 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 79 GLN 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 33 LEU Chi-restraints excluded: chain F residue 63 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 45 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 81 optimal weight: 0.0040 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3665 r_free = 0.3665 target = 0.129607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.108739 restraints weight = 13590.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111143 restraints weight = 8619.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112668 restraints weight = 6480.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113500 restraints weight = 5413.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114196 restraints weight = 4867.732| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8253 Z= 0.133 Angle : 0.688 11.507 11222 Z= 0.345 Chirality : 0.043 0.195 1284 Planarity : 0.004 0.047 1370 Dihedral : 5.642 45.641 1184 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.08 % Allowed : 22.67 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.28), residues: 1008 helix: 1.51 (0.27), residues: 408 sheet: -0.09 (0.34), residues: 224 loop : -0.93 (0.35), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 18 TYR 0.025 0.001 TYR A 645 PHE 0.013 0.001 PHE A 545 TRP 0.015 0.001 TRP E 48 HIS 0.001 0.000 HIS B 583 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8242) covalent geometry : angle 0.68031 (11196) SS BOND : bond 0.00434 ( 7) SS BOND : angle 1.45949 ( 14) hydrogen bonds : bond 0.03265 ( 414) hydrogen bonds : angle 4.64624 ( 1170) link_BETA1-4 : bond 0.00209 ( 2) link_BETA1-4 : angle 1.70716 ( 6) link_NAG-ASN : bond 0.00254 ( 2) link_NAG-ASN : angle 3.58585 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1345.17 seconds wall clock time: 24 minutes 4.90 seconds (1444.90 seconds total)