Starting phenix.real_space_refine on Wed Mar 4 08:56:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wij_32531/03_2026/7wij_32531.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wij_32531/03_2026/7wij_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_32531/03_2026/7wij_32531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wij_32531/03_2026/7wij_32531.map" model { file = "/net/cci-nas-00/data/ceres_data/7wij_32531/03_2026/7wij_32531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wij_32531/03_2026/7wij_32531.cif" } resolution = 3.17 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= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG: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: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG: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: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG: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: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG: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: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG: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: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 2.56, per 1000 atoms: 0.21 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: 0.94 Conformation dependent library (CDL) restraints added in 566.1 milliseconds 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: 0.20 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: 1.55 Time building geometry restraints manager: 1.29 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: 0.01 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: 6.330 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- 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 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: 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 ARG 0.001 0.000 ARG F 504 TYR 0.004 0.001 TYR A 535 PHE 0.007 0.001 PHE B 577 TRP 0.003 0.001 TRP F 487 HIS 0.008 0.001 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00240 (12588) covalent geometry : angle 0.50298 (16986) hydrogen bonds : bond 0.12717 ( 952) hydrogen bonds : angle 4.92995 ( 2856) *********************** 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 : 0.443 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.0787 time to fit residues: 22.6305 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 : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.137219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.105249 restraints weight = 13546.825| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.57 r_work: 0.2854 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12588 Z= 0.184 Angle : 0.595 11.820 16986 Z= 0.302 Chirality : 0.039 0.245 2034 Planarity : 0.004 0.033 2100 Dihedral : 3.650 22.752 1692 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.38 % Allowed : 6.56 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.60 (0.22), residues: 1554 helix: 2.17 (0.14), residues: 1320 sheet: None (None), residues: 0 loop : -0.90 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 504 TYR 0.006 0.001 TYR F 685 PHE 0.014 0.002 PHE D 577 TRP 0.006 0.001 TRP E 523 HIS 0.010 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00455 (12588) covalent geometry : angle 0.59532 (16986) hydrogen bonds : bond 0.06334 ( 952) hydrogen bonds : angle 4.38969 ( 2856) *********************** 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 172 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 167 time to evaluate : 0.447 Fit side-chains REVERT: B 659 ARG cc_start: 0.7300 (ttt-90) cc_final: 0.6834 (ttp-110) REVERT: D 659 ARG cc_start: 0.7231 (ttt-90) cc_final: 0.6814 (ttp-110) outliers start: 5 outliers final: 5 residues processed: 171 average time/residue: 0.0911 time to fit residues: 23.9285 Evaluate side-chains 167 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain E residue 639 LEU Chi-restraints excluded: chain E residue 686 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** 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 = 0.139067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.112124 restraints weight = 13560.065| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.23 r_work: 0.2948 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1080 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= 0.131 Angle : 0.527 11.438 16986 Z= 0.266 Chirality : 0.036 0.218 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.519 22.756 1692 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.83 % Allowed : 9.05 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.98 (0.22), residues: 1554 helix: 2.32 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.38 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 504 TYR 0.004 0.001 TYR A 535 PHE 0.009 0.001 PHE D 577 TRP 0.003 0.001 TRP B 487 HIS 0.009 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00301 (12588) covalent geometry : angle 0.52652 (16986) hydrogen bonds : bond 0.05171 ( 952) hydrogen bonds : angle 4.09328 ( 2856) *********************** 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 181 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 0.494 Fit side-chains REVERT: C 582 ASP cc_start: 0.6906 (m-30) cc_final: 0.6682 (m-30) REVERT: E 582 ASP cc_start: 0.6865 (m-30) cc_final: 0.6642 (m-30) outliers start: 11 outliers final: 5 residues processed: 179 average time/residue: 0.0789 time to fit residues: 22.6785 Evaluate side-chains 171 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 166 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 D residue 586 LEU 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 99 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 0.0570 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 ASN C 517 GLN E 517 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.140517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.112946 restraints weight = 13461.618| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.27 r_work: 0.2952 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1181 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= 0.118 Angle : 0.497 11.294 16986 Z= 0.253 Chirality : 0.035 0.211 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.421 22.473 1692 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.21 % Allowed : 9.80 