Starting phenix.real_space_refine on Wed Jun 11 03:10:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wij_32531/06_2025/7wij_32531.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wij_32531/06_2025/7wij_32531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wij_32531/06_2025/7wij_32531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wij_32531/06_2025/7wij_32531.map" model { file = "/net/cci-nas-00/data/ceres_data/7wij_32531/06_2025/7wij_32531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wij_32531/06_2025/7wij_32531.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 54 5.16 5 C 7950 2.51 5 N 2136 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12396 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2066 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 7, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 8.51, per 1000 atoms: 0.69 Number of scatterers: 12396 At special positions: 0 Unit cell: (115.28, 125.84, 81.84, 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 54 16.00 O 2256 8.00 N 2136 7.00 C 7950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.5 seconds 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 82.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 433 through 453 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 501 through 527 removed outlier: 3.523A pdb=" N ILE A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 557 removed outlier: 4.856A pdb=" N LEU A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 587 Processing helix chain 'A' and resid 608 through 617 removed outlier: 3.572A pdb=" N LYS A 616 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 635 Processing helix chain 'A' and resid 638 through 652 Processing helix chain 'A' and resid 653 through 678 removed outlier: 3.666A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 694 Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 417 through 427 Processing helix chain 'B' and resid 433 through 453 Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 475 through 495 removed outlier: 3.611A pdb=" N THR B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 527 removed outlier: 3.517A pdb=" N ILE B 505 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 524 " --> pdb=" O ASP B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 557 removed outlier: 4.852A pdb=" N LEU B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 587 Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.607A pdb=" N LYS B 616 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 635 Processing helix chain 'B' and resid 638 through 653 Processing helix chain 'B' and resid 653 through 678 removed outlier: 3.687A pdb=" N ARG B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 674 " --> pdb=" O HIS B 670 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 675 " --> pdb=" O ARG B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 693 Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 417 through 427 Processing helix chain 'C' and resid 433 through 453 Processing helix chain 'C' and resid 469 through 475 Processing helix chain 'C' and resid 475 through 495 removed outlier: 3.704A pdb=" N THR C 479 " --> pdb=" O GLY C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 527 removed outlier: 3.532A pdb=" N ILE C 505 " --> pdb=" O LYS C 501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 524 " --> pdb=" O ASP C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 557 removed outlier: 4.823A pdb=" N LEU C 546 " --> pdb=" O LYS C 542 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE C 547 " --> pdb=" O THR C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 587 Processing helix chain 'C' and resid 608 through 617 removed outlier: 3.697A pdb=" N LYS C 616 " --> pdb=" O ILE C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 635 Processing helix chain 'C' and resid 638 through 652 Processing helix chain 'C' and resid 653 through 678 removed outlier: 3.735A pdb=" N ARG C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 675 " --> pdb=" O ARG C 671 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 676 " --> pdb=" O GLU C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 693 Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 417 through 427 Processing helix chain 'D' and resid 433 through 453 Processing helix chain 'D' and resid 469 through 475 Processing helix chain 'D' and resid 475 through 495 removed outlier: 3.610A pdb=" N THR D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 527 removed outlier: 3.517A pdb=" N ILE D 505 " --> pdb=" O LYS D 501 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 524 " --> pdb=" O ASP D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 557 removed outlier: 4.832A