Starting phenix.real_space_refine on Fri Jul 3 16:04:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sc5_25022/07_2026/7sc5_25022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sc5_25022/07_2026/7sc5_25022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sc5_25022/07_2026/7sc5_25022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sc5_25022/07_2026/7sc5_25022.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sc5_25022/07_2026/7sc5_25022.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sc5_25022/07_2026/7sc5_25022.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sc5_25022/07_2026/7sc5_25022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sc5_25022/07_2026/7sc5_25022.cif" } resolution = 3.88 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= 0.001 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 99 5.16 5 C 9192 2.51 5 N 2511 2.21 5 O 2901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14703 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "B" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "D" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 3464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3464 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 4 Chain: "F" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1163 Classifications: {'peptide': 150} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 147} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.70, per 1000 atoms: 0.25 Number of scatterers: 14703 At special positions: 0 Unit cell: (122.57, 130.81, 129.78, 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 99 16.00 O 2901 8.00 N 2511 7.00 C 9192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 330 " distance=2.02 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 443 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 416 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 149 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 330 " distance=2.02 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 443 " distance=2.03 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 416 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 330 " distance=2.02 Simple disulfide: pdb=" SG CYS E 377 " - pdb=" SG CYS E 443 " distance=2.03 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 416 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 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=3, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 601 " - " ASN A 152 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 331 " " NAG A 605 " - " ASN A 446 " " NAG A 606 " - " ASN A 391 " " NAG A 607 " - " ASN A 385 " " NAG A 608 " - " ASN A 88 " " NAG A 609 " - " ASN A 148 " " NAG B 801 " - " ASN B 625 " " NAG B 802 " - " ASN B 618 " " NAG B 803 " - " ASN B 637 " " NAG C 601 " - " ASN C 152 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 331 " " NAG C 605 " - " ASN C 446 " " NAG C 606 " - " ASN C 391 " " NAG C 607 " - " ASN C 385 " " NAG C 608 " - " ASN C 88 " " NAG C 609 " - " ASN C 148 " " NAG D 801 " - " ASN D 625 " " NAG D 802 " - " ASN D 618 " " NAG D 803 " - " ASN D 637 " " NAG E 601 " - " ASN E 152 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 331 " " NAG E 605 " - " ASN E 446 " " NAG E 606 " - " ASN E 391 " " NAG E 607 " - " ASN E 385 " " NAG E 608 " - " ASN E 88 " " NAG E 609 " - " ASN E 148 " " NAG F 801 " - " ASN F 625 " " NAG F 802 " - " ASN F 618 " " NAG F 803 " - " ASN F 637 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 354 " " NAG K 1 " - " ASN C 234 " " NAG L 1 " - " ASN C 354 " " NAG N 1 " - " ASN E 234 " " NAG O 1 " - " ASN E 354 " NAG-SER " NAG G 1 " - " SER A 445 " " NAG J 1 " - " SER C 445 " " NAG M 1 " - " SER E 445 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 656.9 milliseconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3324 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 27 sheets defined 24.4% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.972A pdb=" N LYS A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.936A pdb=" N TRP A 477 " --> pdb=" O MET A 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 539 Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.694A pdb=" N GLN B 551 " --> pdb=" O GLY B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 Processing helix chain 'B' and resid 570 through 596 removed outlier: 4.085A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 652 removed outlier: 4.087A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 660 Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 333 through 352 removed outlier: 3.972A pdb=" N LYS C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS C 351 " --> pdb=" O GLN C 347 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.937A pdb=" N TRP C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 539 Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.693A pdb=" N GLN D 551 " --> pdb=" O GLY D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 Processing helix chain 'D' and resid 570 through 596 removed outlier: 4.086A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 589 " --> pdb=" O ARG D 585 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN D 590 " --> pdb=" O TYR D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 652 removed outlier: 4.087A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 660 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 333 through 352 removed outlier: 3.971A pdb=" N LYS E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS E 351 " --> pdb=" O GLN E 347 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE E 352 " --> pdb=" O LEU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 372 removed outlier: 3.558A pdb=" N THR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 479 removed outlier: 3.937A pdb=" N TRP E 477 " --> pdb=" O MET E 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 539 Processing helix chain 'F' and resid 540 through 542 No H-bonds generated for 'chain 'F' and resid 540 through 542' Processing helix chain 'F' and resid 543 through 551 removed outlier: 3.693A pdb=" N GLN F 551 " --> pdb=" O GLY F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 558 Processing helix chain 'F' and resid 570 through 596 removed outlier: 4.085A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 652 removed outlier: 4.085A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 660 Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 