Starting phenix.real_space_refine on Thu Sep 18 04:19:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lwu_63459/09_2025/9lwu_63459.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lwu_63459/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9lwu_63459/09_2025/9lwu_63459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lwu_63459/09_2025/9lwu_63459.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lwu_63459/09_2025/9lwu_63459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lwu_63459/09_2025/9lwu_63459.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'TYR: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: {'GLU:plan': 2, 'TYR:plan': 7, 'GLN:plan1': 6, 'ASN:plan1': 4, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} 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: {'GLU:plan': 2, 'TYR:plan': 7, 'GLN:plan1': 6, 'ASN:plan1': 4, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} 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: {'ASP:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 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: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'TYR: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: {'GLU:plan': 2, 'TYR:plan': 7, 'GLN:plan1': 6, 'ASN:plan1': 4, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} 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: {'GLU:plan': 2, 'TYR:plan': 7, 'GLN:plan1': 6, 'ASN:plan1': 4, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} 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: {'ASP:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 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: 4.90, per 1000 atoms: 0.35 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: 1.33 Conformation dependent library (CDL) restraints added in 903.8 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.44 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: 2.29 Time building geometry restraints manager: 1.77 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 803)) selection = (chain 'D' and (resid 183 through 516 or resid 518 through 654 or resid 656 thro \ ugh 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: 1.120 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.250 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG B 246 TYR 0.046 0.002 TYR A 192 PHE 0.034 0.002 PHE B 230 TRP 0.023 0.002 TRP B 118 HIS 0.030 0.002 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00570 (14453) covalent geometry : angle 0.99490 (19625) SS BOND : bond 0.01469 ( 10) SS BOND : angle 2.64003 ( 20) hydrogen bonds : bond 0.27502 ( 784) hydrogen bonds : angle 8.57999 ( 2300) link_ALPHA1-3 : bond 0.01569 ( 2) link_ALPHA1-3 : angle 4.52268 ( 6) 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_NAG-ASN : bond 0.01432 ( 8) link_NAG-ASN : angle 10.37226 ( 24) *********************** 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 : 0.539 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: 0.6199 (tptm) REVERT: D 522 PHE cc_start: 0.7785 (m-80) cc_final: 0.7527 (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 74 LYS cc_start: 0.7845 (mmmt) cc_final: 0.7473 (ttpt) 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: 0.1475 time to fit residues: 91.7417 Evaluate side-chains 309 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 304 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 E 110 GLN E 147 HIS ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.267453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.236065 restraints weight = 19650.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.231760 restraints weight = 29170.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.229732 restraints weight = 26915.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.228019 restraints weight = 26916.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.227921 restraints weight = 23390.945| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4500 r_free = 0.4500 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4500 r_free = 0.4500 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14483 Z= 0.178 Angle : 0.858 14.705 19705 Z= 0.403 Chirality : 0.047 0.320 2257 Planarity : 0.005 0.066 2474 Dihedral : 12.433 110.789 2397 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.45 % Favored : 96.33 % Rotamer: Outliers : 4.45 % Allowed : 29.84 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.19), residues: 1799 helix: -0.65 (0.15), residues: 1097 sheet: -0.84 (0.37), residues: 166 loop : -1.23 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 80 TYR 0.024 0.002 TYR F 234 PHE 0.023 0.002 PHE F 269 TRP 0.014 0.001 TRP B 82 HIS 0.009 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00376 (14453) covalent geometry : angle 0.78154 (19625) SS BOND : bond 0.00618 ( 10) SS BOND : angle 1.43571 ( 20) hydrogen bonds : bond 0.05320 ( 784) hydrogen bonds : angle 4.99696 ( 2300) link_ALPHA1-3 : bond 0.02268 ( 2) link_ALPHA1-3 : angle 4.84219 ( 6) link_ALPHA1-4 : bond 0.01782 ( 4) link_ALPHA1-4 : angle 3.86691 ( 12) link_ALPHA1-6 : bond 0.00819 ( 4) link_ALPHA1-6 : angle 2.22588 ( 12) link_BETA1-4 : bond 0.02454 ( 2) link_BETA1-4 : angle 9.53987 ( 6) link_NAG-ASN : bond 0.02108 ( 8) link_NAG-ASN : angle 8.04817 ( 24) *********************** 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 376 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 317 time to evaluate : 0.548 