Starting phenix.real_space_refine on Sat Oct 11 11:13:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kes_37166/10_2025/8kes_37166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kes_37166/10_2025/8kes_37166.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/8kes_37166/10_2025/8kes_37166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kes_37166/10_2025/8kes_37166.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kes_37166/10_2025/8kes_37166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kes_37166/10_2025/8kes_37166.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= 0.039 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 9187 2.51 5 N 2403 2.21 5 O 2616 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-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14290 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: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1934 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 19, 'TRANS': 231} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 11, 'GLN:plan1': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 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: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1934 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 19, 'TRANS': 231} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 11, 'GLN:plan1': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 68 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: 4.66, per 1000 atoms: 0.33 Number of scatterers: 14290 At special positions: 0 Unit cell: (113.42, 149.8, 143.38, 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 2616 8.00 N 2403 7.00 C 9187 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: 1.39 Conformation dependent library (CDL) restraints added in 860.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3482 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 9 sheets defined 62.7% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 1 through 26 removed outlier: 3.819A 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: 4.252A 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: 3.833A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 266 removed outlier: 3.656A 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: 3.576A pdb=" N GLN D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 190 " --> pdb=" O MET D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 215 removed outlier: 4.327A pdb=" N TYR D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 3.629A 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: 4.018A pdb=" N TYR D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 4.341A 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: 3.716A 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: 3.623A 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: 3.513A 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: 4.608A 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: 3.974A pdb=" N GLN D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 512 removed outlier: 3.747A 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: 3.622A 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: 3.550A pdb=" N GLU D 544 " --> pdb=" O HIS D 540 " (cutoff:3.500A) removed outlier: 3.722A 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: 3.571A pdb=" N ASN D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL D 549 " --> pdb=" O LEU D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 568 removed outlier: 3.618A pdb=" N THR D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) removed outlier: 3.660A 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: 3.584A 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: 3.985A pdb=" N LEU D 597 " --> pdb=" O ALA D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 624 removed outlier: 3.645A pdb=" N ALA D 621 " --> pdb=" O HIS D 617 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN D 624 " --> pdb=" O ARG D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 639 removed outlier: 3.636A 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: 3.500A 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: 3.731A 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: 3.869A pdb=" N PHE D 690 " --> pdb=" O LEU D 686 " (cutoff:3.500A) removed outlier: 3.535A 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: 3.500A pdb=" N PHE D 706 " --> pdb=" O GLN D 702 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 708 " --> pdb=" O PRO D 704 " (cutoff:3.500A) removed outlier: 3.718A 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 155 through 169 removed outlier: 3.631A pdb=" N LEU E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU E 160 " --> pdb=" O ALA E 156 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 246 removed outlier: 3.657A 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: 4.061A 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: 4.017A 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: 3.608A 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: 3.568A pdb=" N LEU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.555A 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: 3.949A 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: 3.600A pdb=" N VAL B 210 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.980A pdb=" N LYS B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 266 removed outlier: 3.721A 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: 4.197A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.581A pdb=" N GLN C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR C 189 " --> pdb=" O MET C 185 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 190 " --> pdb=" O MET C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 215 removed outlier: 4.327A 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: 3.541A 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: 4.343A 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: 3.764A pdb=" N LYS C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 268 removed outlier: 4.086A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.639A 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: 