497 removed outlier: 6.264A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE A 151 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 174 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.823A pdb=" N LEU A 260 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU A 450 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 441 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 445 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 328 " --> pdb=" O CYS A 416 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 421 through 423 Processing sheet with id=AB1, first strand: chain 'C' and resid 492 through 497 removed outlier: 6.107A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS D 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB4, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE C 151 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 173 through 174 Processing sheet with id=AB6, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.824A pdb=" N LEU C 260 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU C 450 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 441 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER C 445 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C 328 " --> pdb=" O CYS C 416 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AB9, first strand: chain 'C' and resid 421 through 423 Processing sheet with id=AC1, first strand: chain 'E' and resid 492 through 497 removed outlier: 6.204A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS F 604 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 133 removed outlier: 3.701A pdb=" N PHE E 151 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 173 through 174 Processing sheet with id=AC6, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.823A pdb=" N LEU E 260 " --> pdb=" O THR E 448 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 272 through 273 removed outlier: 3.542A pdb=" N LEU E 450 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 441 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER E 445 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA E 328 " --> pdb=" O CYS E 416 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'E' and resid 421 through 423 441 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4603 1.34 - 1.46: 3045 1.46 - 1.57: 7190 1.57 - 1.69: 3 1.69 - 1.81: 132 Bond restraints: 14973 Sorted by residual: bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.335 1.376 -0.041 9.40e-03 1.13e+04 1.88e+01 bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.335 1.375 -0.040 9.40e-03 1.13e+04 1.83e+01 bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.335 1.375 -0.040 9.40e-03 1.13e+04 1.80e+01 bond pdb=" C1 BMA M 3 " pdb=" C2 BMA M 3 " ideal model delta sigma weight residual 1.519 1.594 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.593 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 14968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 19425 2.35 - 4.69: 731 4.69 - 7.04: 136 7.04 - 9.39: 24 9.39 - 11.74: 15 Bond angle restraints: 20331 Sorted by residual: angle pdb=" C MET E 153 " pdb=" N THR E 154 " pdb=" CA THR E 154 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C MET C 153 " pdb=" N THR C 154 " pdb=" CA THR C 154 " ideal model delta sigma weight residual 121.54 133.26 -11.72 1.91e+00 2.74e-01 3.77e+01 angle pdb=" C MET A 153 " pdb=" N THR A 154 " pdb=" CA THR A 154 " ideal model delta sigma weight residual 121.54 133.23 -11.69 1.91e+00 2.74e-01 3.75e+01 angle pdb=" CA SER F 612 " pdb=" C SER F 612 " pdb=" O SER F 612 " ideal model delta sigma weight residual 118.91 109.69 9.22 1.60e+00 3.91e-01 3.32e+01 angle pdb=" CA SER D 612 " pdb=" C SER D 612 " pdb=" O SER D 612 " ideal model delta sigma weight residual 118.91 109.73 9.18 1.60e+00 3.91e-01 3.29e+01 ... (remaining 20326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 7614 17.55 - 35.10: 804 35.10 - 52.65: 105 52.65 - 70.20: 45 70.20 - 87.75: 18 Dihedral angle restraints: 8586 sinusoidal: 3471 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 172.34 -79.34 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 172.32 -79.32 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 172.31 -79.31 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 8583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2344 0.114 - 0.227: 119 0.227 - 0.341: 9 0.341 - 0.455: 15 0.455 - 0.568: 3 Chirality restraints: 2490 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 7.98e+00 ... (remaining 2487 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 609 " -0.265 2.00e-02 2.50e+03 2.22e-01 6.13e+02 pdb=" C7 NAG E 609 " 0.071 2.00e-02 2.50e+03 pdb=" C8 NAG E 609 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG E 609 " 0.371 2.00e-02 2.50e+03 pdb=" O7 NAG E 609 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 609 " -0.256 2.00e-02 2.50e+03 2.14e-01 5.71e+02 pdb=" C7 NAG C 609 " 0.069 2.00e-02 2.50e+03 pdb=" C8 NAG C 609 " -0.176 2.00e-02 2.50e+03 pdb=" N2 NAG C 609 " 0.357 2.00e-02 2.50e+03 pdb=" O7 NAG C 609 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 609 " -0.242 2.00e-02 2.50e+03 2.01e-01 5.07e+02 pdb=" C7 NAG A 609 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 609 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A 609 " 0.334 2.00e-02 2.50e+03 pdb=" O7 NAG A 609 " 0.012 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 230 2.55 - 3.14: 11369 3.14 - 3.72: 23109 3.72 - 4.31: 30743 4.31 - 4.90: 48887 Nonbonded interactions: 114338 Sorted by model distance: nonbonded pdb=" O ASP C 367 " pdb=" N GLU C 369 " model vdw 1.959 3.120 nonbonded pdb=" O3 NAG A 609 " pdb=" O7 NAG A 609 " model vdw 2.053 3.040 nonbonded pdb=" O3 NAG C 609 " pdb=" O7 NAG C 609 " model vdw 2.060 3.040 nonbonded pdb=" O3 NAG E 609 " pdb=" O7 NAG E 609 " model vdw 2.070 3.040 nonbonded pdb=" ND2 ASN E 362 " pdb=" O THR E 371 " model vdw 2.196 3.120 ... (remaining 114333 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.180 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.030 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 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 : 0.008 0.075 15066 Z= 0.392 Angle : 1.171 13.256 20568 Z= 0.604 Chirality : 0.070 0.568 2490 Planarity : 0.009 0.222 2520 Dihedral : 14.881 87.748 5172 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.30 % Favored : 88.47 % Rotamer: Outliers : 0.97 % Allowed : 7.52 % Favored : 91.50 % 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: -5.17 (0.16), residues: 1734 helix: -3.87 (0.12), residues: 405 sheet: -2.56 (0.22), residues: 474 loop : -3.75 (0.17), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 158 TYR 0.015 0.002 TYR C 165 PHE 0.013 0.002 PHE A 93 TRP 0.018 0.002 TRP C 394 HIS 0.010 0.002 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00781 / 0.39 (14973) covalent geometry : angle 1.10783 / 0.59 (20331) SS BOND : bond 0.00554 / 0.33 ( 30) SS BOND : angle 0.82746 / 0.56 ( 60) hydrogen bonds : bond 0.29926 / 19.82 ( 441) hydrogen bonds : angle 9.86406 / 6.95 ( 1245) Misc. bond : bond 0.00455 / 0.20 ( 3) link_BETA1-4 : bond 0.01422 / 0.84 ( 15) link_BETA1-4 : angle 6.32654 / 4.21 ( 45) link_NAG-ASN : bond 0.00674 / 0.44 ( 42) link_NAG-ASN : angle 3.28601 / 2.08 ( 126) link_NAG-SER : bond 0.00572 / 0.25 ( 3) link_NAG-SER : angle 2.48703 / 1.