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 77 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8084 (tp) REVERT: A 82 TRP cc_start: 0.7676 (OUTLIER) cc_final: 0.7096 (t-100) REVERT: A 121 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7105 (mm-30) REVERT: D 536 MET cc_start: 0.5068 (tmm) cc_final: 0.4527 (tmm) REVERT: B 53 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7356 (mm) REVERT: B 82 TRP cc_start: 0.8138 (OUTLIER) cc_final: 0.6231 (t-100) REVERT: B 246 ARG cc_start: 0.7730 (tpt170) cc_final: 0.7480 (tpt170) REVERT: C 536 MET cc_start: 0.5107 (tmm) cc_final: 0.4639 (tmm) REVERT: F 51 GLU cc_start: 0.6786 (pm20) cc_final: 0.6567 (pm20) REVERT: F 62 LYS cc_start: 0.4908 (mmmm) cc_final: 0.4568 (mmtm) REVERT: F 179 LYS cc_start: 0.8076 (ptmm) cc_final: 0.7846 (ptmm) REVERT: F 248 LYS cc_start: 0.6244 (tppt) cc_final: 0.6011 (tppt) REVERT: F 269 PHE cc_start: 0.7433 (t80) cc_final: 0.7041 (t80) outliers start: 59 outliers final: 26 residues processed: 355 average time/residue: 0.1362 time to fit residues: 68.8254 Evaluate side-chains 322 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU 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 117 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 E residue 216 HIS 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 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 72 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 133 optimal weight: 50.0000 chunk 167 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 158 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN D 653 HIS D 682 GLN D 685 HIS E 262 GLN E 276 GLN B 28 GLN B 171 GLN C 237 GLN C 653 HIS C 682 GLN C 685 HIS F 153 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.240683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.216903 restraints weight = 19232.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.210370 restraints weight = 28364.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.207799 restraints weight = 32053.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.207875 restraints weight = 29100.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.206603 restraints weight = 24107.303| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 14483 Z= 0.288 Angle : 0.939 22.212 19705 Z= 0.435 Chirality : 0.051 0.318 2257 Planarity : 0.005 0.061 2474 Dihedral : 12.353 116.436 2397 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.79 % Favored : 95.99 % Rotamer: Outliers : 6.09 % Allowed : 27.84 % Favored : 66.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.20), residues: 1799 helix: -0.22 (0.15), residues: 1083 sheet: -0.41 (0.36), residues: 168 loop : -0.98 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 250 TYR 0.040 0.002 TYR C 282 PHE 0.026 0.003 PHE D 641 TRP 0.014 0.003 TRP B 82 HIS 0.010 0.002 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00672 (14453) covalent geometry : angle 0.84370 (19625) SS BOND : bond 0.00431 ( 10) SS BOND : angle 1.95364 ( 20) hydrogen bonds : bond 0.04725 ( 784) hydrogen bonds : angle 4.84849 ( 2300) link_ALPHA1-3 : bond 0.01436 ( 2) link_ALPHA1-3 : angle 3.68477 ( 6) link_ALPHA1-4 : bond 0.01490 ( 4) link_ALPHA1-4 : angle 4.41829 ( 12) link_ALPHA1-6 : bond 0.00660 ( 4) link_ALPHA1-6 : angle 2.68278 ( 12) link_BETA1-4 : bond 0.02243 ( 2) link_BETA1-4 : angle 8.18880 ( 6) link_NAG-ASN : bond 0.01120 ( 8) link_NAG-ASN : angle 10.23766 ( 24) *********************** 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 387 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 306 time to evaluate : 0.583 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 77 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8075 (tt) REVERT: A 80 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6865 (mtm180) REVERT: A 82 TRP cc_start: 0.7992 (OUTLIER) cc_final: 0.7520 (t-100) REVERT: A 87 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7179 (mt-10) REVERT: A 177 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7001 (mm-30) REVERT: D 536 MET cc_start: 0.5062 (tmm) cc_final: 0.4545 (tmm) REVERT: D 675 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: D 685 HIS cc_start: 0.4167 (OUTLIER) cc_final: 0.3929 (m90) REVERT: E 280 GLN cc_start: 0.6549 (tt0) cc_final: 0.6325 (tt0) REVERT: B 54 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7792 (p) REVERT: B 82 TRP cc_start: 0.8113 (OUTLIER) cc_final: 0.5968 (t-100) REVERT: B 140 ARG cc_start: 0.5460 (ttp-170) cc_final: 0.5239 (ttp80) REVERT: C 675 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: F 74 LYS cc_start: 0.7468 (mmmt) cc_final: 0.7228 (ttpt) REVERT: F 269 PHE cc_start: 0.7445 (t80) cc_final: 0.7056 (t80) outliers start: 81 outliers final: 45 residues processed: 369 average time/residue: 0.1432 time to fit residues: 74.3557 Evaluate side-chains 326 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 273 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 77 LEU 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 142 VAL Chi-restraints excluded: chain A residue 148 LEU 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 255 PHE 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 575 VAL Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 675 GLU Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 40 SER 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 82 TRP Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 197 VAL 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 307 VAL 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 153 ASN Chi-restraints excluded: chain F residue 185 MET Chi-restraints excluded: chain F residue 199 CYS Chi-restraints excluded: chain F residue 202 LYS Chi-restraints excluded: chain F residue 208 SER Chi-restraints excluded: chain F residue 216 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 27 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 176 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 685 HIS B 171 GLN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.244679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.219714 restraints weight = 19250.