pdb=" N LEU D 546 " --> pdb=" O LYS D 542 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE D 547 " --> pdb=" O THR D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 588 Processing helix chain 'D' and resid 608 through 617 removed outlier: 3.605A pdb=" N LYS D 616 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 635 Processing helix chain 'D' and resid 638 through 653 Processing helix chain 'D' and resid 653 through 678 removed outlier: 3.703A pdb=" N ARG D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 674 " --> pdb=" O HIS D 670 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS D 675 " --> pdb=" O ARG D 671 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 676 " --> pdb=" O GLU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 693 Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 417 through 427 Processing helix chain 'E' and resid 433 through 453 Processing helix chain 'E' and resid 469 through 475 Processing helix chain 'E' and resid 475 through 495 removed outlier: 3.704A pdb=" N THR E 479 " --> pdb=" O GLY E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 527 removed outlier: 3.532A pdb=" N ILE E 505 " --> pdb=" O LYS E 501 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 524 " --> pdb=" O ASP E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 557 removed outlier: 4.823A pdb=" N LEU E 546 " --> pdb=" O LYS E 542 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE E 547 " --> pdb=" O THR E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 587 Processing helix chain 'E' and resid 608 through 617 removed outlier: 3.672A pdb=" N LYS E 616 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 635 Processing helix chain 'E' and resid 638 through 652 Processing helix chain 'E' and resid 653 through 678 removed outlier: 3.715A pdb=" N ARG E 659 " --> pdb=" O LEU E 655 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS E 675 " --> pdb=" O ARG E 671 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 676 " --> pdb=" O GLU E 672 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 693 Processing helix chain 'F' and resid 404 through 411 removed outlier: 3.515A pdb=" N LEU F 410 " --> pdb=" O PRO F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 427 Processing helix chain 'F' and resid 433 through 453 Processing helix chain 'F' and resid 469 through 475 Processing helix chain 'F' and resid 476 through 495 Processing helix chain 'F' and resid 501 through 527 removed outlier: 3.523A pdb=" N ILE F 505 " --> pdb=" O LYS F 501 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 524 " --> pdb=" O ASP F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 557 removed outlier: 4.814A pdb=" N LEU F 546 " --> pdb=" O LYS F 542 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE F 547 " --> pdb=" O THR F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 587 Processing helix chain 'F' and resid 608 through 617 removed outlier: 3.572A pdb=" N LYS F 616 " --> pdb=" O ILE F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 620 through 635 Processing helix chain 'F' and resid 638 through 652 Processing helix chain 'F' and resid 653 through 678 removed outlier: 3.661A pdb=" N ARG F 659 " --> pdb=" O LEU F 655 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS F 675 " --> pdb=" O ARG F 671 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 676 " --> pdb=" O GLU F 672 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 694 952 hydrogen bonds defined for protein. 2856 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: 3.62 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4020 1.34 - 1.46: 1830 1.46 - 1.57: 6636 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 12588 Sorted by residual: bond pdb=" CG1 ILE D 579 " pdb=" CD1 ILE D 579 " ideal model delta sigma weight residual 1.513 1.485 0.028 3.90e-02 6.57e+02 5.30e-01 bond pdb=" CA ILE F 579 " pdb=" C ILE F 579 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.46e-02 4.69e+03 4.54e-01 bond pdb=" C LEU A 609 " pdb=" N PRO A 610 " ideal model delta sigma weight residual 1.335 1.345 -0.009 1.36e-02 5.41e+03 4.53e-01 bond pdb=" CA ILE A 579 " pdb=" C ILE A 579 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.46e-02 4.69e+03 4.48e-01 bond pdb=" C LEU B 609 " pdb=" N PRO B 610 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.36e-02 5.41e+03 4.43e-01 ... (remaining 12583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16848 2.01 - 4.02: 103 4.02 - 6.03: 23 6.03 - 8.05: 6 8.05 - 10.06: 6 Bond angle restraints: 16986 Sorted by residual: angle pdb=" CA LEU D 550 " pdb=" CB LEU D 550 " pdb=" CG LEU D 550 " ideal model delta sigma weight residual 116.30 126.36 -10.06 3.50e+00 8.16e-02 8.26e+00 angle pdb=" CA LEU A 550 " pdb=" CB LEU A 550 " pdb=" CG LEU A 550 " ideal model delta sigma weight residual 116.30 126.07 -9.77 3.50e+00 8.16e-02 7.79e+00 angle pdb=" CA LEU B 550 " pdb=" CB LEU B 550 " pdb=" CG LEU B 550 " ideal model delta sigma weight residual 116.30 126.00 -9.70 3.50e+00 8.16e-02 7.68e+00 angle pdb=" CA LEU F 550 " pdb=" CB LEU F 550 " pdb=" CG LEU F 550 " ideal model delta sigma weight residual 116.30 125.84 -9.54 3.50e+00 8.16e-02 7.44e+00 angle pdb=" C PHE E 547 " pdb=" N HIS E 548 " pdb=" CA HIS E 548 " ideal model delta sigma weight residual 122.06 117.06 5.00 1.86e+00 2.89e-01 7.24e+00 ... (remaining 16981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6879 17.96 - 35.91: 621 35.91 - 53.87: 106 53.87 - 71.82: 32 71.82 - 89.78: 6 Dihedral angle restraints: 7644 sinusoidal: 3006 harmonic: 4638 Sorted by residual: dihedral pdb=" CA HIS E 548 " pdb=" C HIS E 548 " pdb=" N LEU E 549 " pdb=" CA LEU E 549 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA HIS C 548 " pdb=" C HIS C 548 " pdb=" N LEU C 549 " pdb=" CA LEU C 549 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA HIS B 548 " pdb=" C HIS B 548 " pdb=" N LEU B 549 " pdb=" CA LEU B 549 " ideal model delta harmonic sigma weight residual 180.00 159.75 20.25 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 7641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1463 0.034 - 0.069: 481 0.069 - 0.103: 78 0.103 - 0.137: 6 0.137 - 0.172: 6 Chirality restraints: 2034 Sorted by residual: chirality pdb=" CA HIS F 548 " pdb=" N HIS F 548 " pdb=" C HIS F 548 " pdb=" CB HIS F 548 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA HIS A 548 " pdb=" N HIS A 548 " pdb=" C HIS A 548 " pdb=" CB HIS A 548 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA HIS C 548 " pdb=" N HIS C 548 " pdb=" C HIS C 548 " pdb=" CB HIS C 548 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 2031 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 548 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C HIS A 548 " 0.027 2.00e-02 2.50e+03 pdb=" O HIS A 548 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 549 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS F 548 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C HIS F 548 " -0.027 2.00e-02 2.50e+03 pdb=" O HIS F 548 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU F 549 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 548 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C HIS E 548 " -0.027 2.00e-02 2.50e+03 pdb=" O HIS E 548 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU E 549 " 0.009 2.00e-02 2.50e+03 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2287 2.77 - 3.31: 12023 3.31 - 3.84: 20224 3.84 - 4.37: 22294 4.37 - 4.90: 40388 Nonbonded interactions: 97216 Sorted by model distance: nonbonded pdb=" OE1 GLU A 509 " pdb=" NE2 HIS A 548 " model vdw 2.243 3.120 nonbonded pdb=" OE1 GLU B 509 " pdb=" NE2 HIS B 548 " model vdw 2.244 3.120 nonbonded pdb=" OE1 GLU F 509 " pdb=" NE2 HIS F 548 " model vdw 2.244 3.120 nonbonded pdb=" OE1 GLU D 509 " pdb=" NE2 HIS D 548 " model vdw 2.244 3.120 nonbonded pdb=" OE1 GLU E 509 " pdb=" NE2 HIS E 548 " model vdw 2.246 3.120 ... (remaining 97211 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.240 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.002 0.028 12588 Z= 0.111 Angle : 0.503 10.058 16986 Z= 0.251 Chirality : 0.034 0.172 2034 Planarity : 0.003 0.025 2100 Dihedral : 14.486 89.778 4620 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.22), residues: 1554 helix: 2.24 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -0.68 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 487 HIS 0.008 0.001 HIS E 548 PHE 0.007 0.001 PHE B 577 TYR 0.004 0.001 TYR A 535 ARG 0.001 0.000 ARG F 504 Details of bonding type rmsd hydrogen bonds : bond 0.12717 ( 952) hydrogen bonds : angle 4.92995 ( 2856) covalent geometry : bond 0.00240 (12588) covalent geometry : angle 0.50298 (16986) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.285 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1875 time to fit residues: 53.0974 Evaluate side-chains 164 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0970 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.0000 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.140948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.109440 restraints weight = 13384.380| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.56 r_work: 0.2907 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12588 Z= 0.133 Angle : 0.532 11.082 16986 Z= 0.269 Chirality : 0.036 0.222 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.497 22.455 1692 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.08 % Allowed : 6.11 