Starting phenix.real_space_refine on Thu Jul 31 23:43:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwu_63459/07_2025/9lwu_63459.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwu_63459/07_2025/9lwu_63459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lwu_63459/07_2025/9lwu_63459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwu_63459/07_2025/9lwu_63459.map" model { file = "/net/cci-nas-00/data/ceres_data/9lwu_63459/07_2025/9lwu_63459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwu_63459/07_2025/9lwu_63459.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.046 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 84 5.16 5 C 9085 2.51 5 N 2369 2.21 5 O 2582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 14120 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2064 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 258} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 3000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 407, 2999 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 6, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 407, 2999 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 6, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 3058 Chain: "E" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1849 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 19, 'TRANS': 214} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "B" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2064 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 258} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 3008 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 407, 2999 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 6, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 407, 2999 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 6, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 3049 Chain: "F" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1849 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 19, 'TRANS': 214} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.15, per 1000 atoms: 0.79 Number of scatterers: 14120 At special positions: 0 Unit cell: (142.31, 125.19, 132.68, 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 84 16.00 O 2582 8.00 N 2369 7.00 C 9085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 311 " - pdb=" SG CYS D 539 " distance=2.03 Simple disulfide: pdb=" SG CYS E 79 " - pdb=" SG CYS E 261 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 199 " - pdb=" SG CYS E 232 " distance=2.03 Simple disulfide: pdb=" SG CYS E 215 " - pdb=" SG CYS E 244 " distance=2.03 Simple disulfide: pdb=" SG CYS C 311 " - pdb=" SG CYS C 539 " distance=2.03 Simple disulfide: pdb=" SG CYS F 79 " - pdb=" SG CYS F 261 " distance=2.07 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 199 " - pdb=" SG CYS F 232 " distance=2.03 Simple disulfide: pdb=" SG CYS F 215 " - pdb=" SG CYS F 244 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " MAN I 4 " - " MAN I 5 " " MAN J 4 " - " MAN J 5 " ALPHA1-4 " NAG I 2 " - " MAN I 3 " " MAN I 3 " - " MAN I 7 " " NAG J 2 " - " MAN J 3 " " MAN J 3 " - " MAN J 7 " ALPHA1-6 " MAN I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 6 " " MAN J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG C 801 " - " ASN C 217 " " NAG C 802 " - " ASN C 272 " " NAG C 803 " - " ASN C 608 " " NAG D 801 " - " ASN D 217 " " NAG D 802 " - " ASN D 272 " " NAG D 803 " - " ASN D 608 " " NAG I 1 " - " ASN G 350 " " NAG J 1 " - " ASN H 350 " Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 2.4 seconds 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3414 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 9 sheets defined 62.3% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 1 through 26 removed outlier: 3.820A pdb=" N LEU A 14 " --> pdb=" O ALA A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 39 through 66 Processing helix chain 'A' and resid 72 through 95 removed outlier: 4.253A pdb=" N HIS A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 129 removed outlier: 3.929A pdb=" N ARG A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 166 removed outlier: 3.539A pdb=" N HIS A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 200 removed outlier: 4.416A pdb=" N VAL A 173 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 235 removed outlier: 4.359A pdb=" N ALA A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 266 removed outlier: 3.655A pdb=" N MET A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 197 removed outlier: 3.577A pdb=" N GLN D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 190 " --> pdb=" O MET D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 215 removed outlier: 4.326A pdb=" N TYR D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER D 215 " --> pdb=" O GLN D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 removed outlier: 3.546A pdb=" N VAL D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA D 228 " --> pdb=" O ARG D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 253 removed outlier: 4.237A pdb=" N GLU D 244 " --> pdb=" O GLN D 240 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N MET D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS D 248 " --> pdb=" O GLU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 4.074A pdb=" N ALA D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 289 Processing helix chain 'D' and resid 291 through 303 Processing helix chain 'D' and resid 310 through 333 removed outlier: 3.622A pdb=" N LEU D 320 " --> pdb=" O THR D 316 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 321 " --> pdb=" O HIS D 317 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER D 327 " --> pdb=" O ASN D 323 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP D 328 " --> pdb=" O HIS D 324 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 346 removed outlier: 3.705A pdb=" N GLU D 345 " --> pdb=" O ARG D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 496 removed outlier: 3.508A pdb=" N LEU D 487 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 512 removed outlier: 3.746A pdb=" N TYR D 509 " --> pdb=" O GLN D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 Processing helix chain 'D' and resid 519 through 532 removed outlier: 3.621A pdb=" N ALA D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 551 removed outlier: 3.551A pdb=" N GLU D 544 " --> pdb=" O HIS D 540 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 545 " --> pdb=" O THR D 541 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 546 " --> pdb=" O ALA D 542 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL D 549 " --> pdb=" O LEU D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.617A pdb=" N THR D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 565 " --> pdb=" O THR D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 584 Processing helix chain 'D' and resid 587 through 599 removed outlier: 3.586A pdb=" N ASN