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.213389 restraints weight = 26795.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.211769 restraints weight = 28221.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.211702 restraints weight = 27554.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.210257 restraints weight = 23922.735| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14483 Z= 0.147 Angle : 0.827 22.414 19705 Z= 0.374 Chirality : 0.045 0.293 2257 Planarity : 0.004 0.061 2474 Dihedral : 11.608 111.685 2397 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.17 % Favored : 96.60 % Rotamer: Outliers : 4.60 % Allowed : 28.95 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.20), residues: 1799 helix: 0.30 (0.16), residues: 1073 sheet: -0.45 (0.38), residues: 170 loop : -0.72 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 246 TYR 0.019 0.001 TYR C 523 PHE 0.023 0.001 PHE E 269 TRP 0.010 0.001 TRP B 82 HIS 0.012 0.001 HIS D 685 Details of bonding type rmsd covalent geometry : bond 0.00323 (14453) covalent geometry : angle 0.72376 (19625) SS BOND : bond 0.00996 ( 10) SS BOND : angle 1.98331 ( 20) hydrogen bonds : bond 0.03814 ( 784) hydrogen bonds : angle 4.33661 ( 2300) link_ALPHA1-3 : bond 0.02024 ( 2) link_ALPHA1-3 : angle 4.05905 ( 6) link_ALPHA1-4 : bond 0.01363 ( 4) link_ALPHA1-4 : angle 3.61130 ( 12) link_ALPHA1-6 : bond 0.01067 ( 4) link_ALPHA1-6 : angle 2.63807 ( 12) link_BETA1-4 : bond 0.02746 ( 2) link_BETA1-4 : angle 8.18185 ( 6) link_NAG-ASN : bond 0.01575 ( 8) link_NAG-ASN : angle 9.96976 ( 24) *********************** 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 334 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 273 time to evaluate : 0.578 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: 0.7397 (OUTLIER) cc_final: 0.6825 (mtm180) REVERT: A 82 TRP cc_start: 0.7879 (OUTLIER) cc_final: 0.7445 (t-100) REVERT: A 177 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7093 (mm-30) REVERT: E 269 PHE cc_start: 0.7793 (t80) cc_final: 0.7491 (t80) REVERT: B 28 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8050 (mm-40) REVERT: B 46 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7804 (mm) REVERT: B 82 TRP cc_start: 0.7667 (OUTLIER) cc_final: 0.5950 (t-100) REVERT: B 140 ARG cc_start: 0.5388 (ttp-170) cc_final: 0.5179 (ttp80) REVERT: C 248 LYS cc_start: 0.7703 (tppt) cc_final: 0.7260 (tptm) REVERT: C 536 MET cc_start: 0.5062 (tmm) cc_final: 0.4350 (tmm) outliers start: 61 outliers final: 40 residues processed: 311 average time/residue: 0.1507 time to fit residues: 65.1730 Evaluate side-chains 302 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 257 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 7 MET 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 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 283 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 340 ILE 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 191 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 46 LEU 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 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 533 THR 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 84 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 185 MET Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 216 HIS 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 161 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 685 HIS E 280 GLN B 171 GLN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.241978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.214776 restraints weight = 24399.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.210280 restraints weight = 30015.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.208856 restraints weight = 29540.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.209026 restraints weight = 27614.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.207357 restraints weight = 24142.100| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4239 r_free = 0.4239 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4239 r_free = 0.4239 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14483 Z= 0.213 Angle : 0.828 21.067 19705 Z= 0.379 Chirality : 0.046 0.270 2257 Planarity : 0.005 0.058 2474 Dihedral : 11.460 116.882 2397 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.12 % Favored : 95.66 % Rotamer: Outliers : 5.05 % Allowed : 28.80 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.20), residues: 1799 helix: 0.40 (0.16), residues: 1073 sheet: -0.01 (0.39), residues: 164 loop : -0.79 (0.29), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 80 TYR 0.020 0.002 TYR A 83 PHE 0.023 0.002 PHE F 260 TRP 0.012 0.002 TRP D 302 HIS 0.007 