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.5687 (ttt) cc_final: 0.4700 (ttm) REVERT: B 567 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7901 (mmtm) REVERT: B 601 LYS cc_start: 0.9086 (mtmm) cc_final: 0.8586 (mtmm) REVERT: B 632 GLU cc_start: 0.9368 (tp30) cc_final: 0.9099 (tp30) REVERT: B 651 ASN cc_start: 0.9048 (t0) cc_final: 0.8827 (t0) REVERT: B 657 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8776 (mt-10) REVERT: C 69 TRP cc_start: 0.9256 (m-90) cc_final: 0.8715 (m-90) REVERT: C 424 MET cc_start: 0.5931 (ttt) cc_final: 0.4320 (ttm) REVERT: C 447 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9249 (mp) REVERT: D 601 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8465 (mtmm) REVERT: D 632 GLU cc_start: 0.9328 (tp30) cc_final: 0.8971 (tp30) REVERT: D 657 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8691 (mt-10) REVERT: E 69 TRP cc_start: 0.9174 (m-90) cc_final: 0.8697 (m-90) REVERT: E 264 SER cc_start: 0.9099 (t) cc_final: 0.8762 (m) REVERT: F 601 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8276 (mtmm) REVERT: F 632 GLU cc_start: 0.9287 (tp30) cc_final: 0.8969 (tp30) REVERT: F 633 LYS cc_start: 0.9730 (mttt) cc_final: 0.9454 (mttp) REVERT: F 651 ASN cc_start: 0.9097 (t0) cc_final: 0.8681 (t0) REVERT: F 657 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8727 (mt-10) outliers start: 15 outliers final: 9 residues processed: 194 average time/residue: 0.1451 time to fit residues: 40.4126 Evaluate side-chains 119 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain F residue 636 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 295 ASN A 300 ASN ** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS B 550 GLN B 551 GLN B 564 HIS ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN C 276 ASN C 295 ASN C 300 ASN C 373 HIS D 550 GLN D 551 GLN D 564 HIS D 656 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 ASN E 295 ASN E 300 ASN E 373 HIS F 550 GLN F 551 GLN F 564 HIS F 575 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.051544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.041309 restraints weight = 94337.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.042396 restraints weight = 58551.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.043191 restraints weight = 43699.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.043773 restraints weight = 35529.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.044184 restraints weight = 30831.840| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15066 Z= 0.185 Angle : 0.856 10.325 20568 Z= 0.414 Chirality : 0.052 0.303 2490 Planarity : 0.004 0.041 2520 Dihedral : 7.419 59.981 1884 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 2.46 % Allowed : 10.51 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.85 (0.18), residues: 1734 helix: -1.69 (0.22), residues: 408 sheet: -2.05 (0.23), residues: 432 loop : -3.31 (0.18), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 588 TYR 0.017 0.002 TYR C 383 PHE 0.010 0.001 PHE C 93 TRP 0.017 0.002 TRP B 571 HIS 0.004 0.001 HIS B 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (14973) covalent geometry : angle 0.81455 / 0.41 (20331) SS BOND : bond 0.00139 / 0.08 ( 30) SS BOND : angle 0.44906 / 0.31 ( 60) hydrogen bonds : bond 0.05599 / 3.75 ( 441) hydrogen bonds : angle 6.58525 / 4.65 ( 1245) Misc. bond : bond 0.00092 / 0.04 ( 3) link_BETA1-4 : bond 0.01249 / 0.73 ( 15) link_BETA1-4 : angle 4.13846 / 2.64 ( 45) link_NAG-ASN : bond 0.00463 / 0.30 ( 42) link_NAG-ASN : angle 2.52573 / 1.60 ( 126) link_NAG-SER : bond 0.00425 / 0.18 ( 3) link_NAG-SER : angle 1.35844 / 0.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9224 (ttt) cc_final: 0.9024 (ttt) REVERT: A 260 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9063 (pp) REVERT: A 362 ASN cc_start: 0.7344 (t0) cc_final: 0.7106 (t0) REVERT: A 424 MET cc_start: 0.5827 (ttt) cc_final: 0.4853 (ttm) REVERT: B 632 GLU cc_start: 0.9331 (tp30) cc_final: 0.8987 (tp30) REVERT: B 651 ASN cc_start: 0.9119 (t0) cc_final: 0.8784 (t0) REVERT: B 657 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8745 (mt-10) REVERT: C 69 TRP cc_start: 0.9271 (m-90) cc_final: 0.8702 (m-90) REVERT: C 271 MET cc_start: 0.8531 (mmm) cc_final: 0.8218 (mmm) REVERT: C 432 MET cc_start: 0.8506 (ppp) cc_final: 0.8283 (ppp) REVERT: D 530 MET cc_start: 0.6986 (mtm) cc_final: 0.6754 (mtp) REVERT: D 574 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8913 (pttm) REVERT: D 584 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8117 (mp0) REVERT: D 601 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8397 (mtmm) REVERT: D 632 GLU cc_start: 0.9303 (tp30) cc_final: 0.8963 (tp30) REVERT: D 657 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8675 (mt-10) REVERT: E 69 TRP cc_start: 0.9228 (m-90) cc_final: 0.8613 (m-90) REVERT: E 264 SER cc_start: 0.9110 (t) cc_final: 0.8788 (m) REVERT: E 424 MET cc_start: 0.5873 (ttt) cc_final: 0.5243 (ttm) REVERT: F 601 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8120 (mtmm) REVERT: F 632 GLU cc_start: 0.9283 (tp30) cc_final: 0.8987 (tp30) REVERT: F 633 LYS cc_start: 0.9766 (mttt) cc_final: 0.9541 (mttp) REVERT: F 651 ASN cc_start: 0.9116 (t0) cc_final: 0.8804 (t0) REVERT: F 654 GLU cc_start: 0.8577 (tm-30) cc_final: 0.7978 (tm-30) REVERT: F 657 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8704 (mt-10) outliers start: 38 outliers final: 14 residues processed: 159 average time/residue: 0.1334 time to fit residues: 31.3607 Evaluate side-chains 129 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 ASN B 564 HIS B 575 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 ASN E 82 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.050005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.039901 restraints weight = 97192.