D 592 " --> pdb=" O VAL D 588 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 593 " --> pdb=" O ALA D 589 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA D 594 " --> pdb=" O GLN D 590 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU D 597 " --> pdb=" O ALA D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 624 removed outlier: 3.643A pdb=" N ALA D 621 " --> pdb=" O HIS D 617 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN D 624 " --> pdb=" O ARG D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 639 removed outlier: 3.635A pdb=" N TYR D 636 " --> pdb=" O LYS D 632 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS D 637 " --> pdb=" O LEU D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 656 removed outlier: 3.552A pdb=" N ILE D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS D 653 " --> pdb=" O THR D 649 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR D 654 " --> pdb=" O ALA D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.858A pdb=" N PHE D 668 " --> pdb=" O ALA D 664 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 670 " --> pdb=" O ALA D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 698 removed outlier: 3.968A pdb=" N ARG D 689 " --> pdb=" O HIS D 685 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE D 690 " --> pdb=" O LEU D 686 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU D 696 " --> pdb=" O ASP D 692 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 698 " --> pdb=" O ALA D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 723 removed outlier: 3.811A pdb=" N ALA D 708 " --> pdb=" O PRO D 704 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 711 " --> pdb=" O LEU D 707 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 103 No H-bonds generated for 'chain 'E' and resid 101 through 103' Processing helix chain 'E' and resid 104 through 111 removed outlier: 4.000A pdb=" N SER E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 246 removed outlier: 3.655A pdb=" N SER E 245 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 285 removed outlier: 4.280A pdb=" N LEU E 284 " --> pdb=" O GLN E 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 26 removed outlier: 4.062A pdb=" N LEU B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 39 through 66 Processing helix chain 'B' and resid 72 through 95 removed outlier: 4.018A pdb=" N HIS B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 127 Processing helix chain 'B' and resid 134 through 161 removed outlier: 3.570A pdb=" N LEU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 170 through 201 removed outlier: 3.510A pdb=" N PHE B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 175 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 199 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 237 removed outlier: 4.224A pdb=" N ALA B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET B 234 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 235 " --> pdb=" O MET B 231 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 266 removed outlier: 3.720A pdb=" N MET B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.582A pdb=" N GLN C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 189 " --> pdb=" O MET C 185 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 190 " --> pdb=" O MET C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 215 removed outlier: 4.326A pdb=" N TYR C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 215 " --> pdb=" O GLN C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 removed outlier: 3.540A pdb=" N VAL C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA C 228 " --> pdb=" O ARG C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 253 removed outlier: 4.383A pdb=" N GLU C 244 " --> pdb=" O GLN C 240 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N MET C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 268 removed outlier: 4.087A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 288 Processing helix chain 'C' and resid 291 through 303 removed outlier: 3.543A pdb=" N LEU C 297 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 333 removed outlier: 3.586A pdb=" N LEU C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL C 321 " --> pdb=" O HIS C 317 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP C 328 " --> pdb=" O HIS C 324 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 346 removed outlier: 3.698A pdb=" N GLU C 345 " --> pdb=" O ARG C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 removed outlier: 3.506A pdb=" N LEU C 487 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 512 removed outlier: 3.748A pdb=" N TYR C 509 " --> pdb=" O GLN C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 517 Processing helix chain 'C' and resid 519 through 532 removed outlier: 3.619A pdb=" N ALA C 526 " --> pdb=" O PHE C 522 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY C 532 " --> pdb=" O MET C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 551 removed outlier: 3.529A pdb=" N GLU C 544 " --> pdb=" O HIS C 540 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 545 " --> pdb=" O THR C 541 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 546 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 548 " --> pdb=" O GLU C 544 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL C 549 " --> pdb=" O LEU C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.645A pdb=" N THR C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 565 " --> pdb=" O THR C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 584 Processing helix chain 'C' and resid 587 through 599 removed outlier: 3.579A pdb=" N ASN C 592 " --> pdb=" O VAL C 588 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 594 " --> pdb=" O GLN C 590 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU C 597 " --> pdb=" O ALA C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 624 removed outlier: 3.659A pdb=" N ALA C 621 " --> pdb=" O HIS C 617 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 624 " --> pdb=" O ARG C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 639 removed outlier: 3.635A pdb=" N TYR C 636 " --> pdb=" O LYS C 632 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 656 removed outlier: 3.546A pdb=" N ILE C 652 " --> pdb=" O GLU C 648 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS C 653 " --> pdb=" O THR C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 3.849A pdb=" N PHE C 668 " --> pdb=" O ALA C 664 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 670 " --> pdb=" O ALA C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 698 removed outlier: 3.962A pdb=" N ARG C 689 " --> pdb=" O HIS C 685 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE C 690 " --> pdb=" O LEU C 686 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 696 " --> pdb=" O ASP C 692 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 698 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 723 