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00496 (14453) covalent geometry : angle 0.73429 (19625) SS BOND : bond 0.00947 ( 10) SS BOND : angle 2.06554 ( 20) hydrogen bonds : bond 0.03981 ( 784) hydrogen bonds : angle 4.36680 ( 2300) link_ALPHA1-3 : bond 0.01769 ( 2) link_ALPHA1-3 : angle 3.88715 ( 6) link_ALPHA1-4 : bond 0.01108 ( 4) link_ALPHA1-4 : angle 3.79082 ( 12) link_ALPHA1-6 : bond 0.00825 ( 4) link_ALPHA1-6 : angle 2.62227 ( 12) link_BETA1-4 : bond 0.02314 ( 2) link_BETA1-4 : angle 7.65802 ( 6) link_NAG-ASN : bond 0.01489 ( 8) link_NAG-ASN : angle 9.47637 ( 24) *********************** 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 343 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7817 (mm) REVERT: A 54 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7798 (p) REVERT: A 77 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8095 (tt) REVERT: A 80 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6843 (mtm180) REVERT: A 82 TRP cc_start: 0.7844 (OUTLIER) cc_final: 0.7352 (t-100) REVERT: D 243 ARG cc_start: 0.6930 (tmm-80) cc_final: 0.6724 (ttp80) REVERT: D 536 MET cc_start: 0.4970 (tmm) cc_final: 0.4624 (tmm) REVERT: E 269 PHE cc_start: 0.7619 (t80) cc_final: 0.7372 (t80) REVERT: B 54 VAL cc_start: 0.7979 (OUTLIER) cc_final: 0.7728 (p) REVERT: B 82 TRP cc_start: 0.7668 (OUTLIER) cc_final: 0.6055 (t-100) REVERT: B 248 MET cc_start: 0.6131 (ttm) cc_final: 0.5395 (ttm) REVERT: B 252 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.5979 (mpp) outliers start: 67 outliers final: 47 residues processed: 321 average time/residue: 0.1473 time to fit residues: 65.6616 Evaluate side-chains 322 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 267 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 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 77 LEU 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 199 LEU 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 295 MET Chi-restraints excluded: chain D residue 340 ILE 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 633 LEU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 236 VAL Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 40 SER 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 82 TRP Chi-restraints excluded: chain B residue 160 TYR 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 295 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 533 THR 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 185 MET Chi-restraints excluded: chain F residue 199 CYS Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 216 HIS 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 102 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 44 optimal weight: 50.0000 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 280 GLN ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 HIS F 180 ASN ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.264340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.233155 restraints weight = 19584.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.233077 restraints weight = 25350.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.229587 restraints weight = 23634.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.225666 restraints weight = 22862.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.225638 restraints weight = 21018.301| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4514 r_free = 0.4514 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4514 r_free = 0.4514 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14483 Z= 0.215 Angle : 0.826 20.290 19705 Z= 0.378 Chirality : 0.047 0.258 2257 Planarity : 0.004 0.056 2474 Dihedral : 11.325 116.705 2397 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.40 % Favored : 96.38 % Rotamer: Outliers : 5.86 % Allowed : 28.51 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.20), residues: 1799 helix: 0.46 (0.16), residues: 1093 sheet: 0.03 (0.39), residues: 164 loop : -0.85 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 80 TYR 0.019 0.002 TYR A 83 PHE 0.018 0.002 PHE D 641 TRP 0.012 0.002 TRP C 302 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00499 (14453) covalent geometry : angle 0.73520 (19625) SS BOND : bond 0.01062 ( 10) SS BOND : angle 2.09409 ( 20) hydrogen bonds : bond 0.03848 ( 784) hydrogen bonds : angle 4.31246 ( 2300) link_ALPHA1-3 : bond 0.01796 ( 2) link_ALPHA1-3 : angle 3.93783 ( 6) link_ALPHA1-4 : bond 0.01082 ( 4) link_ALPHA1-4 : angle 3.74152 ( 12) link_ALPHA1-6 : bond 0.00861 ( 4) link_ALPHA1-6 : angle 2.68464 ( 12) link_BETA1-4 : bond 0.02240 ( 2) link_BETA1-4 : angle 7.34850 ( 6) link_NAG-ASN : bond 0.01494 ( 8) link_NAG-ASN : angle 9.26799 ( 24) *********************** 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 356 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 278 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7813 (p) REVERT: A 77 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8107 (tt) REVERT: A 80 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6822 (mtm180) REVERT: A 82 TRP cc_start: 0.7829 (OUTLIER) cc_final: 0.7242 (t-100) REVERT: D 243 ARG cc_start: 0.6981 (tmm-80) cc_final: 0.6740 (ttp80) REVERT: D 675 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: E 269 PHE cc_start: 0.7752 (t80) cc_final: 0.7470 (t80) REVERT: B 28 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8081 (mm-40) REVERT: B 30 TYR cc_start: 0.8094 (t80) cc_final: 0.7711 (t80) REVERT: B 54 