3.542A 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: 3.794A 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: 4.714A 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: 3.699A 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: 3.962A pdb=" N GLN C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 512 removed outlier: 3.747A 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: 3.618A 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: 3.672A 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: 3.646A 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: 3.598A pdb=" N ALA C 594 " --> pdb=" O GLN C 590 " (cutoff:3.500A) removed outlier: 3.980A 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: 3.539A pdb=" N GLN C 624 " --> pdb=" O ARG C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 639 removed outlier: 3.636A pdb=" N TYR C 636 " --> pdb=" O LYS C 632 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 656 removed outlier: 3.545A 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: 3.963A 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: 3.521A 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: 3.523A 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: 3.691A pdb=" N LYS C 711 " --> pdb=" O LEU C 707 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 111 removed outlier: 3.999A pdb=" N SER F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 169 removed outlier: 3.717A pdb=" N LEU F 159 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU F 160 " --> pdb=" O ALA F 156 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 167 " --> pdb=" O LYS F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 246 removed outlier: 3.723A pdb=" N SER F 245 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 285 removed outlier: 3.839A 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: 3.631A 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: 6.304A pdb=" N ARG E 44 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 7.542A 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: 7.528A 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: 7.731A pdb=" N GLU E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 3.705A 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: 6.301A pdb=" N ARG F 44 " --> pdb=" O ILE F 259 " (cutoff:3.500A) removed outlier: 7.391A 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: 3.976A pdb=" N PHE F 260 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.628A 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: 6.276A 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: 5.624A 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: 3.507A pdb=" N THR F 210 " --> pdb=" O TYR F 234 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.765A 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 199 799 hydrogen bonds defined for protein. 2345 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: 2.28 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: 4594 1.35 - 1.50: 4078 1.50 - 1.64: 5815 1.64 - 1.78: 19 1.78 - 1.93: 119 Bond restraints: 14625 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 2.01e+01 bond pdb=" CA ASN E 180 " pdb=" C ASN E 180 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.34e-02 5.57e+03 1.96e+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 1.73e+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 1.472 0.051 1.34e-02 5.57e+03 1.44e+01 ... (remaining 14620 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.31: 19761 5.31 - 10.61: 99 10.61 - 15.92: 8 15.92 - 21.23: 0 21.23 - 26.53: 1 Bond angle restraints: 19869 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 114.40 140.93 -26.53 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 119.87 112.92 6.95 1.04e+00 9.25e-01 4.46e+01 angle pdb=" N TRP A 82 " pdb=" CA TRP A 82 " pdb=" C TRP A 82 " ideal model delta sigma weight residual 111.14 104.97 6.17 1.08e+00 8.57e-01 3.27e+01 angle pdb=" C HIS B 238 " pdb=" CA HIS B 238 " pdb=" CB HIS B 238 " ideal model delta sigma weight residual 117.23 109.72 7.51 1.36e+00 5.41e-01 3.05e+01 angle pdb=" CA VAL E 84 " pdb=" CB VAL E 84 " pdb=" CG1 VAL E 84 " ideal model delta sigma weight residual 110.40 119.68 -9.28 1.70e+00 3.46e-01 2.98e+01 ... (remaining 19864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 7869 23.98 - 47.96: 841 47.96 - 71.94: 123 71.94 - 95.92: 27 95.92 - 119.89: 11 Dihedral angle restraints: 8871 sinusoidal: 3439 harmonic: 5432 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 27.32 65.68 1 1.00e+01 1.00e-02 5.65e+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 55.62 37.38 1 1.00e+01 1.00e-02 1.97e+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 56.44 36.56 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 8868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2113 0.095 - 0.191: 164 0.191 - 0.286: 9 0.286 - 0.382: 2 0.382 - 0.477: 3 Chirality restraints: 2291 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 5.69e+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 5.55e+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 3.69e+00 ... (remaining 2288 not shown) Planarity restraints: 2518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 272 " 0.029 2.00e-02 2.50e+03 6.00e-02 3.60e+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 2.97e-02 8.79e+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 2515 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 583 2.72 - 3.27: 14035 3.27 - 3.81: 22952 3.81 - 4.36: 27076 4.36 - 4.90: 44468 Nonbonded interactions: 109114 Sorted by model distance: nonbonded pdb=" OD2 ASP C 683 " pdb=" OG1 THR F 230 " model vdw 2.177 3.040 nonbonded pdb=" OD2 ASP D 683 " pdb=" OG1 THR E 230 " model vdw 2.180 3.040 nonbonded pdb=" OD1 ASP D 635 " pdb=" OH TYR D 654 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASP C 635 " pdb=" OH TYR C 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 109109 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: 1.080 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.450 Find NCS groups from input model: 0.200 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 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 : 0.005 