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.22), residues: 1554 helix: 2.41 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.69 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 523 HIS 0.009 0.001 HIS A 548 PHE 0.009 0.001 PHE A 519 TYR 0.004 0.001 TYR F 685 ARG 0.002 0.000 ARG F 504 Details of bonding type rmsd hydrogen bonds : bond 0.05161 ( 952) hydrogen bonds : angle 4.16177 ( 2856) covalent geometry : bond 0.00305 (12588) covalent geometry : angle 0.53169 (16986) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 1.761 Fit side-chains REVERT: B 659 ARG cc_start: 0.7190 (ttt-90) cc_final: 0.6702 (ttp-110) outliers start: 1 outliers final: 1 residues processed: 170 average time/residue: 0.2974 time to fit residues: 77.7641 Evaluate side-chains 165 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 4.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 584 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 139 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN E 517 GLN ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.140200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.113442 restraints weight = 13515.672| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.23 r_work: 0.2962 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12588 Z= 0.127 Angle : 0.517 11.544 16986 Z= 0.260 Chirality : 0.036 0.215 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.427 22.707 1692 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.06 % Allowed : 7.92 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.22), residues: 1554 helix: 2.52 (0.15), residues: 1320 sheet: None (None), residues: 0 loop : -0.66 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 523 HIS 0.009 0.001 HIS C 548 PHE 0.009 0.001 PHE D 577 TYR 0.004 0.001 TYR A 535 ARG 0.002 0.000 ARG F 504 Details of bonding type rmsd hydrogen bonds : bond 0.05003 ( 952) hydrogen bonds : angle 4.00130 ( 2856) covalent geometry : bond 0.00291 (12588) covalent geometry : angle 0.51718 (16986) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 1.293 Fit side-chains REVERT: C 582 ASP cc_start: 0.6884 (m-30) cc_final: 0.6658 (m-30) REVERT: D 426 MET cc_start: 0.8379 (ttm) cc_final: 0.8159 (ttm) REVERT: E 582 ASP cc_start: 0.6871 (m-30) cc_final: 0.6656 (m-30) outliers start: 14 outliers final: 8 residues processed: 181 average time/residue: 0.1841 time to fit residues: 52.1959 Evaluate side-chains 173 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 120 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 ASN C 517 GLN E 517 GLN ** F 548 HIS ** 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 = 0.3422 r_free = 0.3422 target = 0.137421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.110757 restraints weight = 13381.741| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.23 r_work: 0.2938 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12588 Z= 0.152 Angle : 0.540 11.806 16986 Z= 0.274 Chirality : 0.037 0.226 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.501 22.645 1692 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.06 % Allowed : 9.28 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.22), residues: 1554 helix: 2.41 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.59 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 523 HIS 0.010 0.001 HIS F 548 PHE 0.011 0.002 PHE D 577 TYR 0.004 0.001 TYR A 535 ARG 0.002 0.000 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.05678 ( 952) hydrogen bonds : angle 4.07419 ( 2856) covalent geometry : bond 0.00363 (12588) covalent geometry : angle 0.53968 (16986) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 1.446 Fit side-chains REVERT: C 582 ASP cc_start: 0.6885 (m-30) cc_final: 0.6677 (m-30) REVERT: C 647 GLN cc_start: 0.8064 (tt0) cc_final: 0.7797 (tt0) REVERT: D 572 MET cc_start: 0.8473 (mmp) cc_final: 0.8272 (mmp) REVERT: D 659 ARG cc_start: 0.7263 (ttt-90) cc_final: 0.6847 (ttp-110) REVERT: E 647 GLN cc_start: 0.8080 (tt0) cc_final: 0.7832 (tt0) outliers start: 14 outliers final: 14 residues processed: 176 average time/residue: 0.2151 time to fit residues: 58.3678 Evaluate side-chains 178 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 79 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN E 517 GLN ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.138937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.112925 restraints weight = 13441.962| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.21 r_work: 0.2957 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12588 Z= 0.128 Angle : 0.508 11.426 16986 Z= 0.258 Chirality : 0.035 0.216 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.436 22.299 1692 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.81 % Allowed : 10.26 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.22), residues: 1554 helix: 2.47 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 487 HIS 0.009 0.001 HIS A 548 PHE 0.009 0.001 PHE D 577 TYR 0.004 0.001 TYR A 535 ARG 0.002 0.000 ARG F 504 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 952) hydrogen bonds : angle 3.95414 ( 2856) covalent geometry : bond 0.00292 (12588) covalent geometry : angle 0.50793 (16986) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 1.309 Fit side-chains outliers start: 24 outliers final: 18 residues processed: 187 average time/residue: 0.2008 time to fit residues: 58.5077 Evaluate side-chains 186 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 150 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN E 517 GLN ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.139640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.113061 restraints weight = 13552.430| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.23 r_work: 0.2978 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12588 Z= 0.120 Angle : 0.497 11.486 16986 Z= 0.252 Chirality : 0.035 0.212 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.382 21.957 1692 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.66 % Allowed : 10.48 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.22), residues: 1554 helix: 2.53 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.33 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 487 HIS 0.009 0.001 HIS A 548 PHE 0.008 0.001 PHE A 519 TYR 0.003 0.001 TYR A 535 ARG 0.002 0.000 ARG F 504 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 952) hydrogen bonds : angle 3.88476 ( 2856) covalent geometry : bond 0.00271 (12588) covalent geometry : angle 0.49704 (16986) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.327 Fit side-chains outliers start: 22 outliers final: 18 residues processed: 184 average time/residue: 0.1874 time to fit residues: 54.2115 Evaluate side-chains 185 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 528 GLN Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 28 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN E 517 GLN ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.138213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.110904 restraints weight = 13545.558| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.25 r_work: 0.2935 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12588 Z= 0.138 Angle : 0.519 11.878 16986 Z= 0.263 Chirality : 0.035 0.218 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.420 21.964 1692 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.04 % Allowed : 10.26 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.22), residues: 1554 helix: 2.50 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.58 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 523 HIS 0.009 0.001 HIS A 548 PHE 0.009 0.001 PHE D 577 TYR 0.004 0.001 TYR A 535 ARG 0.002 0.000 ARG F 504 Details of bonding type rmsd hydrogen bonds : bond 0.05313 ( 952) hydrogen bonds : angle 3.96011 ( 2856) covalent geometry : bond 0.00322 (12588) covalent geometry : angle 0.51916 (16986) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.534 Fit side-chains outliers start: 27 outliers final: 25 residues processed: 181 average time/residue: 0.1827 time to fit residues: 52.4531 Evaluate side-chains 185 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 528 GLN Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 119 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN E 517 GLN ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.138471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.111284 restraints weight = 13506.200| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.24 r_work: 0.2934 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12588 Z= 0.134 Angle : 0.515 11.879 16986 Z= 0.261 Chirality : 0.035 0.215 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.413 21.788 1692 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.89 % Allowed : 9.95 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.22), residues: 1554 helix: 2.51 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.58 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 523 HIS 0.009 0.001 HIS A 548 PHE 0.009 0.001 PHE D 577 TYR 0.004 0.001 TYR A 535 ARG 0.002 0.000 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.05196 ( 952) hydrogen bonds : angle 3.94045 ( 2856) covalent geometry : bond 0.00312 (12588) covalent geometry : angle 0.51540 (16986) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 1.476 Fit side-chains outliers start: 25 outliers final: 25 residues processed: 185 average time/residue: 0.1825 time to fit residues: 53.8655 Evaluate