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7743 (p) REVERT: B 82 TRP cc_start: 0.7710 (OUTLIER) cc_final: 0.6026 (t-100) REVERT: B 96 ARG cc_start: 0.5882 (mmm160) cc_final: 0.5537 (mmt180) REVERT: B 246 ARG cc_start: 0.7591 (ttp80) cc_final: 0.7384 (ttp80) REVERT: B 248 MET cc_start: 0.6330 (ttm) cc_final: 0.5541 (ttm) REVERT: B 252 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6077 (mpp) REVERT: C 243 ARG cc_start: 0.6898 (tmm-80) cc_final: 0.6680 (ttp80) REVERT: C 248 LYS cc_start: 0.7572 (tppt) cc_final: 0.7144 (tptm) REVERT: C 675 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7474 (tt0) outliers start: 78 outliers final: 52 residues processed: 333 average time/residue: 0.1455 time to fit residues: 67.9189 Evaluate side-chains 326 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 264 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 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 160 TYR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 186 LEU 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 269 LEU Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 340 ILE 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 633 LEU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 675 GLU Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 199 CYS 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 B residue 28 GLN Chi-restraints excluded: chain B residue 40 SER 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 82 TRP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 160 TYR 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 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 533 THR Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 199 CYS 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 7 optimal weight: 1.9990 chunk 152 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN C 685 HIS ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.243578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.217942 restraints weight = 18616.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.211197 restraints weight = 27189.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.210089 restraints weight = 29412.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.210277 restraints weight = 29173.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.208929 restraints weight = 23403.283| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14483 Z= 0.159 Angle : 0.809 19.834 19705 Z= 0.365 Chirality : 0.045 0.258 2257 Planarity : 0.004 0.055 2474 Dihedral : 11.039 114.439 2397 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.51 % Favored : 96.27 % Rotamer: Outliers : 4.90 % Allowed : 29.70 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.20), residues: 1799 helix: 0.65 (0.16), residues: 1095 sheet: 0.04 (0.39), residues: 164 loop : -0.86 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 80 TYR 0.015 0.001 TYR C 523 PHE 0.027 0.002 PHE A 95 TRP 0.052 0.002 TRP E 121 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00364 (14453) covalent geometry : angle 0.72055 (19625) SS BOND : bond 0.00795 ( 10) SS BOND : angle 2.01087 ( 20) hydrogen bonds : bond 0.03573 ( 784) hydrogen bonds : angle 4.16270 ( 2300) link_ALPHA1-3 : bond 0.01846 ( 2) link_ALPHA1-3 : angle 3.92973 ( 6) link_ALPHA1-4 : bond 0.01043 ( 4) link_ALPHA1-4 : angle 3.57958 ( 12) link_ALPHA1-6 : bond 0.01008 ( 4) link_ALPHA1-6 : angle 2.61600 ( 12) link_BETA1-4 : bond 0.02192 ( 2) link_BETA1-4 : angle 7.20953 ( 6) link_NAG-ASN : bond 0.01542 ( 8) link_NAG-ASN : angle 9.07448 ( 24) *********************** 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 338 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 273 time to evaluate : 0.524 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 54 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7740 (p) REVERT: A 77 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8111 (tt) REVERT: A 80 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6718 (mtm180) REVERT: A 82 TRP cc_start: 0.7727 (OUTLIER) cc_final: 0.7134 (t-100) REVERT: A 234 MET cc_start: 0.7652 (mmt) cc_final: 0.7342 (mmt) REVERT: D 675 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: B 28 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.8043 (mm-40) REVERT: B 30 TYR cc_start: 0.7851 (t80) cc_final: 0.7456 (t80) REVERT: B 54 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7691 (p) REVERT: B 82 TRP cc_start: 0.7566 (OUTLIER) cc_final: 0.6063 (t-100) REVERT: B 246 ARG cc_start: 0.7427 (ttp80) cc_final: 0.7202 (ttp80) REVERT: B 248 MET cc_start: 0.6155 (ttm) cc_final: 0.5374 (ttm) REVERT: B 252 MET cc_start: 0.6932 (OUTLIER) cc_final: 0.5873 (mpp) REVERT: C 536 MET cc_start: 0.5156 (tmm) cc_final: 0.4628 (tmm) outliers start: 65 outliers final: 47 residues processed: 318 average time/residue: 0.1405 time to fit residues: 62.1592 Evaluate side-chains 313 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 257 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 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 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 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 269 LEU 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 633 LEU Chi-restraints excluded: chain D residue 673 MET 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 199 CYS 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 B residue 28 GLN Chi-restraints