0.118 14655 Z= 0.281 Angle : 1.077 26.535 19949 Z= 0.525 Chirality : 0.055 0.477 2291 Planarity : 0.007 0.072 2510 Dihedral : 19.523 119.894 5359 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.25 % Favored : 95.31 % Rotamer: Outliers : 1.86 % Allowed : 31.25 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.86 (0.17), residues: 1837 helix: -2.09 (0.13), residues: 1061 sheet: -1.06 (0.41), residues: 162 loop : -1.35 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 246 TYR 0.045 0.002 TYR A 192 PHE 0.034 0.002 PHE B 230 TRP 0.022 0.002 TRP B 118 HIS 0.030 0.002 HIS F 135 Details of bonding type rmsd covalent geometry : bond 0.00547 (14625) covalent geometry : angle 0.97402 (19869) SS BOND : bond 0.01443 ( 10) SS BOND : angle 2.64246 ( 20) hydrogen bonds : bond 0.27642 ( 799) hydrogen bonds : angle 8.48264 ( 2345) link_ALPHA1-3 : bond 0.01603 ( 2) link_ALPHA1-3 : angle 4.55252 ( 6) link_ALPHA1-4 : bond 0.00998 ( 4) link_ALPHA1-4 : angle 4.85026 ( 12) link_ALPHA1-6 : bond 0.00480 ( 4) link_ALPHA1-6 : angle 1.90680 ( 12) link_BETA1-4 : bond 0.02739 ( 2) link_BETA1-4 : angle 13.59931 ( 6) link_NAG-ASN : bond 0.01446 ( 8) link_NAG-ASN : angle 10.36206 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 500 time to evaluate : 0.554 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 82 TRP cc_start: 0.7811 (OUTLIER) cc_final: 0.6126 (t-100) REVERT: A 102 ARG cc_start: 0.6607 (tpt170) cc_final: 0.5494 (ptp-170) REVERT: D 700 ASP cc_start: 0.6638 (m-30) cc_final: 0.6348 (m-30) REVERT: E 154 MET cc_start: 0.2104 (mmm) cc_final: 0.1570 (mmm) REVERT: E 181 ILE cc_start: 0.7200 (mm) cc_final: 0.6293 (mm) REVERT: E 185 MET cc_start: 0.6975 (mmm) cc_final: 0.6707 (mmm) REVERT: E 272 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5243 (mp) REVERT: E 282 GLU cc_start: 0.5760 (OUTLIER) cc_final: 0.5522 (tp30) REVERT: B 46 LEU cc_start: 0.7082 (mt) cc_final: 0.6682 (mp) REVERT: B 70 ARG cc_start: 0.4569 (ptp-110) cc_final: 0.4299 (ttm110) REVERT: B 163 ILE cc_start: 0.7679 (tp) cc_final: 0.7473 (tt) REVERT: B 242 LEU cc_start: 0.6488 (mp) cc_final: 0.6280 (mm) REVERT: C 297 LEU cc_start: 0.5781 (mt) cc_final: 0.5571 (mt) REVERT: F 247 PRO cc_start: 0.2878 (Cg_exo) cc_final: 0.2197 (Cg_endo) outliers start: 24 outliers final: 3 residues processed: 507 average time/residue: 0.1423 time to fit residues: 100.2399 Evaluate side-chains 326 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 320 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 284 LEU Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 82 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0980 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 0.5980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 ASN D 624 GLN E 110 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 GLN B 158 HIS C 540 HIS C 577 GLN ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN F 135 HIS ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.260251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.232304 restraints weight = 23233.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.226982 restraints weight = 26233.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.222243 restraints weight = 25683.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.222301 restraints weight = 27960.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.221316 restraints weight = 19021.761| |-----------------------------------------------------------------------------| r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4551 r_free = 0.4551 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4550 r_free = 0.4550 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14655 Z= 0.168 Angle : 0.884 18.173 19949 Z= 0.417 Chirality : 0.049 0.333 2291 Planarity : 0.005 0.064 2510 Dihedral : 12.445 110.814 2440 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.49 % Favored : 96.29 % Rotamer: Outliers : 5.12 % Allowed : 27.10 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.34 (0.19), residues: 1837 helix: -0.61 (0.15), residues: 1121 sheet: -0.89 (0.38), residues: 166 loop : -1.12 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 319 TYR 0.021 0.002 TYR C 265 PHE 0.036 0.002 PHE F 108 TRP 0.009 0.002 TRP C 302 HIS 0.007 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00350 (14625) covalent geometry : angle 0.80804 (19869) SS BOND : bond 0.00632 ( 10) SS BOND : angle 1.83092 ( 20) hydrogen bonds : bond 0.05447 ( 799) hydrogen bonds : angle 5.05037 ( 2345) link_ALPHA1-3 : bond 0.01394 ( 2) link_ALPHA1-3 : angle 4.75082 ( 6) link_ALPHA1-4 : bond 0.01618 ( 4) link_ALPHA1-4 : angle 3.94793 ( 12) link_ALPHA1-6 : bond 0.00895 ( 4) link_ALPHA1-6 : angle 2.13248 ( 12) link_BETA1-4 : bond 0.02515 ( 2) link_BETA1-4 : angle 9.50853 ( 6) link_NAG-ASN : bond 0.01214 ( 8) link_NAG-ASN : angle 8.22484 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 359 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7581 (mmm) REVERT: A 82 TRP cc_start: 0.7284 (OUTLIER) cc_final: 0.5609 (t-100) REVERT: A 102 ARG cc_start: 0.6670 (tpt170) cc_final: 0.5578 (ptp-170) REVERT: A 231 MET cc_start: 0.5895 (mmm) cc_final: 0.5694 (mmm) REVERT: D 577 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6815 (mp10) REVERT: E 154 MET cc_start: 0.2323 (mmm) cc_final: 0.2097 (mmm) REVERT: B 12 LEU cc_start: 0.8524 (tp) cc_final: 0.8048 (mt) REVERT: B 38 LYS cc_start: 0.8077 (mtmm) cc_final: 0.7763 (mttp) REVERT: B 48 ILE cc_start: 0.8661 (mm) cc_final: 0.8433 (mt) REVERT: B 145 MET cc_start: 0.5363 (mtp) cc_final: 0.5163 (mtp) REVERT: B 163 ILE cc_start: 0.7489 (tp) cc_final: 0.7234 (tt) REVERT: C 297 LEU cc_start: 0.6490 (mt) cc_final: 0.6182 (mt) REVERT: F 223 ILE cc_start: 0.3106 (OUTLIER) cc_final: 0.2867 (tt) outliers start: 68 outliers final: 24 residues processed: 403 average time/residue: 0.1221 time to fit residues: 71.5015 Evaluate side-chains 338 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 310 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 223 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 64 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 138 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 129 optimal weight: 0.0870 chunk 172 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 161 HIS ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 HIS E 276 GLN B 158 HIS C 240 GLN ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 599 GLN F 153 ASN F 180 ASN F 184 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.255424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.218243 restraints weight = 22871.