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.040993 restraints weight = 59821.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.041814 restraints weight = 43856.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.042335 restraints weight = 35921.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.042697 restraints weight = 31133.803| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15066 Z= 0.276 Angle : 0.866 9.518 20568 Z= 0.420 Chirality : 0.051 0.281 2490 Planarity : 0.004 0.034 2520 Dihedral : 6.908 54.229 1879 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.67 % Favored : 86.16 % Rotamer: Outliers : 3.70 % Allowed : 14.53 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.22 (0.19), residues: 1734 helix: -0.46 (0.26), residues: 399 sheet: -1.95 (0.23), residues: 432 loop : -3.10 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 454 TYR 0.009 0.001 TYR E 484 PHE 0.018 0.002 PHE C 93 TRP 0.019 0.002 TRP A 477 HIS 0.006 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.28 (14973) covalent geometry : angle 0.82851 / 0.41 (20331) SS BOND : bond 0.00245 / 0.13 ( 30) SS BOND : angle 0.69731 / 0.46 ( 60) hydrogen bonds : bond 0.04946 / 3.27 ( 441) hydrogen bonds : angle 6.11479 / 4.33 ( 1245) Misc. bond : bond 0.00102 / 0.04 ( 3) link_BETA1-4 : bond 0.01171 / 0.69 ( 15) link_BETA1-4 : angle 3.84723 / 2.45 ( 45) link_NAG-ASN : bond 0.00517 / 0.33 ( 42) link_NAG-ASN : angle 2.41538 / 1.54 ( 126) link_NAG-SER : bond 0.00475 / 0.23 ( 3) link_NAG-SER : angle 2.02855 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 117 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9123 (pp) REVERT: A 424 MET cc_start: 0.5872 (ttt) cc_final: 0.5082 (ttm) REVERT: B 574 LYS cc_start: 0.9380 (mmmt) cc_final: 0.9018 (ptmt) REVERT: B 632 GLU cc_start: 0.9287 (tp30) cc_final: 0.9083 (tp30) REVERT: B 651 ASN cc_start: 0.9207 (t0) cc_final: 0.8975 (t0) REVERT: B 654 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8136 (tm-30) REVERT: B 657 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8732 (mt-10) REVERT: C 69 TRP cc_start: 0.9258 (m-90) cc_final: 0.8657 (m-90) REVERT: C 432 MET cc_start: 0.8742 (ppp) cc_final: 0.8418 (ppp) REVERT: C 447 ILE cc_start: 0.9425 (OUTLIER) cc_final: 0.9225 (mp) REVERT: D 530 MET cc_start: 0.7610 (mtm) cc_final: 0.7367 (mtp) REVERT: D 574 LYS cc_start: 0.9341 (mmmt) cc_final: 0.9035 (ptmt) REVERT: D 601 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8565 (mtmm) REVERT: D 632 GLU cc_start: 0.9299 (tp30) cc_final: 0.9043 (tp30) REVERT: D 657 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8667 (mt-10) REVERT: E 69 TRP cc_start: 0.9225 (m-90) cc_final: 0.8565 (m-90) REVERT: E 264 SER cc_start: 0.9203 (t) cc_final: 0.8831 (m) REVERT: E 424 MET cc_start: 0.5944 (ttt) cc_final: 0.4664 (ttm) REVERT: F 601 LYS cc_start: 0.8840 (mtmm) cc_final: 0.8212 (mtmm) REVERT: F 632 GLU cc_start: 0.9257 (tp30) cc_final: 0.9035 (tp30) REVERT: F 633 LYS cc_start: 0.9745 (mttt) cc_final: 0.9512 (mttp) REVERT: F 651 ASN cc_start: 0.9148 (t0) cc_final: 0.8810 (t0) REVERT: F 654 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8467 (tm-30) REVERT: F 657 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8708 (mt-10) outliers start: 57 outliers final: 34 residues processed: 165 average time/residue: 0.1302 time to fit residues: 31.8746 Evaluate side-chains 143 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 47 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 136 optimal weight: 5.9990 chunk 176 optimal weight: 50.0000 chunk 48 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 117 optimal weight: 50.0000 chunk 77 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.049516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.039402 restraints weight = 97821.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.040459 restraints weight = 60716.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.041228 restraints weight = 45275.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.041720 restraints weight = 37186.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.042078 restraints weight = 32428.437| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 15066 Z= 0.312 Angle : 0.878 9.432 20568 Z= 0.425 Chirality : 0.051 0.270 2490 Planarity : 0.004 0.086 2520 Dihedral : 6.889 55.044 1877 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.65 % Favored : 85.35 % Rotamer: Outliers : 3.57 % Allowed : 17.06 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 (0.19), residues: 1734 helix: -0.36 (0.26), residues: 417 sheet: -1.93 (0.23), residues: 426 loop : -3.10 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 427 TYR 0.007 0.001 TYR C 217 PHE 0.017 0.002 PHE C 93 TRP 0.017 0.002 TRP B 571 HIS 0.005 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00671 / 0.31 (14973) covalent geometry : angle 0.84295 / 0.42 (20331) SS BOND : bond 0.00283 / 0.16 ( 30) SS BOND : angle 0.66501 / 0.45 ( 60) hydrogen bonds : bond 0.04729 / 3.11 ( 441) hydrogen bonds : angle 6.04170 / 4.27 ( 1245) Misc. bond : bond 0.00100 / 0.04 ( 3) link_BETA1-4 : bond 0.01060 / 0.62 ( 15) link_BETA1-4 : angle 3.83345 / 2.42 ( 45) link_NAG-ASN : bond 0.00491 / 0.32 ( 42) link_NAG-ASN : angle 2.36477 / 1.52 ( 126) link_NAG-SER : bond 0.00457 / 0.21 ( 3) link_NAG-SER : angle 2.19023 / 1.