excluded: chain B residue 40 SER 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 98 ASP Chi-restraints excluded: chain B residue 160 TYR 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 C residue 250 THR Chi-restraints excluded: chain C residue 295 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 533 THR 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 84 VAL Chi-restraints excluded: chain F residue 199 CYS 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 263 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 136 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 124 optimal weight: 0.0770 chunk 33 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 685 HIS ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN C 685 HIS F 130 HIS F 180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.266889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.236475 restraints weight = 16965.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.236327 restraints weight = 25306.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.233816 restraints weight = 23061.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.229815 restraints weight = 21539.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.230835 restraints weight = 22909.194| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4545 r_free = 0.4545 target_work(ls_wunit_k1) = 0.230 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4545 r_free = 0.4545 target_work(ls_wunit_k1) = 0.230 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14483 Z= 0.165 Angle : 0.808 19.427 19705 Z= 0.366 Chirality : 0.046 0.258 2257 Planarity : 0.004 0.076 2474 Dihedral : 10.823 114.267 2393 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.56 % Favored : 96.21 % Rotamer: Outliers : 5.20 % Allowed : 29.40 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.20), residues: 1799 helix: 0.69 (0.16), residues: 1109 sheet: 0.11 (0.40), residues: 160 loop : -0.99 (0.29), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 140 TYR 0.014 0.001 TYR A 83 PHE 0.044 0.002 PHE F 260 TRP 0.071 0.003 TRP E 121 HIS 0.009 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00376 (14453) covalent geometry : angle 0.72346 (19625) SS BOND : bond 0.00735 ( 10) SS BOND : angle 1.91503 ( 20) hydrogen bonds : bond 0.03564 ( 784) hydrogen bonds : angle 4.14442 ( 2300) link_ALPHA1-3 : bond 0.01793 ( 2) link_ALPHA1-3 : angle 3.89302 ( 6) link_ALPHA1-4 : bond 0.00958 ( 4) link_ALPHA1-4 : angle 3.56167 ( 12) link_ALPHA1-6 : bond 0.00988 ( 4) link_ALPHA1-6 : angle 2.59178 ( 12) link_BETA1-4 : bond 0.02147 ( 2) link_BETA1-4 : angle 7.11305 ( 6) link_NAG-ASN : bond 0.01515 ( 8) link_NAG-ASN : angle 8.89975 ( 24) *********************** 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 334 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 265 time to evaluate : 0.526 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 54 VAL cc_start: 0.8050 (OUTLIER) cc_final: 0.7805 (p) REVERT: A 77 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8086 (tt) REVERT: A 82 TRP cc_start: 0.7739 (OUTLIER) cc_final: 0.7139 (t-100) REVERT: A 234 MET cc_start: 0.7690 (mmt) cc_final: 0.7359 (mmt) REVERT: D 243 ARG cc_start: 0.7302 (ttp80) cc_final: 0.6820 (tmm-80) REVERT: D 536 MET cc_start: 0.5085 (tmm) cc_final: 0.4362 (tmm) REVERT: D 675 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: B 30 TYR cc_start: 0.8046 (t80) cc_final: 0.7703 (t80) REVERT: B 54 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7756 (p) REVERT: B 82 TRP cc_start: 0.7626 (OUTLIER) cc_final: 0.6152 (t-100) REVERT: B 246 ARG cc_start: 0.7467 (ttp80) cc_final: 0.7237 (ttp80) REVERT: B 248 MET cc_start: 0.6362 (ttm) cc_final: 0.5561 (ttm) REVERT: B 252 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6147 (mpp) REVERT: C 243 ARG cc_start: 0.7078 (ttp80) cc_final: 0.6595 (tmm-80) REVERT: C 536 MET cc_start: 0.5231 (tmm) cc_final: 0.4735 (tmm) REVERT: C 675 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7485 (tt0) outliers start: 69 outliers final: 48 residues processed: 311 average time/residue: 0.1370 time to fit residues: 59.5342 Evaluate side-chains 313 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 257 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 LEU 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 160 TYR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 186 LEU 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 269 LEU 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 673 MET Chi-restraints excluded: chain D residue 675 GLU Chi-restraints excluded: chain D residue 685 HIS 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 191 VAL Chi-restraints excluded: chain E residue 199 CYS 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 B residue 19 VAL Chi-restraints excluded: chain B residue 40 SER 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 160 TYR 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 295 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 673 MET Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 199 CYS Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 215 CYS 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 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 64 optimal weight: 0.0060 chunk 19 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.268255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.235927 restraints weight = 17132.