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.23 (0.22), residues: 1554 helix: 2.50 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.33 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 504 TYR 0.003 0.001 TYR F 535 PHE 0.008 0.001 PHE A 519 TRP 0.002 0.001 TRP D 487 HIS 0.008 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00261 (12588) covalent geometry : angle 0.49737 (16986) hydrogen bonds : bond 0.04752 ( 952) hydrogen bonds : angle 3.92030 ( 2856) *********************** 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 189 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 time to evaluate : 0.487 Fit side-chains REVERT: C 582 ASP cc_start: 0.6763 (m-30) cc_final: 0.6559 (m-30) outliers start: 16 outliers final: 15 residues processed: 186 average time/residue: 0.0753 time to fit residues: 22.1814 Evaluate side-chains 184 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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 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 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 20 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 ASN C 517 GLN E 517 GLN F 585 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.138113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.111691 restraints weight = 13517.892| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.25 r_work: 0.2939 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12588 Z= 0.139 Angle : 0.523 11.578 16986 Z= 0.266 Chirality : 0.036 0.221 2034 Planarity : 0.003 0.032 2100 Dihedral : 3.459 22.209 1692 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.96 % Allowed : 10.48 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.13 (0.22), residues: 1554 helix: 2.48 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.62 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 504 TYR 0.004 0.001 TYR F 535 PHE 0.009 0.001 PHE B 577 TRP 0.003 0.001 TRP B 523 HIS 0.009 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00326 (12588) covalent geometry : angle 0.52303 (16986) hydrogen bonds : bond 0.05370 ( 952) hydrogen bonds : angle 3.99634 ( 2856) *********************** 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 193 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.445 Fit side-chains REVERT: D 426 MET cc_start: 0.8297 (ttm) cc_final: 0.8088 (ttm) outliers start: 26 outliers final: 23 residues processed: 188 average time/residue: 0.0760 time to fit residues: 23.1854 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 : 0.421 ------------------------------------------------------------------------------- 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 452 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 430 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 555 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 129 optimal weight: 0.0270 chunk 139 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 153 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.140141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.114291 restraints weight = 13502.717| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.28 r_work: 0.2961 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1287 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= 0.119 Angle : 0.496 11.364 16986 Z= 0.252 Chirality : 0.035 0.209 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.386 21.969 1692 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.81 % Allowed : 11.01 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.29 (0.22), residues: 1554 helix: 2.54 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 504 TYR 0.003 0.001 TYR A 535 PHE 0.008 0.001 PHE A 519 TRP 0.002 0.001 TRP A 487 HIS 0.008 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00267 (12588) covalent geometry : angle 0.49618 (16986) hydrogen bonds : bond 0.04783 ( 952) hydrogen bonds : angle 3.88573 ( 2856) *********************** 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 190 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.388 Fit side-chains REVERT: F 647 GLN cc_start: 0.7865 (tt0) cc_final: 0.7640 (tt0) outliers start: 24 outliers final: 22 residues processed: 186 average time/residue: 0.0809 time to fit residues: 23.9662 Evaluate side-chains 187 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 555 ILE 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 555 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 153 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 26 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.140497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.112793 restraints weight = 13366.295| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.27 r_work: 0.2962 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1331 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= 0.114 Angle : 0.491 11.604 16986 Z= 0.248 Chirality : 0.034 0.206 2034 Planarity : 0.003 0.031 2100 Dihedral : 3.331 21.551 1692 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.11 % Allowed : 10.56 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.36 (0.22), residues: 1554 helix: 2.59 (0.15), residues: 1344 sheet: None (None), residues: 0 loop : -0.35 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 504 TYR 0.003 0.001 TYR A 535 PHE 0.008 0.001 PHE A 519 TRP 0.002 0.001 TRP A 487 HIS 0.009 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00253 (12588) covalent geometry : angle 0.49059 (16986) hydrogen bonds : bond 0.04637 ( 952) hydrogen bonds : angle 3.83279 ( 2856) *********************** 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 195 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.381 Fit side-chains REVERT: B 585 ASN cc_start: 0.7337 (m-40) cc_final: 0.7026 (t0) REVERT: D 426 MET cc_start: 0.8252 (ttm) cc_final: 0.8033 (ttm) REVERT: D 572 MET cc_start: 0.8333 (mmp) cc_final: 0.7956 (mmp) outliers start: 28 outliers final: 23 residues processed: 186 average time/residue: 0.0755 time to fit residues: 22.7799 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 : 0.454 ------------------------------------------------------------------------------- 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 555 ILE Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 586 LEU 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 25 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3440 r_free = 0.3440 target = 