side-chains 192 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 528 GLN Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 95 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 103 optimal weight: 0.0270 chunk 73 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 45 optimal weight: 0.0070 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 517 GLN E 517 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.142340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.114812 restraints weight = 13403.014| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.28 r_work: 0.2993 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12588 Z= 0.102 Angle : 0.472 11.418 16986 Z= 0.238 Chirality : 0.034 0.197 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.272 21.511 1692 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.66 % Allowed : 10.26 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.22), residues: 1554 helix: 2.68 (0.15), residues: 1344 sheet: None (None), residues: 0 loop : -0.27 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 487 HIS 0.009 0.001 HIS A 548 PHE 0.008 0.001 PHE A 519 TYR 0.003 0.000 TYR A 535 ARG 0.001 0.000 ARG F 504 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 952) hydrogen bonds : angle 3.74382 ( 2856) covalent geometry : bond 0.00214 (12588) covalent geometry : angle 0.47178 (16986) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 1.324 Fit side-chains REVERT: B 585 ASN cc_start: 0.7305 (m-40) cc_final: 0.7081 (t0) outliers start: 22 outliers final: 21 residues processed: 188 average time/residue: 0.2007 time to fit residues: 59.7022 Evaluate side-chains 192 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 528 GLN Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 120 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 134 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN E 517 GLN ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.138275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.112745 restraints weight = 13460.569| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.24 r_work: 0.2946 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12588 Z= 0.135 Angle : 0.517 12.022 16986 Z= 0.261 Chirality : 0.035 0.214 2034 Planarity : 0.003 0.030 2100 Dihedral : 3.369 21.480 1692 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.73 % Allowed : 10.11 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.22), residues: 1554 helix: 2.56 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.51 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 523 HIS 0.010 0.001 HIS A 548 PHE 0.009 0.001 PHE D 577 TYR 0.004 0.001 TYR F 535 ARG 0.002 0.000 ARG F 504 Details of bonding type rmsd hydrogen bonds : bond 0.05203 ( 952) hydrogen bonds : angle 3.90737 ( 2856) covalent geometry : bond 0.00317 (12588) covalent geometry : angle 0.51687 (16986) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3108 Ramachandran restraints generated. 1554 Oldfield, 0 Emsley, 1554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 2.505 Fit side-chains outliers start: 23 outliers final: 23 residues processed: 180 average time/residue: 0.2073 time to fit residues: 58.3996 Evaluate side-chains 186 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 534 GLU Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 528 GLN Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 528 GLN Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 430 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 583 LEU Chi-restraints excluded: chain F residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 130 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.137783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.112162 restraints weight = 13540.301| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.26 r_work: 0.2932 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12588 Z= 0.141 Angle : 0.526 12.160 16986 Z= 0.267 Chirality : 0.036 0.218 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.424 21.627 1692 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.81 % Allowed : 10.11 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.22), residues: 1554 helix: 2.50 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.52 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 523 HIS 0.009 0.001 HIS A 548 PHE 0.009 0.001 PHE D 577 TYR 0.004 0.001 TYR A 535 ARG 0.002 0.000 ARG F 504 Details of bonding type rmsd hydrogen bonds : bond 0.05360 ( 952) hydrogen bonds : angle 3.96951 ( 2856) covalent geometry : bond 0.00333 (12588) covalent geometry : angle 0.52639 (16986) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7121.92 seconds wall clock time: 126 minutes 45.71 seconds (7605.71 seconds total)