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.232897 restraints weight = 27084.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.230599 restraints weight = 23578.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.229578 restraints weight = 23250.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.229903 restraints weight = 20856.961| |-----------------------------------------------------------------------------| r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4537 r_free = 0.4537 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4537 r_free = 0.4537 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14483 Z= 0.143 Angle : 0.804 19.096 19705 Z= 0.362 Chirality : 0.046 0.278 2257 Planarity : 0.004 0.071 2474 Dihedral : 10.566 111.915 2393 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.17 % Favored : 96.60 % Rotamer: Outliers : 4.01 % Allowed : 30.66 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.20), residues: 1799 helix: 0.80 (0.16), residues: 1109 sheet: -0.16 (0.40), residues: 166 loop : -0.94 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 243 TYR 0.014 0.001 TYR C 523 PHE 0.078 0.002 PHE F 260 TRP 0.046 0.002 TRP E 121 HIS 0.012 0.001 HIS D 685 Details of bonding type rmsd covalent geometry : bond 0.00319 (14453) covalent geometry : angle 0.72118 (19625) SS BOND : bond 0.00730 ( 10) SS BOND : angle 1.91838 ( 20) hydrogen bonds : bond 0.03421 ( 784) hydrogen bonds : angle 4.06346 ( 2300) link_ALPHA1-3 : bond 0.01913 ( 2) link_ALPHA1-3 : angle 3.99542 ( 6) link_ALPHA1-4 : bond 0.01010 ( 4) link_ALPHA1-4 : angle 3.47111 ( 12) link_ALPHA1-6 : bond 0.01177 ( 4) link_ALPHA1-6 : angle 2.52301 ( 12) link_BETA1-4 : bond 0.02156 ( 2) link_BETA1-4 : angle 7.01292 ( 6) link_NAG-ASN : bond 0.01515 ( 8) link_NAG-ASN : angle 8.76723 ( 24) *********************** 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 314 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 261 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7791 (p) REVERT: A 77 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8039 (tt) REVERT: A 82 TRP cc_start: 0.7653 (OUTLIER) cc_final: 0.7129 (t-100) REVERT: A 234 MET cc_start: 0.7737 (mmt) cc_final: 0.7458 (mmt) REVERT: D 243 ARG cc_start: 0.7174 (ttp80) cc_final: 0.6698 (tmm-80) REVERT: D 536 MET cc_start: 0.5192 (tmm) cc_final: 0.4715 (pmm) REVERT: B 82 TRP cc_start: 0.7511 (OUTLIER) cc_final: 0.6060 (t-100) REVERT: B 96 ARG cc_start: 0.5834 (mmm160) cc_final: 0.5536 (mmt180) REVERT: B 246 ARG cc_start: 0.7512 (ttp80) cc_final: 0.7281 (ttp80) REVERT: B 248 MET cc_start: 0.6422 (ttm) cc_final: 0.5621 (ttm) REVERT: B 252 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6169 (mpp) REVERT: C 243 ARG cc_start: 0.6954 (ttp80) cc_final: 0.6479 (tmm-80) REVERT: C 248 LYS cc_start: 0.7520 (tppt) cc_final: 0.7141 (tptm) REVERT: C 536 MET cc_start: 0.5193 (tmm) cc_final: 0.4734 (tmm) REVERT: C 675 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: F 258 ASP cc_start: 0.6981 (p0) cc_final: 0.6610 (p0) outliers start: 53 outliers final: 39 residues processed: 300 average time/residue: 0.1424 time to fit residues: 60.1244 Evaluate side-chains 299 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 LEU 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 160 TYR Chi-restraints excluded: chain A residue 173 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 269 LEU 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 84 VAL Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 199 CYS 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 B residue 19 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 160 TYR 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 295 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 675 GLU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 199 CYS Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 168 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 173 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 49 optimal weight: 0.4980 chunk 146 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 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 685 HIS ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 HIS F 147 HIS F 257 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 = 0.4825 r_free = 0.4825 target = 0.268526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.229612 restraints weight = 17069.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 85)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.223427 restraints weight = 27153.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.218732 restraints weight = 25092.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.217212 restraints weight = 24999.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.217898 restraints weight = 21967.462| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4387 r_free = 0.4387 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4386 r_free = 0.4386 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14483 Z= 0.143 Angle : 0.805 18.731 19705 Z= 0.363 Chirality : 0.046 0.260 2257 Planarity : 0.004 0.054 2474 Dihedral : 10.339 111.707 2393 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.34 % Favored : 96.44 % Rotamer: Outliers : 4.53 % Allowed : 29.