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.216135 restraints weight = 34850.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.213085 restraints weight = 24224.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.213684 restraints weight = 21660.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.213769 restraints weight = 15988.432| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4485 r_free = 0.4485 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4485 r_free = 0.4485 target_work(ls_wunit_k1) = 0.213 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 14655 Z= 0.181 Angle : 0.842 17.734 19949 Z= 0.390 Chirality : 0.049 0.433 2291 Planarity : 0.005 0.058 2510 Dihedral : 11.316 111.518 2433 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.38 % Favored : 96.40 % Rotamer: Outliers : 4.90 % Allowed : 28.36 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.70 (0.19), residues: 1837 helix: 0.03 (0.15), residues: 1117 sheet: -0.52 (0.38), residues: 156 loop : -1.22 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 253 TYR 0.025 0.002 TYR A 160 PHE 0.028 0.002 PHE E 269 TRP 0.011 0.002 TRP B 82 HIS 0.010 0.001 HIS C 518 Details of bonding type rmsd covalent geometry : bond 0.00395 (14625) covalent geometry : angle 0.75468 (19869) SS BOND : bond 0.01120 ( 10) SS BOND : angle 1.47005 ( 20) hydrogen bonds : bond 0.04559 ( 799) hydrogen bonds : angle 4.61773 ( 2345) link_ALPHA1-3 : bond 0.01912 ( 2) link_ALPHA1-3 : angle 3.67472 ( 6) link_ALPHA1-4 : bond 0.01734 ( 4) link_ALPHA1-4 : angle 3.96796 ( 12) link_ALPHA1-6 : bond 0.01015 ( 4) link_ALPHA1-6 : angle 2.43404 ( 12) link_BETA1-4 : bond 0.02521 ( 2) link_BETA1-4 : angle 9.22051 ( 6) link_NAG-ASN : bond 0.01671 ( 8) link_NAG-ASN : angle 8.97280 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 345 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6355 (ttp) cc_final: 0.6032 (ttp) REVERT: A 43 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7438 (mmm) REVERT: A 82 TRP cc_start: 0.7352 (OUTLIER) cc_final: 0.5510 (t-100) REVERT: D 220 LYS cc_start: 0.7180 (tmtt) cc_final: 0.6839 (tmmt) REVERT: D 537 ARG cc_start: 0.5757 (ptm-80) cc_final: 0.5366 (ptt180) REVERT: D 577 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: D 655 ARG cc_start: 0.7499 (ptt-90) cc_final: 0.7294 (ptt90) REVERT: D 711 LYS cc_start: 0.7990 (tttp) cc_final: 0.7549 (ttmm) REVERT: E 154 MET cc_start: 0.2424 (mmm) cc_final: 0.2218 (mmm) REVERT: E 193 MET cc_start: 0.6341 (ptp) cc_final: 0.6074 (ptp) REVERT: E 279 GLN cc_start: 0.7335 (tm-30) cc_final: 0.6907 (tm-30) REVERT: B 96 ARG cc_start: 0.5643 (mmm160) cc_final: 0.5322 (mmm160) REVERT: B 163 ILE cc_start: 0.7400 (tp) cc_final: 0.7197 (tt) REVERT: C 295 MET cc_start: 0.6592 (tpp) cc_final: 0.6251 (tpt) REVERT: C 315 LEU cc_start: 0.6905 (mm) cc_final: 0.6652 (mm) REVERT: C 528 MET cc_start: 0.6629 (ttt) cc_final: 0.6229 (ttm) REVERT: C 638 PHE cc_start: 0.4518 (t80) cc_final: 0.4093 (t80) REVERT: F 116 ARG cc_start: 0.4380 (ttt-90) cc_final: 0.3830 (ttt-90) outliers start: 65 outliers final: 34 residues processed: 382 average time/residue: 0.1244 time to fit residues: 68.3705 Evaluate side-chains 354 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 317 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain H residue 350 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 1 optimal weight: 0.9990 chunk 117 optimal weight: 0.2980 chunk 120 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 158 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 151 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 GLN B 158 HIS ** C 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 HIS F 135 HIS F 180 ASN F 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.256304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.224908 restraints weight = 20656.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.220431 restraints weight = 29985.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.216094 restraints weight = 26274.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.216475 restraints weight = 25654.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.214894 restraints weight = 20263.643| |-----------------------------------------------------------------------------| r_work (final): 0.4494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4492 r_free = 0.4492 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4492 r_free = 0.4492 target_work(ls_wunit_k1) = 0.214 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14655 Z= 0.143 Angle : 0.785 16.564 19949 Z= 0.362 Chirality : 0.046 0.389 2291 Planarity : 0.005 0.069 2510 Dihedral : 10.908 111.407 2433 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.11 % Favored : 96.67 % Rotamer: Outliers : 4.23 % Allowed : 30.36 % 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: -0.29 (0.20), residues: 1837 helix: 0.48 (0.16), residues: 1115 sheet: -0.46 (0.40), residues: 142 loop : -1.28 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 70 TYR 0.018 0.001 TYR A 160 PHE 0.019 0.002 PHE B 218 TRP 0.019 0.001 TRP E 121 HIS 0.008 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00304 (14625) covalent geometry : angle 0.70482 (19869) SS BOND : bond 0.00316 ( 10) SS BOND : angle 1.41540 ( 20) hydrogen bonds : bond 0.03919 ( 799) hydrogen bonds : angle 4.35436 ( 2345) link_ALPHA1-3 : bond 0.01866 ( 2) link_ALPHA1-3 : angle 3.54518 ( 6) link_ALPHA1-4 : bond 0.01467 ( 4) link_ALPHA1-4 : angle 3.52724 ( 12) link_ALPHA1-6 : bond 0.01161 ( 4) link_ALPHA1-6 : angle 2.43939 ( 12) link_BETA1-4 : bond 0.02231 ( 2) link_BETA1-4 : angle 9.15030 ( 6) link_NAG-ASN : bond 0.01466 ( 8) link_NAG-ASN : angle 8.15787 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 336 time to evaluate : 0.408 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 