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 113 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9125 (pp) REVERT: A 432 MET cc_start: 0.8666 (ppp) cc_final: 0.8374 (ppp) REVERT: B 574 LYS cc_start: 0.9377 (mmmt) cc_final: 0.9010 (ptpt) REVERT: B 651 ASN cc_start: 0.9238 (t0) cc_final: 0.9035 (t0) REVERT: B 654 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8220 (tm-30) REVERT: B 657 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8733 (mt-10) REVERT: C 69 TRP cc_start: 0.9302 (m-90) cc_final: 0.8685 (m-90) REVERT: C 104 MET cc_start: 0.9251 (ttt) cc_final: 0.9020 (ttt) REVERT: C 432 MET cc_start: 0.8826 (ppp) cc_final: 0.8429 (ppp) REVERT: C 447 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9299 (mp) REVERT: D 601 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8575 (mtmm) REVERT: D 632 GLU cc_start: 0.9287 (tp30) cc_final: 0.9066 (tp30) REVERT: D 657 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8622 (mt-10) REVERT: E 69 TRP cc_start: 0.9184 (m-90) cc_final: 0.8524 (m-90) REVERT: E 432 MET cc_start: 0.8857 (ppp) cc_final: 0.8551 (ppp) REVERT: F 601 LYS cc_start: 0.8881 (mtmm) cc_final: 0.8285 (mtmm) REVERT: F 633 LYS cc_start: 0.9729 (mttt) cc_final: 0.9513 (mttp) REVERT: F 651 ASN cc_start: 0.9199 (t0) cc_final: 0.8936 (t0) REVERT: F 654 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8235 (tm-30) REVERT: F 657 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8718 (mt-10) outliers start: 55 outliers final: 40 residues processed: 156 average time/residue: 0.1292 time to fit residues: 29.5644 Evaluate side-chains 147 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 HIS Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 564 HIS Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 85 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 167 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 ASN A 279 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 279 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.050847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.040577 restraints weight = 95634.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.041724 restraints weight = 58791.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.042541 restraints weight = 43094.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.043068 restraints weight = 34887.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.043509 restraints weight = 30259.202| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15066 Z= 0.132 Angle : 0.767 9.602 20568 Z= 0.368 Chirality : 0.050 0.255 2490 Planarity : 0.004 0.080 2520 Dihedral : 6.291 58.645 1876 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.59 % Favored : 88.24 % Rotamer: Outliers : 3.83 % Allowed : 18.22 % Favored : 77.95 % 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: -2.94 (0.19), residues: 1734 helix: -0.21 (0.26), residues: 414 sheet: -1.81 (0.24), residues: 411 loop : -2.95 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 557 TYR 0.008 0.001 TYR C 383 PHE 0.007 0.001 PHE C 390 TRP 0.023 0.002 TRP B 571 HIS 0.003 0.001 HIS A 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (14973) covalent geometry : angle 0.73203 / 0.36 (20331) SS BOND : bond 0.00173 / 0.10 ( 30) SS BOND : angle 0.40523 / 0.28 ( 60) hydrogen bonds : bond 0.04011 / 2.65 ( 441) hydrogen bonds : angle 5.73429 / 4.02 ( 1245) Misc. bond : bond 0.00090 / 0.04 ( 3) link_BETA1-4 : bond 0.01180 / 0.69 ( 15) link_BETA1-4 : angle 3.65268 / 2.34 ( 45) link_NAG-ASN : bond 0.00405 / 0.27 ( 42) link_NAG-ASN : angle 2.11681 / 1.37 ( 126) link_NAG-SER : bond 0.00592 / 0.27 ( 3) link_NAG-SER : angle 2.05342 / 1.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8922 (pp) REVERT: A 424 MET cc_start: 0.6072 (ttt) cc_final: 0.5281 (ttm) REVERT: A 432 MET cc_start: 0.8452 (ppp) cc_final: 0.8207 (ppp) REVERT: B 574 LYS cc_start: 0.9270 (mmmt) cc_final: 0.9005 (ptmt) REVERT: B 626 MET cc_start: 0.8492 (ttm) cc_final: 0.8163 (ttm) REVERT: B 651 ASN cc_start: 0.9101 (t0) cc_final: 0.8876 (t0) REVERT: B 657 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8741 (mt-10) REVERT: C 69 TRP cc_start: 0.9288 (m-90) cc_final: 0.8940 (m-90) REVERT: C 113 ASP cc_start: 0.9163 (m-30) cc_final: 0.8900 (m-30) REVERT: C 432 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8289 (ppp) REVERT: D 530 MET cc_start: 0.6965 (mtm) cc_final: 0.6644 (mtm) REVERT: D 574 LYS cc_start: 0.9192 (mmmt) cc_final: 0.8956 (ptmt) REVERT: D 601 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8614 (mtpp) REVERT: D 632 GLU cc_start: 0.9308 (tp30) cc_final: 0.9066 (tp30) REVERT: D 633 LYS cc_start: 0.9717 (mtpp) cc_final: 0.9440 (mttp) REVERT: D 657 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8625 (mt-10) REVERT: E 69 TRP cc_start: 0.9184 (m-90) cc_final: 0.8674 (m-90) REVERT: E 125 LEU cc_start: 0.9685 (tp) cc_final: 0.9138 (tt) REVERT: E 271 MET cc_start: 0.8256 (tpp) cc_final: 0.8031 (tpp) REVERT: E 424 MET cc_start: 0.6111 (ttt) cc_final: 0.5452 (ttm) REVERT: F 601 LYS cc_start: 0.8803 (mtmm) cc_final: 0.8578 (mtpp) REVERT: F 633 LYS cc_start: 0.9737 (mttt) cc_final: 0.9526 (mttp) REVERT: F 651 ASN cc_start: 0.9097 (t0) cc_final: 0.8831 (t0) REVERT: F 654 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8323 (tm-30) REVERT: F 657 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8701 (mt-10) outliers start: 59 outliers final: 42 residues processed: 172 average time/residue: 0.1205 time to fit residues: 30.7509 Evaluate side-chains 155 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 111 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 85 HIS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 23 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.050194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.040002 restraints weight = 95977.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.041146 restraints weight = 59111.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041926 restraints weight = 43304.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.042462 restraints weight = 35188.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.042850 restraints weight = 30461.546| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15066 Z= 0.185 Angle : 0.773 9.429 20568 Z= 0.371 Chirality : 0.049 0.264 2490 Planarity : 0.004 0.068 2520 Dihedral : 6.152 56.135 1875 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.26 % Favored : 86.68 % Rotamer: Outliers : 3.76 % Allowed : 19.78 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.86 (0.19), residues: 1734 helix: -0.08 (0.26), residues: 417 sheet: -1.72 (0.23), residues: 426 loop : -2.99 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 617 TYR 0.007 0.001 TYR A 217 PHE 0.010 0.001 PHE C 93 TRP 0.020 0.002 TRP B 571 HIS 0.002 0.001 HIS E 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (14973) covalent geometry : angle 0.74147 / 0.36 (20331) SS BOND : bond 0.00190 / 0.11 ( 30) SS BOND : angle 0.46325 / 0.31 ( 60) hydrogen bonds : bond 0.03994 / 2.63 ( 441) hydrogen bonds : angle 5.65633 / 3.97 ( 1245) Misc. bond : bond 0.00096 / 0.04 ( 3) link_BETA1-4 : bond 0.01083 / 0.64 ( 15) link_BETA1-4 : angle 3.46804 / 2.23 ( 45) link_NAG-ASN : bond 0.00380 / 0.25 ( 42) link_NAG-ASN : angle 2.06716 / 1.34 ( 126) link_NAG-SER : bond 0.00674 / 0.31 ( 3) link_NAG-SER : angle 2.32712 / 1.