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.21), residues: 1799 helix: 0.91 (0.16), residues: 1109 sheet: -0.14 (0.40), residues: 166 loop : -0.94 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 243 TYR 0.013 0.001 TYR A 83 PHE 0.022 0.001 PHE A 95 TRP 0.032 0.002 TRP E 121 HIS 0.009 0.001 HIS E 130 Details of bonding type rmsd covalent geometry : bond 0.00322 (14453) covalent geometry : angle 0.72511 (19625) SS BOND : bond 0.00769 ( 10) SS BOND : angle 1.79938 ( 20) hydrogen bonds : bond 0.03394 ( 784) hydrogen bonds : angle 4.02495 ( 2300) link_ALPHA1-3 : bond 0.01909 ( 2) link_ALPHA1-3 : angle 3.93080 ( 6) link_ALPHA1-4 : bond 0.00961 ( 4) link_ALPHA1-4 : angle 3.45549 ( 12) link_ALPHA1-6 : bond 0.01205 ( 4) link_ALPHA1-6 : angle 2.48329 ( 12) link_BETA1-4 : bond 0.02168 ( 2) link_BETA1-4 : angle 6.91970 ( 6) link_NAG-ASN : bond 0.01486 ( 8) link_NAG-ASN : angle 8.62223 ( 24) ********************** 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 319 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 259 time to evaluate : 0.533 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 54 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7841 (p) REVERT: A 77 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 82 TRP cc_start: 0.7662 (OUTLIER) cc_final: 0.7167 (t-100) REVERT: A 182 MET cc_start: 0.7430 (mtp) cc_final: 0.7073 (mtp) REVERT: A 234 MET cc_start: 0.7913 (mmt) cc_final: 0.7678 (mmt) REVERT: D 243 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6520 (tmm-80) REVERT: D 536 MET cc_start: 0.5282 (tmm) cc_final: 0.4750 (pmm) REVERT: B 54 VAL cc_start: 0.8016 (OUTLIER) cc_final: 0.7787 (p) REVERT: B 82 TRP cc_start: 0.7479 (OUTLIER) cc_final: 0.6024 (t-100) REVERT: B 96 ARG cc_start: 0.6121 (mmm160) cc_final: 0.5628 (mmt180) REVERT: B 246 ARG cc_start: 0.7579 (ttp80) cc_final: 0.7348 (ttp80) REVERT: B 248 MET cc_start: 0.6850 (ttm) cc_final: 0.6088 (ttm) REVERT: B 252 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.6451 (mpp) REVERT: C 243 ARG cc_start: 0.6832 (ttp80) cc_final: 0.6444 (tmm-80) REVERT: C 248 LYS cc_start: 0.7558 (tppt) cc_final: 0.7048 (tptm) REVERT: C 536 MET cc_start: 0.5389 (tmm) cc_final: 0.4903 (tmm) REVERT: C 675 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: F 258 ASP cc_start: 0.7154 (p0) cc_final: 0.6542 (p0) REVERT: F 260 PHE cc_start: 0.6511 (m-80) cc_final: 0.5993 (m-80) outliers start: 60 outliers final: 44 residues processed: 303 average time/residue: 0.1238 time to fit residues: 53.6190 Evaluate side-chains 306 residues out of total 1555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 77 LEU 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 160 TYR Chi-restraints excluded: chain A residue 173 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 269 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 633 LEU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 685 HIS 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 199 CYS 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 B residue 6 VAL 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 160 TYR 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 295 MET Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 675 GLU 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 201 LEU Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 240 THR 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 150 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 157 optimal weight: 20.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 685 HIS ** E 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 HIS ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.267997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.237555 restraints weight = 16915.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.233369 restraints weight = 24133.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.230535 restraints weight = 23570.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.230534 restraints weight = 24243.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.229582 restraints weight = 20207.697| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4534 r_free = 0.4534 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4534 r_free = 0.4534 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14483 Z= 0.152 Angle : 0.818 18.474 19705 Z= 0.368 Chirality : 0.047 0.279 2257 Planarity : 0.004 0.054 2474 Dihedral : 10.271 112.127 2393 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.67 % Favored : 96.10 % Rotamer: Outliers : 4.31 % Allowed : 30.36 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.21), residues: 1799 helix: 0.92 (0.16), residues: 1109 sheet: -0.12 (0.40), residues: 166 loop : -0.92 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 243 TYR 0.015 0.001 TYR F 188 PHE 0.021 0.001 PHE A 95 TRP 0.026 0.002 TRP E 121 HIS 0.011 0.001 HIS D 685 Details of bonding type rmsd covalent geometry : bond 0.00345 (14453) covalent geometry : angle 0.74091 (19625) SS BOND : bond 0.00755 ( 10) SS BOND : angle 1.84468 ( 20) hydrogen bonds : bond 0.03420 ( 784) hydrogen bonds : angle 4.02814 ( 2300) link_ALPHA1-3 : bond 0.01888 ( 2) link_ALPHA1-3 : angle 3.90900 ( 6) link_ALPHA1-4 : bond 0.00936 ( 4) link_ALPHA1-4 : angle 3.48504 ( 12) link_ALPHA1-6 : bond 0.01167 ( 4) link_ALPHA1-6 : angle 2.48237 ( 12) link_BETA1-4 : bond 0.02187 ( 2) link_BETA1-4 : angle 6.90277 ( 6) link_NAG-ASN : bond 0.01470 ( 8) link_NAG-ASN : angle 8.54147 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2964.75 seconds wall clock time: 51 minutes 50.08 seconds (3110.08 seconds total)