7 MET cc_start: 0.6325 (ttp) cc_final: 0.6015 (ttp) REVERT: A 43 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7428 (mmm) REVERT: A 82 TRP cc_start: 0.6942 (OUTLIER) cc_final: 0.5292 (t-100) REVERT: A 96 ARG cc_start: 0.6125 (tpp-160) cc_final: 0.5730 (ttm110) REVERT: A 234 MET cc_start: 0.7206 (mmt) cc_final: 0.6933 (mmt) REVERT: A 246 ARG cc_start: 0.7619 (tmt-80) cc_final: 0.7383 (tmt170) REVERT: A 249 TYR cc_start: 0.7772 (t80) cc_final: 0.7527 (t80) REVERT: A 256 LYS cc_start: 0.6714 (mttm) cc_final: 0.6320 (mttm) REVERT: D 577 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6832 (mt0) REVERT: D 655 ARG cc_start: 0.7498 (ptt-90) cc_final: 0.7284 (ptt90) REVERT: E 129 LYS cc_start: 0.7239 (mmmt) cc_final: 0.6972 (mmtm) REVERT: E 193 MET cc_start: 0.6348 (ptp) cc_final: 0.6043 (ptp) REVERT: B 163 ILE cc_start: 0.7343 (tp) cc_final: 0.7139 (tt) REVERT: B 254 GLN cc_start: 0.6568 (mm110) cc_final: 0.6334 (mm110) REVERT: C 295 MET cc_start: 0.6741 (tpp) cc_final: 0.6291 (tpt) REVERT: C 528 MET cc_start: 0.6713 (ttt) cc_final: 0.6306 (ttm) REVERT: C 638 PHE cc_start: 0.4351 (t80) cc_final: 0.4042 (t80) REVERT: F 84 VAL cc_start: 0.2717 (OUTLIER) cc_final: 0.2438 (m) outliers start: 56 outliers final: 35 residues processed: 367 average time/residue: 0.1342 time to fit residues: 70.0053 Evaluate side-chains 341 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 302 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 150 TYR Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain H residue 350 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 13 optimal weight: 6.9990 chunk 163 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 40.0000 chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 276 GLN B 158 HIS C 527 GLN C 661 GLN C 719 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.253316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.215644 restraints weight = 20392.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.213228 restraints weight = 33325.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.208275 restraints weight = 26191.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.208775 restraints weight = 24875.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.209086 restraints weight = 17319.906| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4439 r_free = 0.4439 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4439 r_free = 0.4439 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14655 Z= 0.175 Angle : 0.802 15.783 19949 Z= 0.370 Chirality : 0.047 0.384 2291 Planarity : 0.005 0.055 2510 Dihedral : 10.720 112.731 2433 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.22 % Favored : 96.56 % Rotamer: Outliers : 5.05 % Allowed : 30.36 % Favored : 64.59 % 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: -0.08 (0.20), residues: 1837 helix: 0.64 (0.16), residues: 1115 sheet: -0.39 (0.41), residues: 142 loop : -1.19 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 250 TYR 0.018 0.002 TYR A 160 PHE 0.028 0.002 PHE E 269 TRP 0.030 0.002 TRP E 121 HIS 0.009 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00391 (14625) covalent geometry : angle 0.72858 (19869) SS BOND : bond 0.00522 ( 10) SS BOND : angle 1.98987 ( 20) hydrogen bonds : bond 0.03898 ( 799) hydrogen bonds : angle 4.33574 ( 2345) link_ALPHA1-3 : bond 0.01727 ( 2) link_ALPHA1-3 : angle 3.65395 ( 6) link_ALPHA1-4 : bond 0.01378 ( 4) link_ALPHA1-4 : angle 3.45627 ( 12) link_ALPHA1-6 : bond 0.01107 ( 4) link_ALPHA1-6 : angle 2.47484 ( 12) link_BETA1-4 : bond 0.02163 ( 2) link_BETA1-4 : angle 8.78002 ( 6) link_NAG-ASN : bond 0.01371 ( 8) link_NAG-ASN : angle 7.76059 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 327 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6327 (ttp) cc_final: 0.6010 (ttp) REVERT: A 43 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7459 (mmm) REVERT: A 82 TRP cc_start: 0.7239 (OUTLIER) cc_final: 0.5342 (t-100) REVERT: A 96 ARG cc_start: 0.6345 (tpp-160) cc_final: 0.5999 (ttm170) REVERT: A 234 MET cc_start: 0.7339 (mmt) cc_final: 0.7095 (mmt) REVERT: A 246 ARG cc_start: 0.7832 (tmt-80) cc_final: 0.7508 (tmt170) REVERT: A 256 LYS cc_start: 0.6775 (mttm) cc_final: 0.6368 (mttm) REVERT: D 220 LYS cc_start: 0.7390 (tmtt) cc_final: 0.7050 (tmmt) REVERT: D 577 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: D 655 ARG cc_start: 0.7663 (ptt-90) cc_final: 0.7443 (ptt90) REVERT: B 96 ARG cc_start: 0.6037 (mmm160) cc_final: 0.5273 (mmm160) REVERT: C 245 MET cc_start: 0.2452 (ppp) cc_final: 0.2156 (ppp) REVERT: C 295 MET cc_start: 0.6981 (tpp) cc_final: 0.6493 (tpt) REVERT: C 528 MET cc_start: 0.6802 (ttt) cc_final: 0.6391 (ttm) outliers start: 67 outliers final: 46 residues processed: 365 average time/residue: 0.1274 time to fit residues: 66.4137 Evaluate side-chains 350 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 76 HIS Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 89 CYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain H residue 350 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 127 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 162 optimal weight: 30.0000 chunk 113 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 126 optimal weight: 0.0010 chunk 8 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN E 130 HIS E 262 GLN B 158 HIS F 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.254273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.219869 restraints weight = 28936.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.216754 restraints weight = 34779.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.211894 restraints weight = 27253.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.212650 restraints weight = 23562.