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 116 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8880 (pp) REVERT: A 432 MET cc_start: 0.8547 (ppp) cc_final: 0.8248 (ppp) REVERT: B 651 ASN cc_start: 0.9132 (t0) cc_final: 0.8910 (t0) REVERT: B 654 GLU cc_start: 0.8361 (tm-30) cc_final: 0.8160 (tm-30) REVERT: B 657 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8734 (mt-10) REVERT: C 69 TRP cc_start: 0.9291 (m-90) cc_final: 0.8759 (m-90) REVERT: C 113 ASP cc_start: 0.9208 (m-30) cc_final: 0.8969 (m-30) REVERT: C 432 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8322 (ppp) REVERT: D 530 MET cc_start: 0.7285 (mtm) cc_final: 0.7022 (mtm) REVERT: D 574 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8974 (ptmt) REVERT: D 601 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8638 (mtpp) REVERT: D 632 GLU cc_start: 0.9303 (tp30) cc_final: 0.9084 (tp30) REVERT: D 633 LYS cc_start: 0.9702 (mtpp) cc_final: 0.9424 (mttp) REVERT: D 654 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8119 (tm-30) REVERT: D 657 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8614 (mt-10) REVERT: E 69 TRP cc_start: 0.9207 (m-90) cc_final: 0.8644 (m-90) REVERT: E 153 MET cc_start: 0.7434 (tpt) cc_final: 0.7147 (tpt) REVERT: E 424 MET cc_start: 0.6126 (ttt) cc_final: 0.5426 (ttm) REVERT: F 530 MET cc_start: 0.7430 (mtm) cc_final: 0.7137 (mtm) REVERT: F 601 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8710 (mtpp) REVERT: F 626 MET cc_start: 0.8448 (ttm) cc_final: 0.8171 (ttm) REVERT: F 633 LYS cc_start: 0.9748 (mttt) cc_final: 0.9547 (mttp) REVERT: F 651 ASN cc_start: 0.9123 (t0) cc_final: 0.8861 (t0) REVERT: F 654 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8342 (tm-30) REVERT: F 657 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8705 (mt-10) outliers start: 58 outliers final: 45 residues processed: 162 average time/residue: 0.1166 time to fit residues: 28.2519 Evaluate side-chains 157 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 110 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 161 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 176 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.051211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.040981 restraints weight = 94671.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.042084 restraints weight = 58839.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.042907 restraints weight = 43829.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.043472 restraints weight = 35477.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.043863 restraints weight = 30697.179| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15066 Z= 0.133 Angle : 0.753 13.043 20568 Z= 0.360 Chirality : 0.049 0.273 2490 Planarity : 0.004 0.093 2520 Dihedral : 5.912 44.840 1874 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.71 % Favored : 88.12 % Rotamer: Outliers : 3.50 % Allowed : 20.10 % Favored : 76.39 % 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: -2.67 (0.19), residues: 1734 helix: -0.08 (0.26), residues: 417 sheet: -1.36 (0.26), residues: 363 loop : -2.85 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 427 TYR 0.006 0.001 TYR A 217 PHE 0.007 0.001 PHE C 93 TRP 0.029 0.001 TRP F 571 HIS 0.002 0.000 HIS D 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14973) covalent geometry : angle 0.72247 / 0.35 (20331) SS BOND : bond 0.00158 / 0.08 ( 30) SS BOND : angle 0.41276 / 0.28 ( 60) hydrogen bonds : bond 0.03763 / 2.48 ( 441) hydrogen bonds : angle 5.58833 / 3.90 ( 1245) Misc. bond : bond 0.00089 / 0.04 ( 3) link_BETA1-4 : bond 0.01058 / 0.62 ( 15) link_BETA1-4 : angle 3.44012 / 2.21 ( 45) link_NAG-ASN : bond 0.00362 / 0.24 ( 42) link_NAG-ASN : angle 1.95383 / 1.27 ( 126) link_NAG-SER : bond 0.00617 / 0.28 ( 3) link_NAG-SER : angle 2.29109 / 1.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8877 (pp) REVERT: A 424 MET cc_start: 0.6363 (ttt) cc_final: 0.6010 (ttm) REVERT: A 432 MET cc_start: 0.8468 (ppp) cc_final: 0.8175 (ppp) REVERT: B 574 LYS cc_start: 0.9239 (mmmt) cc_final: 0.9036 (ptmt) REVERT: B 651 ASN cc_start: 0.9111 (t0) cc_final: 0.8887 (t0) REVERT: B 657 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8727 (mt-10) REVERT: C 69 TRP cc_start: 0.9304 (m-90) cc_final: 0.8815 (m-90) REVERT: C 113 ASP cc_start: 0.9149 (m-30) cc_final: 0.8907 (m-30) REVERT: C 432 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8203 (ppp) REVERT: D 530 MET cc_start: 0.7087 (mtm) cc_final: 0.6838 (mtm) REVERT: D 574 LYS cc_start: 0.9179 (mmmt) cc_final: 0.8970 (ptmt) REVERT: D 633 LYS cc_start: 0.9697 (mtpp) cc_final: 0.9412 (mttp) REVERT: D 657 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8641 (mt-10) REVERT: E 69 TRP cc_start: 0.9208 (m-90) cc_final: 0.8736 (m-90) REVERT: E 153 MET cc_start: 0.7368 (tpt) cc_final: 0.7151 (tpt) REVERT: E 352 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.7787 (p90) REVERT: E 424 MET cc_start: 0.6341 (ttt) cc_final: 0.5511 (ttm) REVERT: F 601 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8625 (mtpp) REVERT: F 626 MET cc_start: 0.8344 (ttm) cc_final: 0.8047 (ttm) REVERT: F 633 LYS cc_start: 0.9744 (mttt) cc_final: 0.9538 (mttp) REVERT: F 651 ASN cc_start: 0.9081 (t0) cc_final: 0.8793 (t0) REVERT: F 654 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8340 (tm-30) REVERT: F 657 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8799 (mt-10) outliers start: 54 outliers final: 45 residues processed: 167 average time/residue: 0.1258 time to fit residues: 31.6606 Evaluate side-chains 162 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 114 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 114 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 140 optimal weight: 0.0270 chunk 117 optimal weight: 50.0000 chunk 142 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** 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 = 0.3203 r_free = 0.3203 target = 0.049811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.039710 restraints weight = 97006.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.040845 restraints weight = 60508.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.041619 restraints weight = 44224.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.042138 restraints weight = 35829.