removed outlier: 3.524A pdb=" N PHE C 706 " --> pdb=" O GLN C 702 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C 708 " --> pdb=" O PRO C 704 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 711 " --> pdb=" O LEU C 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 111 removed outlier: 4.000A pdb=" N SER F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 246 removed outlier: 3.724A pdb=" N SER F 245 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 285 removed outlier: 3.838A pdb=" N GLU F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN F 279 " --> pdb=" O ARG F 275 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN F 280 " --> pdb=" O GLN F 276 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 43 through 49 removed outlier: 6.305A pdb=" N ARG E 44 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N CYS E 261 " --> pdb=" O ARG E 44 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASN E 46 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N SER E 263 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ASP E 258 " --> pdb=" O PRO E 82 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL E 67 " --> pdb=" O CYS E 79 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU E 81 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN E 65 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 116 through 117 removed outlier: 5.559A pdb=" N ILE E 131 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 189 through 193 removed outlier: 3.540A pdb=" N THR E 210 " --> pdb=" O TYR E 234 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL E 229 " --> pdb=" O GLU E 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 198 through 199 Processing sheet with id=AA5, first strand: chain 'F' and resid 43 through 46 removed outlier: 6.300A pdb=" N ARG F 44 " --> pdb=" O ILE F 259 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N CYS F 261 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASN F 46 " --> pdb=" O CYS F 261 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N SER F 263 " --> pdb=" O ASN F 46 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP F 258 " --> pdb=" O PRO F 82 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE F 260 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL F 67 " --> pdb=" O CYS F 79 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU F 81 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASN F 65 " --> pdb=" O LEU F 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 116 through 117 removed outlier: 5.623A pdb=" N ILE F 131 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 178 through 181 removed outlier: 3.980A pdb=" N THR F 186 " --> pdb=" O LYS F 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 189 through 193 removed outlier: 3.508A pdb=" N THR F 210 " --> pdb=" O TYR F 234 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLU F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL F 229 " --> pdb=" O GLU F 233 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 198 through 199 784 hydrogen bonds defined for protein. 2300 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: 4.10 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 4526 1.35 - 1.50: 4048 1.50 - 1.64: 5741 1.64 - 1.78: 19 1.78 - 1.93: 119 Bond restraints: 14453 Sorted by residual: bond pdb=" CA TRP A 82 " pdb=" C TRP A 82 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.26e-02 6.30e+03 2.04e+01 bond pdb=" CA ASN E 180 " pdb=" C ASN E 180 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.34e-02 5.57e+03 2.00e+01 bond pdb=" CA ARG D 319 " pdb=" C ARG D 319 " ideal model delta sigma weight residual 1.524 1.471 0.054 1.29e-02 6.01e+03 1.72e+01 bond pdb=" N ASN E 180 " pdb=" CA ASN E 180 " ideal model delta sigma weight residual 1.457 1.404 0.053 1.29e-02 6.01e+03 1.69e+01 bond pdb=" CA LYS E 179 " pdb=" C LYS E 179 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.34e-02 5.57e+03 1.40e+01 ... (remaining 14448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.30: 19512 5.30 - 10.61: 104 10.61 - 15.91: 8 15.91 - 21.22: 0 21.22 - 26.52: 1 Bond angle restraints: 19625 Sorted by residual: angle pdb=" CA CYS F 261 " pdb=" CB CYS F 261 " pdb=" SG CYS F 261 " ideal model delta sigma weight residual 114.40 140.92 -26.52 2.30e+00 1.89e-01 1.33e+02 angle pdb=" C ARG A 246 " pdb=" N PRO A 247 " pdb=" CA PRO A 247 " ideal model delta sigma weight residual 119.87 112.88 6.99 1.04e+00 9.25e-01 4.52e+01 angle pdb=" N PHE A 189 " pdb=" CA PHE A 189 " pdb=" C PHE A 189 " ideal model delta sigma weight residual 111.03 103.83 7.20 1.11e+00 8.12e-01 4.21e+01 angle pdb=" C ILE A 188 " pdb=" N PHE A 189 " pdb=" CA PHE A 189 " ideal model delta sigma weight residual 120.63 112.72 7.91 1.36e+00 5.41e-01 3.39e+01 angle pdb=" N TRP A 82 " pdb=" CA TRP A 82 " pdb=" C TRP A 82 " ideal model delta sigma weight residual 111.14 104.93 6.21 1.08e+00 8.57e-01 3.31e+01 ... (remaining 19620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.99: 7774 23.99 - 47.98: 830 47.98 - 71.97: 125 71.97 - 95.96: 27 95.96 - 119.95: 11 Dihedral angle restraints: 8767 sinusoidal: 3439 harmonic: 5328 Sorted by residual: dihedral pdb=" CB CYS F 79 " pdb=" SG CYS F 79 " pdb=" SG CYS F 261 " pdb=" CB CYS F 261 " ideal model delta sinusoidal sigma weight residual 93.00 27.36 65.64 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS D 311 " pdb=" SG CYS D 311 " pdb=" SG CYS D 539 " pdb=" CB CYS D 539 " ideal model delta sinusoidal sigma weight residual 93.00 55.50 37.50 1 1.00e+01 1.00e-02 1.98e+01 dihedral pdb=" CB CYS C 311 " pdb=" SG CYS C 311 " pdb=" SG CYS C 539 " pdb=" CB CYS C 539 " ideal model delta sinusoidal sigma weight residual 93.00 56.41 36.59 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 8764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2077 0.096 - 0.191: 164 0.191 - 0.287: 10 0.287 - 0.383: 3 0.383 - 0.478: 3 Chirality restraints: 2257 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN G 350 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN H 350 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" C1 NAG D 801 " pdb=" ND2 ASN D 217 " pdb=" C2 NAG D 801 " pdb=" O5 NAG D 801 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 2254 not shown) Planarity restraints: 2482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 272 " 0.029 2.00e-02 2.50e+03 6.01e-02 3.61e+01 pdb=" C LEU E 272 " -0.104 2.00e-02 2.50e+03 pdb=" O LEU E 272 " 0.040 2.00e-02 2.50e+03 pdb=" N THR E 273 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 178 " 0.024 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C THR E 178 " -0.085 2.00e-02 2.50e+03 pdb=" O THR E 178 " 0.032 2.00e-02 2.50e+03 pdb=" N LYS E 179 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 75 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C GLU A 75 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU A 75 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS A 76 " 0.017 2.00e-02 2.50e+03 ... (remaining 2479 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 598 2.72 - 3.27: 13874 3.27 - 3.81: 22670 3.81 - 4.36: 26821 4.36 - 4.90: 44032 Nonbonded interactions: 107995 Sorted by model distance: nonbonded pdb=" OD2 ASP C 683 " pdb=" OG1 THR F 230 " model vdw 2.176 3.040 nonbonded pdb=" OD2 ASP D 683 " pdb=" OG1 THR E 230 " model vdw 2.181 3.040 nonbonded pdb=" OD1 ASP C 635 " pdb=" OH TYR C 654 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP D 635 " pdb=" OH TYR D 654 " model vdw 2.214 3.040 nonbonded pdb=" O MET A 184 " pdb=" OG1 THR A 187 " model vdw 2.233 3.040 ... (remaining 107990 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 183 through 516 or resid 518 through 654 or resid 656 thro \ ugh 723 or resid 801 through 803)) selection = (chain 'D' and (resid 183 through 516 or resid 518 through 654 or resid 656 thro \ ugh 723 or resid 801 through 803)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.24 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 36.840 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.090 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 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 : 0.006 0.118 14483 Z= 0.303 Angle : 1.097 26.525 19705 Z= 0.543 Chirality : 0.056 0.478 2257 Planarity : 0.007 0.072 2474 Dihedral : 19.564 119.953 5323 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.34 % Favored : 95.10 % Rotamer: Outliers : 1.93 % Allowed : 31.03 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.18), residues: 1799 helix: -2.08 (0.13), residues: 1033 sheet: -1.06 (0.41), residues: 162 loop : -1.31 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 118 HIS 0.030 0.002 HIS F 135 PHE 0.034 0.002 PHE B 230 TYR 0.046 0.002 TYR A 192 ARG 0.006 0.001 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.01432 ( 8) link_NAG-ASN : angle 10.37226 ( 24) link_ALPHA1-4 : bond 0.01005 ( 4) link_ALPHA1-4 : angle 4.85682 ( 12) link_ALPHA1-6 : bond 0.00467 ( 4) link_ALPHA1-6 : angle 1.90501 ( 12) link_BETA1-4 : bond 0.02755 ( 2) link_BETA1-4 : angle 13.59034 ( 6) link_ALPHA1-3 : bond 0.01569 ( 2) link_ALPHA1-3 : angle 4.52268 ( 6) hydrogen bonds : bond 0.27502 ( 784) hydrogen bonds : angle 8.57999 ( 2300) SS BOND : bond 0.01469 ( 10) SS BOND : angle 2.64003 ( 20) covalent geometry : bond 0.00570 (14453) covalent geometry : angle 0.99490 (19625) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 437 time to evaluate : 1.367 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 49 GLN cc_start: 0.8043 (tp40) cc_final: 0.7799 (tp40) REVERT: A 81 SER cc_start: 0.8253 (t) cc_final: 0.8051 (p) REVERT: A 82 TRP cc_start: 0.7728 (OUTLIER) cc_final: 0.7160 (t-100) REVERT: A 141 ILE cc_start: 0.7860 (tp) cc_final: 0.7456 (tp) REVERT: D 248 LYS cc_start: 0.6421 (ttmt) cc_final: 0.6200 (tptm) REVERT: D 522 PHE cc_start: 0.7785 (m-80) cc_final: 0.7528 (m-80) REVERT: B 49 GLN cc_start: 0.8198 (tp40) cc_final: 0.7846 (tp40) REVERT: B 82 TRP cc_start: 0.7920 (OUTLIER) cc_final: 0.6190 (t-100) REVERT: F 185 MET cc_start: 0.4343 (mmm) cc_final: 0.3849 (mtp) REVERT: F 189 TYR cc_start: 0.5128 (t80) cc_final: 0.4899 (t80) outliers start: 25 outliers final: 3 residues processed: 448 average time/residue: 0.2938 time to fit residues: 182.1206 Evaluate side-chains 310 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 305 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain C residue 283 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 139 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 161 optimal weight: 20.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN D 524 ASN D 624 GLN E 110 GLN E 147 HIS E 153 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN B 28 GLN B 171 GLN C 524 ASN C 572 ASN F 110 GLN F 147 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.265597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.242795 restraints weight = 25237.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.240566 restraints weight = 31415.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.238165 restraints weight = 19738.873| |-----------------------------------------------------------------------------| r_work (final): 0.4608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4608 r_free = 0.4608 target_work(ls_wunit_k1) = 0.239 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4609 r_free = 0.4609 target_work(ls_wunit_k1) = 0.238 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14483 Z= 0.167 Angle : 0.856 15.032 19705 Z= 0.403 Chirality : 0.046 0.316 2257 Planarity : 0.005 0.066 2474 Dihedral : 12.419 110.930 2397 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.34 % Favored : 96.44 % Rotamer: Outliers : 4.08 % Allowed : 30.14 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.19), residues: 1799 helix: -0.57 (0.15), residues: 1089 sheet: -0.83 (0.37), residues: 166 loop : -1.18 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.008 0.001 HIS B 76 PHE 0.021 0.002 PHE F 269 TYR 0.023 0.002 TYR F 234 ARG 0.007 0.001 ARG B 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01332 ( 8) link_NAG-ASN : angle 7.90710 ( 24) link_ALPHA1-4 : bond 0.01679 ( 4) link_ALPHA1-4 : angle 3.81636 ( 12) link_ALPHA1-6 : bond 0.00989 ( 4) link_ALPHA1-6 : angle 2.21774 ( 12) link_BETA1-4 : bond 0.02555 ( 2) link_BETA1-4 : angle 9.59497 ( 6) link_ALPHA1-3 : bond 0.02108 ( 2) link_ALPHA1-3 : angle 5.02691 ( 6) hydrogen bonds : bond 0.05505 ( 784) hydrogen bonds : angle 4.98952 ( 2300) SS BOND : bond 0.00660 ( 10) SS BOND : angle 1.50728 ( 20) covalent geometry : bond 0.00352 (14453) covalent geometry : angle 0.78087 (19625) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 320 time to evaluate : 1.399 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 82 TRP cc_start: 0.7635 (OUTLIER) cc_final: 0.7037 (t-100) REVERT: A 121 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6911 (mm-30) REVERT: D 536 MET cc_start: 0.4986 (tmm) cc_final: 0.4519 (tmm) REVERT: B 53 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7349 (mm) REVERT: B 82 TRP cc_start: 0.8104 (OUTLIER) cc_final: 0.6244 (t-100) REVERT: B 246 ARG cc_start: 0.7592 (tpt170) cc_final: 0.7307 (tpt170) REVERT: C 536 MET cc_start: 0.5048 (tmm) cc_final: 0.4640 (tmm) REVERT: F 179 LYS cc_start: 0.7953 (ptmm) cc_final: 0.7733 (ptmm) REVERT: F 248 LYS cc_start: 0.5824 (tppt) cc_final: 0.5593 (tppt) REVERT: F 269 PHE cc_start: 0.7274 (t80) cc_final: 0.6959 (t80) outliers start: 54 outliers final: 25 residues processed: 353 average time/residue: 0.2664 time to fit residues: 134.2065 Evaluate side-chains 317 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 289 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 683 ASP Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 117 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 263 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 109 optimal weight: 50.