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.212870 restraints weight = 16864.844| |-----------------------------------------------------------------------------| r_work (final): 0.4476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4475 r_free = 0.4475 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4475 r_free = 0.4475 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14655 Z= 0.140 Angle : 0.774 15.626 19949 Z= 0.357 Chirality : 0.046 0.362 2291 Planarity : 0.004 0.077 2510 Dihedral : 10.371 110.184 2433 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.27 % Favored : 96.51 % Rotamer: Outliers : 4.38 % Allowed : 31.48 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.20), residues: 1837 helix: 0.83 (0.16), residues: 1117 sheet: -0.71 (0.40), residues: 146 loop : -1.15 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 275 TYR 0.018 0.001 TYR C 523 PHE 0.018 0.001 PHE B 218 TRP 0.036 0.002 TRP E 121 HIS 0.008 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00306 (14625) covalent geometry : angle 0.70225 (19869) SS BOND : bond 0.00645 ( 10) SS BOND : angle 2.08722 ( 20) hydrogen bonds : bond 0.03560 ( 799) hydrogen bonds : angle 4.19553 ( 2345) link_ALPHA1-3 : bond 0.01824 ( 2) link_ALPHA1-3 : angle 3.67490 ( 6) link_ALPHA1-4 : bond 0.01310 ( 4) link_ALPHA1-4 : angle 3.28790 ( 12) link_ALPHA1-6 : bond 0.01288 ( 4) link_ALPHA1-6 : angle 2.39623 ( 12) link_BETA1-4 : bond 0.02116 ( 2) link_BETA1-4 : angle 8.48458 ( 6) link_NAG-ASN : bond 0.01372 ( 8) link_NAG-ASN : angle 7.50299 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 321 time to evaluate : 0.543 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 7 MET cc_start: 0.6249 (ttp) cc_final: 0.5968 (ttp) REVERT: A 43 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7459 (mmm) REVERT: A 82 TRP cc_start: 0.7353 (OUTLIER) cc_final: 0.5400 (t-100) REVERT: A 96 ARG cc_start: 0.6411 (tpp-160) cc_final: 0.6147 (ttm170) REVERT: A 246 ARG cc_start: 0.7806 (tmt-80) cc_final: 0.7504 (tmt170) REVERT: A 256 LYS cc_start: 0.6756 (mttm) cc_final: 0.6350 (mttm) REVERT: D 220 LYS cc_start: 0.7227 (tmtt) cc_final: 0.6903 (tmmt) REVERT: D 328 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7221 (t70) REVERT: D 577 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: B 96 ARG cc_start: 0.5890 (mmm160) cc_final: 0.5298 (mmm160) REVERT: B 196 SER cc_start: 0.7013 (m) cc_final: 0.6572 (t) REVERT: C 295 MET cc_start: 0.7089 (tpp) cc_final: 0.6632 (tpt) REVERT: C 528 MET cc_start: 0.6699 (ttt) cc_final: 0.6238 (ttm) outliers start: 58 outliers final: 41 residues processed: 356 average time/residue: 0.1311 time to fit residues: 66.6923 Evaluate side-chains 343 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 298 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 76 HIS Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 32 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain H residue 350 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 17 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 71 optimal weight: 0.0050 chunk 176 optimal weight: 7.9990 chunk 153 optimal weight: 0.0970 chunk 27 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 GLN C 685 HIS F 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.253533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.220120 restraints weight = 29367.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.215867 restraints weight = 32155.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.209018 restraints weight = 28057.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.209630 restraints weight = 26414.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.208719 restraints weight = 18172.434| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4433 r_free = 0.4433 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4433 r_free = 0.4433 target_work(ls_wunit_k1) = 0.207 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14655 Z= 0.143 Angle : 0.777 17.453 19949 Z= 0.355 Chirality : 0.045 0.358 2291 Planarity : 0.004 0.079 2510 Dihedral : 10.195 110.539 2433 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.22 % Favored : 96.56 % Rotamer: Outliers : 4.45 % Allowed : 31.77 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.20), residues: 1837 helix: 0.93 (0.16), residues: 1119 sheet: -0.47 (0.42), residues: 140 loop : -1.17 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 224 TYR 0.017 0.001 TYR A 160 PHE 0.028 0.002 PHE E 269 TRP 0.021 0.001 TRP E 121 HIS 0.010 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00313 (14625) covalent geometry : angle 0.70672 (19869) SS BOND : bond 0.00858 ( 10) SS BOND : angle 1.65314 ( 20) hydrogen bonds : bond 0.03501 ( 799) hydrogen bonds : angle 4.11929 ( 2345) link_ALPHA1-3 : bond 0.01830 ( 2) link_ALPHA1-3 : angle 3.74024 ( 6) link_ALPHA1-4 : bond 0.01268 ( 4) link_ALPHA1-4 : angle 3.35189 ( 12) link_ALPHA1-6 : bond 0.01326 ( 4) link_ALPHA1-6 : angle 2.33139 ( 12) link_BETA1-4 : bond 0.02097 ( 2) link_BETA1-4 : angle 8.31825 ( 6) link_NAG-ASN : bond 0.01354 ( 8) link_NAG-ASN : angle 7.55654 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 304 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6255 (ttp) cc_final: 0.5990 (ttp) REVERT: A 43 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7449 (mmm) REVERT: A 82 TRP cc_start: 0.7300 (OUTLIER) cc_final: 0.5322 (t-100) REVERT: A 121 GLU cc_start: 0.7285 (tt0) cc_final: 0.7075 (mt-10) REVERT: A 246 ARG cc_start: 0.7836 (tmt-80) cc_final: 0.7560 (tmt170) REVERT: A 256 LYS cc_start: 0.6648 (mttm) cc_final: 0.6218 (mttm) REVERT: D 220 LYS cc_start: 0.7238 (tmtt) cc_final: 0.6920 (tmmt) REVERT: D 577 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6941 (mp10) REVERT: B 76 HIS cc_start: 0.7202 (t-90) cc_final: 0.6785 (t-90) REVERT: B 80 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.5777 (mtt90) REVERT: B 96 ARG cc_start: 0.5884 (mmm160) cc_final: 0.5468 (mmm160) REVERT: B 196 SER cc_start: 0.7192 (m) cc_final: 0.6695 (t) REVERT: C 245 MET cc_start: 0.2107 (ppp) cc_final: 0.1879 (ppp) REVERT: C 295 MET cc_start: 0.7154 (tpp) cc_final: 0.6693 (tpt) REVERT: C 528 MET cc_start: 0.6755 (ttt) cc_final: 0.6301 (ttm) REVERT: F 69 MET cc_start: -0.0374 (ptt) cc_final: -0.0703 (ptt) outliers start: 59 outliers final: 42 residues processed: 341 average time/residue: 0.1258 time to fit residues: 61.9240 Evaluate side-chains 344 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 298 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 76 HIS Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 120 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 HIS D 540 HIS E 221 HIS ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 GLN F 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.252321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.212178 restraints weight = 22111.