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.042545 restraints weight = 30987.563| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15066 Z= 0.213 Angle : 0.801 12.022 20568 Z= 0.385 Chirality : 0.049 0.259 2490 Planarity : 0.004 0.078 2520 Dihedral : 5.956 31.058 1873 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.61 % Favored : 86.22 % Rotamer: Outliers : 4.28 % Allowed : 20.82 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.72 (0.20), residues: 1734 helix: -0.04 (0.27), residues: 423 sheet: -1.69 (0.24), residues: 426 loop : -2.83 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 427 TYR 0.008 0.001 TYR A 217 PHE 0.012 0.001 PHE C 93 TRP 0.029 0.002 TRP F 571 HIS 0.003 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (14973) covalent geometry : angle 0.77359 / 0.38 (20331) SS BOND : bond 0.00217 / 0.12 ( 30) SS BOND : angle 0.48618 / 0.33 ( 60) hydrogen bonds : bond 0.03898 / 2.57 ( 441) hydrogen bonds : angle 5.56641 / 3.91 ( 1245) Misc. bond : bond 0.00090 / 0.04 ( 3) link_BETA1-4 : bond 0.01028 / 0.61 ( 15) link_BETA1-4 : angle 3.36103 / 2.15 ( 45) link_NAG-ASN : bond 0.00398 / 0.26 ( 42) link_NAG-ASN : angle 1.97512 / 1.28 ( 126) link_NAG-SER : bond 0.00430 / 0.19 ( 3) link_NAG-SER : angle 2.26037 / 1.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 118 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8901 (pp) REVERT: A 424 MET cc_start: 0.6626 (ttt) cc_final: 0.6148 (ttm) REVERT: A 432 MET cc_start: 0.8561 (ppp) cc_final: 0.8252 (ppp) REVERT: B 574 LYS cc_start: 0.9286 (mmmt) cc_final: 0.9057 (ptmt) REVERT: B 651 ASN cc_start: 0.9115 (t0) cc_final: 0.8848 (t0) REVERT: B 654 GLU cc_start: 0.8431 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 657 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8722 (mt-10) REVERT: C 69 TRP cc_start: 0.9262 (m-90) cc_final: 0.8744 (m-90) REVERT: C 113 ASP cc_start: 0.9200 (m-30) cc_final: 0.8938 (m-30) REVERT: C 432 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8275 (ppp) REVERT: D 530 MET cc_start: 0.7416 (mtm) cc_final: 0.7122 (mtm) REVERT: D 601 LYS cc_start: 0.8858 (mtpp) cc_final: 0.8434 (ptpp) REVERT: D 633 LYS cc_start: 0.9698 (mtpp) cc_final: 0.9375 (mttp) REVERT: D 657 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8690 (mt-10) REVERT: E 69 TRP cc_start: 0.9184 (m-90) cc_final: 0.8622 (m-90) REVERT: E 424 MET cc_start: 0.6243 (ttt) cc_final: 0.5761 (ttm) REVERT: F 626 MET cc_start: 0.8463 (ttm) cc_final: 0.8203 (ttm) REVERT: F 651 ASN cc_start: 0.9116 (t0) cc_final: 0.8860 (t0) REVERT: F 654 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8373 (tm-30) REVERT: F 657 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8775 (mt-10) outliers start: 66 outliers final: 55 residues processed: 167 average time/residue: 0.1315 time to fit residues: 32.6365 Evaluate side-chains 172 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 115 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 427 ARG Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 14 optimal weight: 0.0980 chunk 166 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 93 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.051241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.041124 restraints weight = 95787.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.042228 restraints weight = 58638.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.043063 restraints weight = 43028.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.043634 restraints weight = 34534.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.044067 restraints weight = 29667.269| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15066 Z= 0.126 Angle : 0.781 13.375 20568 Z= 0.372 Chirality : 0.050 0.254 2490 Planarity : 0.003 0.072 2520 Dihedral : 5.739 28.898 1873 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.84 % Favored : 88.99 % Rotamer: Outliers : 3.37 % Allowed : 22.37 % Favored : 74.25 % 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: -2.61 (0.19), residues: 1734 helix: -0.10 (0.27), residues: 426 sheet: -1.31 (0.26), residues: 363 loop : -2.81 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 427 TYR 0.010 0.001 TYR E 217 PHE 0.006 0.001 PHE E 390 TRP 0.033 0.001 TRP B 571 HIS 0.002 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (14973) covalent geometry : angle 0.75360 / 0.37 (20331) SS BOND : bond 0.00154 / 0.08 ( 30) SS BOND : angle 0.43026 / 0.29 ( 60) hydrogen bonds : bond 0.03675 / 2.39 ( 441) hydrogen bonds : angle 5.57276 / 3.91 ( 1245) Misc. bond : bond 0.00080 / 0.04 ( 3) link_BETA1-4 : bond 0.01030 / 0.59 ( 15) link_BETA1-4 : angle 3.36983 / 2.17 ( 45) link_NAG-ASN : bond 0.00341 / 0.23 ( 42) link_NAG-ASN : angle 1.87405 / 1.23 ( 126) link_NAG-SER : bond 0.00611 / 0.28 ( 3) link_NAG-SER : angle 2.31817 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9573 (tp) cc_final: 0.9155 (tt) REVERT: A 260 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8808 (pp) REVERT: A 424 MET cc_start: 0.6419 (ttt) cc_final: 0.6022 (ttm) REVERT: A 432 MET cc_start: 0.8425 (ppp) cc_final: 0.8162 (ppp) REVERT: B 651 ASN cc_start: 0.8769 (t0) cc_final: 0.8465 (t0) REVERT: B 657 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8834 (mt-10) REVERT: C 69 TRP cc_start: 0.9281 (m-90) cc_final: 0.8871 (m-90) REVERT: C 113 ASP cc_start: 0.9104 (m-30) cc_final: 0.8853 (m-30) REVERT: C 125 LEU cc_start: 0.9620 (tp) cc_final: 0.9209 (tt) REVERT: C 432 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8150 (ppp) REVERT: D 530 MET cc_start: 0.6905 (mtm) cc_final: 0.6656 (mtm) REVERT: D 601 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8435 (ptpp) REVERT: D 633 LYS cc_start: 0.9694 (mtpp) cc_final: 0.9346 (mttp) REVERT: D 651 ASN cc_start: 0.8609 (t0) cc_final: 0.8343 (t0) REVERT: D 657 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8727 (mt-10) REVERT: E 69 TRP cc_start: 0.9172 (m-90) cc_final: 0.8748 (m-90) REVERT: E 125 LEU cc_start: 0.9658 (tp) cc_final: 0.9178 (tt) REVERT: E 424 MET cc_start: 0.6298 (ttt) cc_final: 0.5592 (ttm) REVERT: F 584 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8243 (mp0) REVERT: F 601 LYS cc_start: 0.8980 (mtpp) cc_final: 0.8733 (ptpp) REVERT: F 626 MET cc_start: 0.8458 (ttm) cc_final: 0.8114 (ttm) REVERT: F 651 ASN cc_start: 0.8952 (t0) cc_final: 0.8658 (t0) REVERT: F 654 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8309 (tm-30) REVERT: F 657 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8764 (mt-10) outliers start: 52 outliers final: 45 residues processed: 168 average time/residue: 0.1256 time to fit residues: 31.7126 Evaluate side-chains 170 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 453 THR Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 137 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 167 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** 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 = 0.3247 r_free = 0.3247 target = 0.051505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.041432 restraints weight = 95623.