0.138831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.113363 restraints weight = 13499.769| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.19 r_work: 0.2950 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1367 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= 0.130 Angle : 0.512 11.867 16986 Z= 0.259 Chirality : 0.035 0.211 2034 Planarity : 0.003 0.030 2100 Dihedral : 3.374 21.279 1692 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.96 % Allowed : 10.41 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.23 (0.22), residues: 1554 helix: 2.54 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.59 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 504 TYR 0.003 0.001 TYR A 535 PHE 0.008 0.001 PHE D 577 TRP 0.003 0.001 TRP B 523 HIS 0.009 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00301 (12588) covalent geometry : angle 0.51185 (16986) hydrogen bonds : bond 0.05122 ( 952) hydrogen bonds : angle 3.91534 ( 2856) *********************** 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 187 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.315 Fit side-chains REVERT: D 572 MET cc_start: 0.8358 (mmp) cc_final: 0.7970 (mmp) REVERT: F 647 GLN cc_start: 0.7841 (tt0) cc_final: 0.7618 (tt0) outliers start: 26 outliers final: 24 residues processed: 180 average time/residue: 0.0788 time to fit residues: 22.6216 Evaluate side-chains 185 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 555 ILE Chi-restraints excluded: chain D residue 584 SER Chi-restraints excluded: chain D residue 586 LEU 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 76 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 153 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.139989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.114807 restraints weight = 13502.313| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.18 r_work: 0.2967 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1365 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 : 0.498 11.785 16986 Z= 0.252 Chirality : 0.035 0.206 2034 Planarity : 0.003 0.030 2100 Dihedral : 3.343 21.110 1692 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.89 % Allowed : 10.71 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.32 (0.22), residues: 1554 helix: 2.56 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.33 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 504 TYR 0.003 0.001 TYR A 535 PHE 0.008 0.001 PHE A 519 TRP 0.002 0.001 TRP D 523 HIS 0.008 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00270 (12588) covalent geometry : angle 0.49835 (16986) hydrogen bonds : bond 0.04803 ( 952) hydrogen bonds : angle 3.86244 ( 2856) *********************** 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 192 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.351 Fit side-chains REVERT: B 585 ASN cc_start: 0.7300 (m-40) cc_final: 0.7033 (t0) REVERT: D 572 MET cc_start: 0.8331 (mmp) cc_final: 0.7942 (mmp) outliers start: 25 outliers final: 25 residues processed: 184 average time/residue: 0.0787 time to fit residues: 23.0380 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 : 0.432 ------------------------------------------------------------------------------- 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 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 555 ILE 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 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.139265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.113343 restraints weight = 13557.650| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.24 r_work: 0.2964 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1377 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= 0.125 Angle : 0.506 11.976 16986 Z= 0.256 Chirality : 0.035 0.207 2034 Planarity : 0.003 0.030 2100 Dihedral : 3.355 21.152 1692 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.96 % Allowed : 10.48 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.27 (0.22), residues: 1554 helix: 2.57 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.55 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 504 TYR 0.003 0.001 TYR A 535 PHE 0.008 0.001 PHE A 519 TRP 0.002 0.001 TRP B 523 HIS 0.009 0.001 HIS A 548 Details of bonding type rmsd covalent geometry : bond 0.00286 (12588) covalent geometry : angle 0.50603 (16986) hydrogen bonds : bond 0.04967 ( 952) hydrogen bonds : angle 3.88769 ( 2856) ********************** 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 192 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.436 Fit side-chains REVERT: B 585 ASN cc_start: 0.7340 (m-40) cc_final: 0.7072 (t0) REVERT: D 572 MET cc_start: 0.8340 (mmp) cc_final: 0.7946 (mmp) REVERT: F 647 GLN cc_start: 0.7832 (tt0) cc_final: 0.7606 (tt0) outliers start: 26 outliers final: 26 residues processed: 184 average time/residue: 0.0815 time to fit residues: 23.8603 Evaluate side-chains 192 residues out of total 1416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 555 ILE 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 57 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 107 optimal weight: 0.0970 chunk 28 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 104 optimal weight: 0.0470 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.142777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.116985 restraints weight = 13386.357| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.35 r_work: 0.3014 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1400 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= 0.099 Angle : 0.470 11.487 16986 Z= 0.237 Chirality : 0.034 0.195 2034 Planarity : 0.003 0.030 2100 Dihedral : 3.243 20.940 1692 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.81 % Allowed : 10.71 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.54 (0.22), residues: 1554 helix: 2.71 (0.15), residues: 1344 sheet: None (None), residues: 0 loop : -0.26 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 504 TYR 0.003 0.001 TYR A 576 PHE 0.008 0.001 PHE A 519 TRP 0.004 0.001 TRP A 487 HIS 0.008 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00204 (12588) covalent geometry : angle 0.46967 (16986) hydrogen bonds : bond 0.04082 ( 952) hydrogen bonds : angle 3.72659 ( 2856) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2907.62 seconds wall clock time: 50 minutes 30.75 seconds (3030.75 seconds total)