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.210270 restraints weight = 31932.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.204273 restraints weight = 25725.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.204804 restraints weight = 25290.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.203744 restraints weight = 18446.944| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4383 r_free = 0.4383 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4383 r_free = 0.4383 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14655 Z= 0.159 Angle : 0.798 17.001 19949 Z= 0.365 Chirality : 0.046 0.350 2291 Planarity : 0.005 0.113 2510 Dihedral : 10.133 112.921 2433 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.44 % Favored : 96.35 % Rotamer: Outliers : 4.75 % Allowed : 31.03 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.20), residues: 1837 helix: 0.96 (0.16), residues: 1133 sheet: -0.37 (0.43), residues: 140 loop : -1.26 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 70 TYR 0.032 0.001 TYR D 523 PHE 0.017 0.002 PHE B 218 TRP 0.023 0.002 TRP F 121 HIS 0.008 0.001 HIS A 117 Details of bonding type rmsd covalent geometry : bond 0.00351 (14625) covalent geometry : angle 0.72325 (19869) SS BOND : bond 0.00339 ( 10) SS BOND : angle 1.47413 ( 20) hydrogen bonds : bond 0.03519 ( 799) hydrogen bonds : angle 4.08538 ( 2345) link_ALPHA1-3 : bond 0.01806 ( 2) link_ALPHA1-3 : angle 3.69145 ( 6) link_ALPHA1-4 : bond 0.00931 ( 4) link_ALPHA1-4 : angle 3.25655 ( 12) link_ALPHA1-6 : bond 0.01358 ( 4) link_ALPHA1-6 : angle 2.31137 ( 12) link_BETA1-4 : bond 0.02807 ( 2) link_BETA1-4 : angle 7.13887 ( 6) link_NAG-ASN : bond 0.01425 ( 8) link_NAG-ASN : angle 8.41302 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 306 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7493 (mmm) REVERT: A 82 TRP cc_start: 0.7317 (OUTLIER) cc_final: 0.5302 (t-100) REVERT: A 121 GLU cc_start: 0.7352 (tt0) cc_final: 0.7069 (mt-10) REVERT: A 148 LEU cc_start: 0.7374 (mt) cc_final: 0.6744 (mt) REVERT: A 246 ARG cc_start: 0.7871 (tmt-80) cc_final: 0.7610 (tmt170) REVERT: A 256 LYS cc_start: 0.6506 (mttm) cc_final: 0.6166 (mttm) REVERT: D 220 LYS cc_start: 0.7239 (tmtt) cc_final: 0.6893 (tmmt) REVERT: D 577 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6918 (mp10) REVERT: E 193 MET cc_start: 0.4117 (OUTLIER) cc_final: 0.3713 (ptt) REVERT: E 269 PHE cc_start: 0.7458 (t80) cc_final: 0.7232 (t80) REVERT: B 12 LEU cc_start: 0.8512 (tp) cc_final: 0.8158 (mt) REVERT: B 96 ARG cc_start: 0.5776 (mmm160) cc_final: 0.5219 (mmm160) REVERT: C 245 MET cc_start: 0.2152 (ppp) cc_final: 0.1878 (ppp) REVERT: C 528 MET cc_start: 0.6788 (ttt) cc_final: 0.6339 (ttm) REVERT: F 101 ARG cc_start: 0.5245 (tpt90) cc_final: 0.4948 (tpp-160) outliers start: 63 outliers final: 48 residues processed: 343 average time/residue: 0.1313 time to fit residues: 64.5887 Evaluate side-chains 348 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 76 HIS Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 40 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 55 optimal weight: 0.1980 chunk 92 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 chunk 131 optimal weight: 0.0970 chunk 170 optimal weight: 40.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.251785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.212871 restraints weight = 23197.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.210663 restraints weight = 32184.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.206015 restraints weight = 24036.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.206628 restraints weight = 22638.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.206949 restraints weight = 15401.291| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4424 r_free = 0.4424 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4424 r_free = 0.4424 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14655 Z= 0.139 Angle : 0.809 16.616 19949 Z= 0.365 Chirality : 0.046 0.340 2291 Planarity : 0.004 0.075 2510 Dihedral : 9.902 111.040 2429 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.60 % Favored : 96.18 % Rotamer: Outliers : 3.93 % Allowed : 31.85 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.20), residues: 1837 helix: 1.02 (0.16), residues: 1135 sheet: -0.47 (0.43), residues: 144 loop : -1.25 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 246 TYR 0.021 0.001 TYR B 227 PHE 0.017 0.001 PHE B 112 TRP 0.019 0.002 TRP F 121 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00301 (14625) covalent geometry : angle 0.74968 (19869) SS BOND : bond 0.00548 ( 10) SS BOND : angle 1.78293 ( 20) hydrogen bonds : bond 0.03439 ( 799) hydrogen bonds : angle 4.05223 ( 2345) link_ALPHA1-3 : bond 0.01808 ( 2) link_ALPHA1-3 : angle 3.69111 ( 6) link_ALPHA1-4 : bond 0.01291 ( 4) link_ALPHA1-4 : angle 3.28002 ( 12) link_ALPHA1-6 : bond 0.01369 ( 4) link_ALPHA1-6 : angle 2.29030 ( 12) link_BETA1-4 : bond 0.02244 ( 2) link_BETA1-4 : angle 7.04665 ( 6) link_NAG-ASN : bond 0.01334 ( 8) link_NAG-ASN : angle 7.23305 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7468 (mmm) REVERT: A 82 TRP cc_start: 0.7223 (OUTLIER) cc_final: 0.5320 (t-100) REVERT: A 121 GLU cc_start: 0.7353 (tt0) cc_final: 0.7040 (mt-10) REVERT: A 148 LEU cc_start: 0.7414 (mt) cc_final: 0.7005 (mt) REVERT: A 234 MET cc_start: 0.7114 (mmt) cc_final: 0.6876 (mmt) REVERT: A 256 LYS cc_start: 0.6485 (mttm) cc_final: 0.6143 (mttm) REVERT: D 220 LYS cc_start: 0.7154 (tmtt) cc_final: 0.6840 (tmmt) REVERT: E 77 TYR cc_start: 0.7749 (m-80) cc_final: 0.7526 (m-80) REVERT: B 246 ARG cc_start: 0.6142 (ttp80) cc_final: 0.5687 (ttp80) REVERT: C 245 MET cc_start: 0.2166 (ppp) cc_final: 0.1891 (ppp) REVERT: C 528 MET cc_start: 0.6668 (ttt) cc_final: 0.6239 (ttm) outliers start: 52 outliers final: 43 residues processed: 332 average time/residue: 0.1328 time to fit residues: 63.2404 Evaluate side-chains 335 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 290 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 76 HIS Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 714 VAL Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 10 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 chunk 128 optimal weight: 0.7980 chunk 135 optimal weight: 0.0980 chunk 166 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 50 optimal weight: 0.1980 chunk 120 optimal weight: 20.