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.042565 restraints weight = 58678.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.043403 restraints weight = 42537.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043992 restraints weight = 33973.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.044376 restraints weight = 29035.058| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15066 Z= 0.128 Angle : 0.772 13.670 20568 Z= 0.370 Chirality : 0.049 0.257 2490 Planarity : 0.003 0.061 2520 Dihedral : 5.616 28.428 1873 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 3.37 % Allowed : 22.50 % Favored : 74.12 % 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: -2.55 (0.20), residues: 1734 helix: -0.03 (0.27), residues: 420 sheet: -1.02 (0.28), residues: 330 loop : -2.84 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 557 TYR 0.006 0.001 TYR C 316 PHE 0.006 0.001 PHE C 93 TRP 0.033 0.001 TRP B 571 HIS 0.002 0.001 HIS D 564 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (14973) covalent geometry : angle 0.74607 / 0.36 (20331) SS BOND : bond 0.00142 / 0.08 ( 30) SS BOND : angle 0.40406 / 0.27 ( 60) hydrogen bonds : bond 0.03550 / 2.32 ( 441) hydrogen bonds : angle 5.50683 / 3.86 ( 1245) Misc. bond : bond 0.00085 / 0.04 ( 3) link_BETA1-4 : bond 0.01090 / 0.63 ( 15) link_BETA1-4 : angle 3.25270 / 2.10 ( 45) link_NAG-ASN : bond 0.00325 / 0.22 ( 42) link_NAG-ASN : angle 1.81507 / 1.19 ( 126) link_NAG-SER : bond 0.00559 / 0.25 ( 3) link_NAG-SER : angle 2.30505 / 1.32 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 130 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LEU cc_start: 0.9565 (tp) cc_final: 0.9206 (tt) REVERT: A 260 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8804 (pp) REVERT: A 424 MET cc_start: 0.6487 (ttt) cc_final: 0.6094 (ttm) REVERT: A 432 MET cc_start: 0.8379 (ppp) cc_final: 0.8103 (ppp) REVERT: B 651 ASN cc_start: 0.8816 (t0) cc_final: 0.8545 (t0) REVERT: B 657 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8772 (mt-10) REVERT: C 69 TRP cc_start: 0.9258 (m-90) cc_final: 0.8876 (m-90) REVERT: C 107 ASP cc_start: 0.8685 (m-30) cc_final: 0.8438 (m-30) REVERT: C 113 ASP cc_start: 0.9070 (m-30) cc_final: 0.8827 (m-30) REVERT: C 125 LEU cc_start: 0.9577 (tp) cc_final: 0.9163 (tt) REVERT: D 530 MET cc_start: 0.6847 (mtm) cc_final: 0.6630 (mtm) REVERT: D 548 ILE cc_start: 0.8241 (mt) cc_final: 0.8010 (mt) REVERT: D 549 VAL cc_start: 0.6987 (t) cc_final: 0.6681 (m) REVERT: D 601 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8444 (ptpp) REVERT: D 633 LYS cc_start: 0.9699 (mtpp) cc_final: 0.9353 (mttp) REVERT: D 651 ASN cc_start: 0.8715 (t0) cc_final: 0.8447 (t0) REVERT: D 657 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8694 (mt-10) REVERT: E 69 TRP cc_start: 0.9175 (m-90) cc_final: 0.8762 (m-90) REVERT: E 125 LEU cc_start: 0.9655 (tp) cc_final: 0.9179 (tt) REVERT: E 424 MET cc_start: 0.6308 (ttt) cc_final: 0.5653 (ttm) REVERT: F 530 MET cc_start: 0.7215 (mtm) cc_final: 0.6970 (pmm) REVERT: F 601 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8744 (ptpp) REVERT: F 651 ASN cc_start: 0.9017 (t0) cc_final: 0.8780 (t0) REVERT: F 654 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8365 (tm-30) REVERT: F 657 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8757 (mt-10) outliers start: 52 outliers final: 47 residues processed: 173 average time/residue: 0.1200 time to fit residues: 31.4878 Evaluate side-chains 170 residues out of total 1569 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 347 GLN Chi-restraints excluded: chain A residue 445 SER Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 448 THR Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 347 GLN Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 347 GLN Chi-restraints excluded: chain E residue 352 PHE Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain F residue 537 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 638 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 76 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.050106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.040111 restraints weight = 97104.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.041226 restraints weight = 60123.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.041952 restraints weight = 43963.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.042505 restraints weight = 35816.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.042914 restraints weight = 30847.788| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15066 Z= 0.198 Angle : 0.807 13.600 20568 Z= 0.388 Chirality : 0.049 0.259 2490 Planarity : 0.004 0.062 2520 Dihedral : 5.780 30.309 1873 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.26 % Favored : 86.56 % Rotamer: Outliers : 3.50 % Allowed : 22.18 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.66 (0.20), residues: 1734 helix: -0.02 (0.27), residues: 420 sheet: -1.62 (0.25), residues: 387 loop : -2.76 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 557 TYR 0.007 0.001 TYR F 643 PHE 0.012 0.001 PHE A 360 TRP 0.030 0.002 TRP B 571 HIS 0.002 0.001 HIS E 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (14973) covalent geometry : angle 0.78169 / 0.38 (20331) SS BOND : bond 0.00191 / 0.11 ( 30) SS BOND : angle 0.44932 / 0.30 ( 60) hydrogen bonds : bond 0.03719 / 2.44 ( 441) hydrogen bonds : angle 5.46477 / 3.82 ( 1245) Misc. bond : bond 0.00085 / 0.04 ( 3) link_BETA1-4 : bond 0.01021 / 0.61 ( 15) link_BETA1-4 : angle 3.26786 / 2.10 ( 45) link_NAG-ASN : bond 0.00353 / 0.23 ( 42) link_NAG-ASN : angle 1.87015 / 1.22 ( 126) link_NAG-SER : bond 0.00757 / 0.35 ( 3) link_NAG-SER : angle 2.35911 / 1.35 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2154.49 seconds wall clock time: 38 minutes 37.09 seconds (2317.09 seconds total)