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 HIS D 682 GLN D 685 HIS ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN C 624 GLN C 653 HIS C 682 GLN C 685 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.255926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.227356 restraints weight = 17109.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.223833 restraints weight = 24004.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.221605 restraints weight = 27325.408| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4398 r_free = 0.4398 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4397 r_free = 0.4397 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14483 Z= 0.152 Angle : 0.847 23.345 19705 Z= 0.380 Chirality : 0.047 0.330 2257 Planarity : 0.004 0.061 2474 Dihedral : 11.851 109.957 2397 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.73 % Favored : 96.05 % Rotamer: Outliers : 3.86 % Allowed : 29.03 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1799 helix: 0.15 (0.16), residues: 1095 sheet: -0.65 (0.37), residues: 166 loop : -1.03 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS B 195 PHE 0.023 0.002 PHE A 66 TYR 0.027 0.001 TYR C 523 ARG 0.012 0.001 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.01488 ( 8) link_NAG-ASN : angle 10.51379 ( 24) link_ALPHA1-4 : bond 0.01640 ( 4) link_ALPHA1-4 : angle 3.89794 ( 12) link_ALPHA1-6 : bond 0.00770 ( 4) link_ALPHA1-6 : angle 2.36372 ( 12) link_BETA1-4 : bond 0.02872 ( 2) link_BETA1-4 : angle 8.72387 ( 6) link_ALPHA1-3 : bond 0.02198 ( 2) link_ALPHA1-3 : angle 4.21625 ( 6) hydrogen bonds : bond 0.04187 ( 784) hydrogen bonds : angle 4.44198 ( 2300) SS BOND : bond 0.01326 ( 10) SS BOND : angle 1.54605 ( 20) covalent geometry : bond 0.00332 (14453) covalent geometry : angle 0.73581 (19625) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 308 time to evaluate : 1.790 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 82 TRP cc_start: 0.7532 (OUTLIER) cc_final: 0.6867 (t-100) REVERT: A 177 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6750 (mm-30) REVERT: B 53 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7361 (mm) REVERT: C 536 MET cc_start: 0.5029 (tmm) cc_final: 0.4566 (tmm) REVERT: F 269 PHE cc_start: 0.7413 (t80) cc_final: 0.7088 (t80) outliers start: 51 outliers final: 29 residues processed: 343 average time/residue: 0.3253 time to fit residues: 160.4014 Evaluate side-chains 311 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 280 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 587 GLU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 185 MET Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 263 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 166 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 chunk 147 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN D 599 GLN D 685 HIS E 276 GLN C 237 GLN C 682 GLN C 685 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.251621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.224409 restraints weight = 19123.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.218978 restraints weight = 25885.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.216554 restraints weight = 27216.910| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4297 r_free = 0.4297 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4297 r_free = 0.4297 target_work(ls_wunit_k1) = 0.211 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 14483 Z= 0.141 Angle : 0.807 22.545 19705 Z= 0.361 Chirality : 0.045 0.317 2257 Planarity : 0.004 0.060 2474 Dihedral : 11.476 109.872 2395 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.23 % Favored : 96.55 % Rotamer: Outliers : 4.75 % Allowed : 28.36 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1799 helix: 0.43 (0.16), residues: 1089 sheet: -0.33 (0.39), residues: 166 loop : -0.92 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS A 195 PHE 0.015 0.001 PHE C 284 TYR 0.020 0.001 TYR C 282 ARG 0.007 0.001 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.01568 ( 8) link_NAG-ASN : angle 9.98712 ( 24) link_ALPHA1-4 : bond 0.01447 ( 4) link_ALPHA1-4 : angle 3.46603 ( 12) link_ALPHA1-6 : bond 0.00936 ( 4) link_ALPHA1-6 : angle 2.35201 ( 12) link_BETA1-4 : bond 0.02709 ( 2) link_BETA1-4 : angle 8.41714 ( 6) link_ALPHA1-3 : bond 0.02330 ( 2) link_ALPHA1-3 : angle 4.19689 ( 6) hydrogen bonds : bond 0.03718 ( 784) hydrogen bonds : angle 4.21596 ( 2300) SS BOND : bond 0.00524 ( 10) SS BOND : angle 1.74172 ( 20) covalent geometry : bond 0.00312 (14453) covalent geometry : angle 0.70076 (19625) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 288 time to evaluate : 1.252 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: A 80 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.6985 (mtm180) REVERT: A 82 TRP cc_start: 0.7591 (OUTLIER) cc_final: 0.6778 (t-100) REVERT: D 536 MET cc_start: 0.4982 (tmm) cc_final: 0.4724 (tmm) REVERT: E 205 ARG cc_start: 0.5132 (ttp-110) cc_final: 0.4782 (ttm110) REVERT: E 269 PHE cc_start: 0.7743 (t80) cc_final: 0.7491 (t80) REVERT: B 53 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7391 (mm) REVERT: B 54 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7537 (p) REVERT: B 246 ARG cc_start: 0.7521 (tpt90) cc_final: 0.7141 (ttp80) REVERT: C 536 MET cc_start: 0.5031 (tmm) cc_final: 0.4698 (tmm) REVERT: C 700 ASP cc_start: 0.6345 (m-30) cc_final: 0.6113 (m-30) REVERT: F 269 PHE cc_start: 0.7471 (t80) cc_final: 0.7122 (t80) outliers start: 63 outliers final: 41 residues processed: 328 average time/residue: 0.3163 time to fit residues: 148.6341 Evaluate side-chains 317 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 272 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 276 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 263 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 53 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 151 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 116 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 682 GLN D 685 HIS ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN F 180 ASN ** F 262 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 = 0.4607 r_free = 0.4607 target = 0.248277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.220756 restraints weight = 17106.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.214025 restraints weight = 21303.