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.251909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.213808 restraints weight = 22820.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.211760 restraints weight = 33729.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.210363 restraints weight = 24346.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.210223 restraints weight = 19232.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.207579 restraints weight = 18966.087| |-----------------------------------------------------------------------------| r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4399 r_free = 0.4399 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4399 r_free = 0.4399 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.6315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14655 Z= 0.156 Angle : 0.808 15.880 19949 Z= 0.369 Chirality : 0.046 0.338 2291 Planarity : 0.005 0.080 2510 Dihedral : 9.801 113.059 2429 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.60 % Favored : 96.18 % Rotamer: Outliers : 3.64 % Allowed : 31.92 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.20), residues: 1837 helix: 1.04 (0.16), residues: 1135 sheet: -0.46 (0.43), residues: 144 loop : -1.24 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 246 TYR 0.018 0.001 TYR B 227 PHE 0.018 0.002 PHE A 218 TRP 0.024 0.002 TRP B 118 HIS 0.006 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00347 (14625) covalent geometry : angle 0.75127 (19869) SS BOND : bond 0.00353 ( 10) SS BOND : angle 1.78923 ( 20) hydrogen bonds : bond 0.03534 ( 799) hydrogen bonds : angle 4.07373 ( 2345) link_ALPHA1-3 : bond 0.01728 ( 2) link_ALPHA1-3 : angle 3.58453 ( 6) link_ALPHA1-4 : bond 0.01179 ( 4) link_ALPHA1-4 : angle 3.26952 ( 12) link_ALPHA1-6 : bond 0.01333 ( 4) link_ALPHA1-6 : angle 2.32420 ( 12) link_BETA1-4 : bond 0.02144 ( 2) link_BETA1-4 : angle 7.33857 ( 6) link_NAG-ASN : bond 0.01310 ( 8) link_NAG-ASN : angle 6.95347 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3674 Ramachandran restraints generated. 1837 Oldfield, 0 Emsley, 1837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 291 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7443 (mmm) REVERT: A 82 TRP cc_start: 0.7253 (OUTLIER) cc_final: 0.5217 (t-100) REVERT: A 96 ARG cc_start: 0.6621 (tpp-160) cc_final: 0.6396 (ttt180) REVERT: A 121 GLU cc_start: 0.7410 (tt0) cc_final: 0.7074 (mt-10) REVERT: A 256 LYS cc_start: 0.6497 (mttm) cc_final: 0.6129 (mttm) REVERT: D 220 LYS cc_start: 0.7203 (tmtt) cc_final: 0.6889 (tmmt) REVERT: D 609 GLU cc_start: 0.7190 (mp0) cc_final: 0.6888 (mp0) REVERT: E 77 TYR cc_start: 0.7786 (m-80) cc_final: 0.7558 (m-80) REVERT: E 193 MET cc_start: 0.3774 (ptm) cc_final: 0.3441 (ptt) REVERT: B 12 LEU cc_start: 0.8487 (tp) cc_final: 0.8143 (mt) REVERT: B 82 TRP cc_start: 0.7763 (OUTLIER) cc_final: 0.7551 (m100) REVERT: B 196 SER cc_start: 0.7113 (m) cc_final: 0.6763 (t) REVERT: B 246 ARG cc_start: 0.6348 (ttp80) cc_final: 0.5890 (ttp80) REVERT: C 245 MET cc_start: 0.2217 (ppp) cc_final: 0.1926 (ppp) REVERT: C 528 MET cc_start: 0.6692 (ttt) cc_final: 0.6279 (ttm) REVERT: F 40 ASP cc_start: 0.6547 (OUTLIER) cc_final: 0.6175 (p0) outliers start: 48 outliers final: 42 residues processed: 320 average time/residue: 0.1278 time to fit residues: 59.0641 Evaluate side-chains 331 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 76 HIS Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 99 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 155 PHE Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 111 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 122 optimal weight: 0.0670 chunk 47 optimal weight: 0.4980 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 527 GLN B 76 HIS ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 GLN F 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.253243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.215077 restraints weight = 23127.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.212696 restraints weight = 32722.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.207895 restraints weight = 25350.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.208564 restraints weight = 23826.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.208963 restraints weight = 16480.746| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4411 r_free = 0.4411 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4411 r_free = 0.4411 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14655 Z= 0.136 Angle : 0.813 15.319 19949 Z= 0.368 Chirality : 0.046 0.332 2291 Planarity : 0.004 0.074 2510 Dihedral : 9.598 110.796 2429 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.65 % Favored : 96.13 % Rotamer: Outliers : 3.79 % Allowed : 32.15 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.20), residues: 1837 helix: 1.14 (0.16), residues: 1131 sheet: -0.54 (0.43), residues: 140 loop : -1.33 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 246 TYR 0.018 0.001 TYR C 654 PHE 0.026 0.002 PHE E 269 TRP 0.022 0.002 TRP B 118 HIS 0.006 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00294 (14625) covalent geometry : angle 0.75852 (19869) SS BOND : bond 0.00328 ( 10) SS BOND : angle 1.49337 ( 20) hydrogen bonds : bond 0.03439 ( 799) hydrogen bonds : angle 4.05241 ( 2345) link_ALPHA1-3 : bond 0.01906 ( 2) link_ALPHA1-3 : angle 3.72854 ( 6) link_ALPHA1-4 : bond 0.01254 ( 4) link_ALPHA1-4 : angle 3.22421 ( 12) link_ALPHA1-6 : bond 0.01504 ( 4) link_ALPHA1-6 : angle 2.30814 ( 12) link_BETA1-4 : bond 0.02120 ( 2) link_BETA1-4 : angle 7.43831 ( 6) link_NAG-ASN : bond 0.01315 ( 8) link_NAG-ASN : angle 6.76872 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2969.56 seconds wall clock time: 51 minutes 52.55 seconds (3112.55 seconds total)