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.213296 restraints weight = 23068.716| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4289 r_free = 0.4289 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4289 r_free = 0.4289 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14483 Z= 0.164 Angle : 0.797 21.296 19705 Z= 0.358 Chirality : 0.045 0.285 2257 Planarity : 0.004 0.058 2474 Dihedral : 11.184 111.008 2395 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.45 % Favored : 96.33 % Rotamer: Outliers : 4.45 % Allowed : 28.66 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1799 helix: 0.60 (0.16), residues: 1087 sheet: -0.26 (0.39), residues: 166 loop : -0.84 (0.28), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS A 195 PHE 0.022 0.002 PHE F 260 TYR 0.021 0.001 TYR C 282 ARG 0.005 0.001 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.01535 ( 8) link_NAG-ASN : angle 9.53177 ( 24) link_ALPHA1-4 : bond 0.01264 ( 4) link_ALPHA1-4 : angle 3.45840 ( 12) link_ALPHA1-6 : bond 0.01004 ( 4) link_ALPHA1-6 : angle 2.53068 ( 12) link_BETA1-4 : bond 0.02417 ( 2) link_BETA1-4 : angle 7.94424 ( 6) link_ALPHA1-3 : bond 0.01971 ( 2) link_ALPHA1-3 : angle 3.96387 ( 6) hydrogen bonds : bond 0.03624 ( 784) hydrogen bonds : angle 4.12905 ( 2300) SS BOND : bond 0.00976 ( 10) SS BOND : angle 1.87345 ( 20) covalent geometry : bond 0.00373 (14453) covalent geometry : angle 0.69813 (19625) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 287 time to evaluate : 2.229 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 80 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6964 (mtm180) REVERT: A 82 TRP cc_start: 0.7727 (OUTLIER) cc_final: 0.6957 (t-100) REVERT: A 177 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6753 (mm-30) REVERT: D 705 VAL cc_start: 0.7363 (OUTLIER) cc_final: 0.7080 (p) REVERT: E 269 PHE cc_start: 0.7699 (t80) cc_final: 0.7385 (t80) REVERT: B 54 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7552 (p) REVERT: B 82 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.6151 (t-100) REVERT: B 246 ARG cc_start: 0.7454 (tpt90) cc_final: 0.7057 (ttp80) REVERT: B 248 MET cc_start: 0.5940 (ttm) cc_final: 0.5192 (ttm) REVERT: B 249 TYR cc_start: 0.7767 (t80) cc_final: 0.7521 (t80) REVERT: B 252 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.5867 (mpp) REVERT: F 269 PHE cc_start: 0.7445 (t80) cc_final: 0.7141 (t80) outliers start: 59 outliers final: 36 residues processed: 322 average time/residue: 0.3535 time to fit residues: 164.7578 Evaluate side-chains 310 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 258 ASP Chi-restraints excluded: chain F residue 263 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 11 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 82 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN D 685 HIS ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN C 237 GLN C 685 HIS F 180 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.265317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.234166 restraints weight = 19409.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.233968 restraints weight = 24442.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.231430 restraints weight = 23369.099| |-----------------------------------------------------------------------------| r_work (final): 0.4555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4555 r_free = 0.4555 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4556 r_free = 0.4556 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 14483 Z= 0.227 Angle : 0.844 20.432 19705 Z= 0.387 Chirality : 0.047 0.281 2257 Planarity : 0.004 0.056 2474 Dihedral : 11.150 115.749 2395 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.90 % Favored : 95.82 % Rotamer: Outliers : 5.20 % Allowed : 27.84 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.20), residues: 1799 helix: 0.51 (0.16), residues: 1087 sheet: 0.17 (0.40), residues: 160 loop : -0.93 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 302 HIS 0.006 0.001 HIS A 195 PHE 0.017 0.002 PHE D 641 TYR 0.028 0.002 TYR D 282 ARG 0.004 0.001 ARG C 620 Details of bonding type rmsd link_NAG-ASN : bond 0.01506 ( 8) link_NAG-ASN : angle 9.24909 ( 24) link_ALPHA1-4 : bond 0.01046 ( 4) link_ALPHA1-4 : angle 3.65027 ( 12) link_ALPHA1-6 : bond 0.00851 ( 4) link_ALPHA1-6 : angle 2.60422 ( 12) link_BETA1-4 : bond 0.02090 ( 2) link_BETA1-4 : angle 7.41545 ( 6) link_ALPHA1-3 : bond 0.01839 ( 2) link_ALPHA1-3 : angle 3.92519 ( 6) hydrogen bonds : bond 0.03939 ( 784) hydrogen bonds : angle 4.29335 ( 2300) SS BOND : bond 0.00764 ( 10) SS BOND : angle 2.12414 ( 20) covalent geometry : bond 0.00529 (14453) covalent geometry : angle 0.75680 (19625) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 290 time to evaluate : 2.070 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 80 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6874 (mtm180) REVERT: D 239 ILE cc_start: 0.8073 (mm) cc_final: 0.7870 (mm) REVERT: D 675 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: E 269 PHE cc_start: 0.7460 (t80) cc_final: 0.7244 (t80) REVERT: B 54 VAL cc_start: 0.7888 (OUTLIER) cc_final: 0.7668 (p) REVERT: B 77 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8039 (tt) REVERT: B 82 TRP cc_start: 0.7929 (OUTLIER) cc_final: 0.6157 (t-100) REVERT: B 141 ILE cc_start: 0.7824 (tp) cc_final: 0.7485 (tp) REVERT: B 248 MET cc_start: 0.5941 (ttm) cc_final: 0.5170 (ttm) REVERT: B 252 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.5836 (mpp) REVERT: C 243 ARG cc_start: 0.6917 (tmm-80) cc_final: 0.6687 (ttp80) REVERT: C 324 HIS cc_start: 0.7026 (OUTLIER) cc_final: 0.6405 (m-70) REVERT: C 675 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: F 269 PHE cc_start: 0.7451 (t80) cc_final: 0.7188 (t80) REVERT: F 275 ARG cc_start: 0.6875 (mtt90) cc_final: 0.6577 (mtt90) outliers start: 69 outliers final: 43 residues processed: 343 average time/residue: 0.3582 time to fit residues: 176.0825 Evaluate side-chains 324 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 675 GLU Chi-restraints excluded: chain D residue 705 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 18 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 153 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 ASN D 577 GLN D 685 HIS ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN C 685 HIS ** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.245461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.220263 restraints weight = 19322.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.214066 restraints weight = 28529.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.211625 restraints weight = 30208.962| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14483 Z= 0.149 Angle : 0.818 19.958 19705 Z= 0.369 Chirality : 0.045 0.277 2257 Planarity : 0.004 0.080 2474 Dihedral : 10.720 111.148 2391 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.40 % Favored : 96.38 % Rotamer: Outliers : 4.97 % Allowed : 28.73 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1799 helix: 0.71 (0.16), residues: 1105 sheet: 0.24 (0.41), residues: 160 loop : -0.95 (0.29), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 121 HIS 0.008 0.001 HIS F 130 PHE 0.015 0.001 PHE D 690 TYR 0.016 0.001 TYR D 578 ARG 0.013 0.001 ARG B 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01571 ( 8) link_NAG-ASN : angle 9.07909 ( 24) link_ALPHA1-4 : bond 0.01057 ( 4) link_ALPHA1-4 : angle 3.45003 ( 12) link_ALPHA1-6 : bond 0.01080 ( 4) link_ALPHA1-6 : angle 2.53328 ( 12) link_BETA1-4 : bond 0.02246 ( 2) link_BETA1-4 : angle 7.26862 ( 6) link_ALPHA1-3 : bond 0.01811 ( 2) link_ALPHA1-3 : angle 3.85086 ( 6) hydrogen bonds : bond 0.03570 ( 784) hydrogen bonds : angle 4.08531 ( 2300) SS BOND : bond 0.01764 ( 10) SS BOND : angle 1.92784 ( 20) covalent geometry : bond 0.00334 (14453) covalent geometry : angle 0.73197 (19625) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 3.261 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 46 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7369 (mt) REVERT: A 54 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7780 (p) REVERT: A 80 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6762 (mtm180) REVERT: A 82 TRP cc_start: 0.7669 (OUTLIER) cc_final: 0.5702 (t-100) REVERT: A 234 MET cc_start: 0.7616 (mmt) cc_final: 0.7414 (mmt) REVERT: D 578 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.8134 (m-10) REVERT: D 675 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: E 269 PHE cc_start: 0.7623 (t80) cc_final: 0.7329 (t80) REVERT: B 54 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7651 (p) REVERT: B 82 TRP cc_start: 0.7779 (OUTLIER) cc_final: 0.6129 (t-100) REVERT: B 248 MET cc_start: 0.6030 (ttm) cc_final: 0.5269 (ttm) REVERT: B 252 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6033 (mpp) REVERT: C 324 HIS cc_start: 0.6997 (OUTLIER) cc_final: 0.6416 (m-70) REVERT: C 536 MET cc_start: 0.5107 (tmm) cc_final: 0.4310 (tmm) outliers start: 66 outliers final: 42 residues processed: 326 average time/residue: 0.4281 time to fit residues: 195.5024 Evaluate side-chains 317 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 265 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 675 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 263 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 93 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN D 685 HIS ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 HIS ** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.264634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.236606 restraints weight = 24693.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.230297 restraints weight = 30307.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.227968 restraints weight = 31702.187| |-----------------------------------------------------------------------------| r_work (final): 0.4470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4471 r_free = 0.4471 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4471 r_free = 0.4471 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14483 Z= 0.240 Angle : 0.870 19.560 19705 Z= 0.399 Chirality : 0.048 0.276 2257 Planarity : 0.005 0.058 2474 Dihedral : 10.969 116.105 2391 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.23 % Favored : 95.55 % Rotamer: Outliers : 5.79 % Allowed : 28.29 % Favored : 65.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1799 helix: 0.60 (0.16), residues: 1103 sheet: 0.24 (0.41), residues: 160 loop : -1.02 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP E 121 HIS 0.008 0.001 HIS F 130 PHE 0.028 0.002 PHE F 260 TYR 0.026 0.002 TYR D 578 ARG 0.009 0.001 ARG B 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01513 ( 8) link_NAG-ASN : angle 8.96688 ( 24) link_ALPHA1-4 : bond 0.00869 ( 4) link_ALPHA1-4 : angle 3.67739 ( 12) link_ALPHA1-6 : bond 0.00759 ( 4) link_ALPHA1-6 : angle 2.68098 ( 12) link_BETA1-4 : bond 0.02225 ( 2) link_BETA1-4 : angle 7.20349 ( 6) link_ALPHA1-3 : bond 0.01532 ( 2) link_ALPHA1-3 : angle 3.74737 ( 6) hydrogen bonds : bond 0.03904 ( 784) hydrogen bonds : angle 4.29348 ( 2300) SS BOND : bond 0.00760 ( 10) SS BOND : angle 1.94524 ( 20) covalent geometry : bond 0.00557 (14453) covalent geometry : angle 0.79031 (19625) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 275 time to evaluate : 1.817 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 46 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7906 (mm) REVERT: A 54 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7920 (p) REVERT: A 80 ARG cc_start: 0.7551 (OUTLIER) cc_final: 0.6907 (mtm180) REVERT: A 82 TRP cc_start: 0.7834 (OUTLIER) cc_final: 0.5860 (t-100) REVERT: A 96 ARG cc_start: 0.5768 (mmm160) cc_final: 0.5368 (tpp-160) REVERT: A 234 MET cc_start: 0.7658 (mmt) cc_final: 0.7415 (mmt) REVERT: D 675 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7513 (tt0) REVERT: B 54 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7815 (p) REVERT: B 82 TRP cc_start: 0.7829 (OUTLIER) cc_final: 0.6073 (t-100) REVERT: B 248 MET cc_start: 0.6294 (ttm) cc_final: 0.5552 (ttm) REVERT: B 249 TYR cc_start: 0.7779 (t80) cc_final: 0.7282 (t80) REVERT: B 252 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6239 (mpp) REVERT: C 675 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7509 (tt0) outliers start: 77 outliers final: 50 residues processed: 327 average time/residue: 0.3521 time to fit residues: 162.6185 Evaluate side-chains 329 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 270 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 675 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 109 optimal weight: 50.0000 chunk 146 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN D 685 HIS ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 HIS ** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.245201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.221230 restraints weight = 24587.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.213925 restraints weight = 27111.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.211422 restraints weight = 30480.856| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4276 r_free = 0.4276 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4275 r_free = 0.4275 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14483 Z= 0.150 Angle : 0.834 19.292 19705 Z= 0.379 Chirality : 0.045 0.272 2257 Planarity : 0.004 0.054 2474 Dihedral : 10.604 110.713 2391 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.45 % Favored : 96.33 % Rotamer: Outliers : 4.75 % Allowed : 28.51 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1799 helix: 0.82 (0.16), residues: 1103 sheet: 0.33 (0.42), residues: 154 loop : -0.96 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP E 121 HIS 0.016 0.001 HIS E 130 PHE 0.018 0.001 PHE D 690 TYR 0.025 0.001 TYR B 249 ARG 0.013 0.001 ARG B 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01543 ( 8) link_NAG-ASN : angle 8.81946 ( 24) link_ALPHA1-4 : bond 0.01161 ( 4) link_ALPHA1-4 : angle 3.48021 ( 12) link_ALPHA1-6 : bond 0.01194 ( 4) link_ALPHA1-6 : angle 2.59053 ( 12) link_BETA1-4 : bond 0.02298 ( 2) link_BETA1-4 : angle 7.06387 ( 6) link_ALPHA1-3 : bond 0.01783 ( 2) link_ALPHA1-3 : angle 3.86276 ( 6) hydrogen bonds : bond 0.03585 ( 784) hydrogen bonds : angle 4.12627 ( 2300) SS BOND : bond 0.00725 ( 10) SS BOND : angle 1.80247 ( 20) covalent geometry : bond 0.00341 (14453) covalent geometry : angle 0.75395 (19625) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 277 time to evaluate : 1.420 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 46 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7849 (mm) REVERT: A 54 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7753 (p) REVERT: A 80 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6696 (mtm180) REVERT: A 82 TRP cc_start: 0.7739 (OUTLIER) cc_final: 0.6021 (t-100) REVERT: A 96 ARG cc_start: 0.5712 (mmm160) cc_final: 0.5398 (tpp-160) REVERT: A 234 MET cc_start: 0.7413 (mmt) cc_final: 0.7170 (mmt) REVERT: D 578 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: B 54 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7607 (p) REVERT: B 82 TRP cc_start: 0.7739 (OUTLIER) cc_final: 0.6165 (t-100) REVERT: B 145 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6457 (mtp) REVERT: B 248 MET cc_start: 0.5708 (ttm) cc_final: 0.4982 (ttm) REVERT: B 249 TYR cc_start: 0.7432 (t80) cc_final: 0.7088 (t80) REVERT: B 252 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.5839 (mpp) outliers start: 63 outliers final: 45 residues processed: 318 average time/residue: 0.2798 time to fit residues: 125.8712 Evaluate side-chains 327 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 273 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 167 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 30.0000 chunk 157 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 168 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 577 GLN D 685 HIS E 221 HIS ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 HIS ** F 246 HIS ** 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 = 0.4822 r_free = 0.4822 target = 0.264354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.239572 restraints weight = 24294.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.232816 restraints weight = 27567.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.229350 restraints weight = 31438.395| |-----------------------------------------------------------------------------| r_work (final): 0.4541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4541 r_free = 0.4541 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4541 r_free = 0.4541 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14483 Z= 0.243 Angle : 0.889 18.788 19705 Z= 0.410 Chirality : 0.049 0.273 2257 Planarity : 0.005 0.053 2474 Dihedral : 10.913 117.721 2391 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.40 % Favored : 95.38 % Rotamer: Outliers : 4.68 % Allowed : 28.36 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.20), residues: 1799 helix: 0.55 (0.16), residues: 1115 sheet: 0.36 (0.41), residues: 164 loop : -1.19 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 302 HIS 0.016 0.001 HIS F 130 PHE 0.026 0.002 PHE F 260 TYR 0.029 0.002 TYR E 188 ARG 0.009 0.001 ARG B 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01460 ( 8) link_NAG-ASN : angle 8.73663 ( 24) link_ALPHA1-4 : bond 0.00826 ( 4) link_ALPHA1-4 : angle 3.80282 ( 12) link_ALPHA1-6 : bond 0.00640 ( 4) link_ALPHA1-6 : angle 2.61251 ( 12) link_BETA1-4 : bond 0.02244 ( 2) link_BETA1-4 : angle 7.03935 ( 6) link_ALPHA1-3 : bond 0.01674 ( 2) link_ALPHA1-3 : angle 3.78006 ( 6) hydrogen bonds : bond 0.04041 ( 784) hydrogen bonds : angle 4.41092 ( 2300) SS BOND : bond 0.00720 ( 10) SS BOND : angle 2.04288 ( 20) covalent geometry : bond 0.00570 (14453) covalent geometry : angle 0.81460 (19625) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3598 Ramachandran restraints generated. 1799 Oldfield, 0 Emsley, 1799 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 276 time to evaluate : 1.463 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 46 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7895 (mm) REVERT: A 54 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7810 (p) REVERT: A 80 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6728 (mtm180) REVERT: A 82 TRP cc_start: 0.7771 (OUTLIER) cc_final: 0.5970 (t-100) REVERT: A 96 ARG cc_start: 0.5696 (mmm160) cc_final: 0.5384 (tpp-160) REVERT: A 246 ARG cc_start: 0.6768 (ttp80) cc_final: 0.6561 (ttp80) REVERT: D 675 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: D 693 MET cc_start: 0.7945 (ptp) cc_final: 0.7666 (mtm) REVERT: B 54 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7709 (p) REVERT: B 82 TRP cc_start: 0.7795 (OUTLIER) cc_final: 0.6025 (t-100) REVERT: B 145 MET cc_start: 0.6748 (OUTLIER) cc_final: 0.6526 (mtp) REVERT: B 248 MET cc_start: 0.5882 (ttm) cc_final: 0.5134 (ttm) REVERT: B 252 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6008 (mpp) REVERT: C 536 MET cc_start: 0.5204 (tmm) cc_final: 0.4747 (tmm) REVERT: C 675 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7472 (tt0) outliers start: 62 outliers final: 44 residues processed: 317 average time/residue: 0.2916 time to fit residues: 129.8120 Evaluate side-chains 319 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 80 ARG Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 675 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 685 HIS ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.264125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.230979 restraints weight = 18829.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.226212 restraints weight = 25380.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.222104 restraints weight = 25546.436| |-----------------------------------------------------------------------------| r_work (final): 0.4473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4473 r_free = 0.4473 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4473 r_free = 0.4473 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.208 14483 Z= 0.288 Angle : 1.071 59.167 19705 Z= 0.556 Chirality : 0.048 0.273 2257 Planarity : 0.005 0.058 2474 Dihedral : 10.927 117.785 2391 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.29 % Favored : 95.49 % Rotamer: Outliers : 4.53 % Allowed : 28.88 % Favored : 66.59 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1799 helix: 0.59 (0.16), residues: 1111 sheet: 0.37 (0.41), residues: 164 loop : -1.23 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.005 TRP F 121 HIS 0.011 0.001 HIS F 130 PHE 0.017 0.002 PHE C 641 TYR 0.020 0.002 TYR E 188 ARG 0.024 0.001 ARG E 250 Details of bonding type rmsd link_NAG-ASN : bond 0.01521 ( 8) link_NAG-ASN : angle 8.82919 ( 24) link_ALPHA1-4 : bond 0.00815 ( 4) link_ALPHA1-4 : angle 3.79720 ( 12) link_ALPHA1-6 : bond 0.00494 ( 4) link_ALPHA1-6 : angle 2.59453 ( 12) link_BETA1-4 : bond 0.02250 ( 2) link_BETA1-4 : angle 7.04217 ( 6) link_ALPHA1-3 : bond 0.00971 ( 2) link_ALPHA1-3 : angle 4.01329 ( 6) hydrogen bonds : bond 0.03989 ( 784) hydrogen bonds : angle 4.39849 ( 2300) SS BOND : bond 0.00727 ( 10) SS BOND : angle 1.99745 ( 20) covalent geometry : bond 0.00620 (14453) covalent geometry : angle 1.00909 (19625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6201.74 seconds wall clock time: 115 minutes 33.88 seconds (6933.88 seconds total)