Starting phenix.real_space_refine on Thu Jun 12 17:33:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kes_37166/06_2025/8kes_37166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kes_37166/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kes_37166/06_2025/8kes_37166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kes_37166/06_2025/8kes_37166.map" model { file = "/net/cci-nas-00/data/ceres_data/8kes_37166/06_2025/8kes_37166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kes_37166/06_2025/8kes_37166.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.039 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 3000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 407, 2999 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 6, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 407, 2999 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 6, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 3058 Chain: "E" Number of atoms: 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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 11, '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: {'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "C" Number of atoms: 3008 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 407, 2999 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 6, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 407, 2999 Classifications: {'peptide': 407} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 6, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 3049 Chain: "F" Number of atoms: 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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 11, '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: 11.86, per 1000 atoms: 0.83 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: 4.12 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.40 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: 4.24 Time building geometry restraints manager: 4.67 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 723 or resid 801 through 803)) selection = (chain 'D' and (resid 183 through 516 or resid 518 through 654 or resid 656 thro \ ugh 723 or resid 801 through 803)) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.24 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 39.010 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.490 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (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 TRP 0.022 0.002 TRP B 118 HIS 0.030 0.002 HIS F 135 PHE 0.034 0.002 PHE B 230 TYR 0.045 0.002 TYR A 192 ARG 0.006 0.001 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.01446 ( 8) link_NAG-ASN : angle 10.36206 ( 24) 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_ALPHA1-3 : bond 0.01603 ( 2) link_ALPHA1-3 : angle 4.55252 ( 6) hydrogen bonds : bond 0.27642 ( 799) hydrogen bonds : angle 8.48264 ( 2345) SS BOND : bond 0.01443 ( 10) SS BOND : angle 2.64246 ( 20) covalent geometry : bond 0.00547 (14625) covalent geometry : angle 0.97402 (19869) *********************** 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 : 1.584 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: 0.1571 (mmm) REVERT: E 181 ILE cc_start: 0.7200 (mm) cc_final: 0.6286 (mm) REVERT: E 185 MET cc_start: 0.6975 (mmm) cc_final: 0.6710 (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: 0.6683 (mp) REVERT: B 163 ILE cc_start: 0.7679 (tp) cc_final: 0.7476 (tt) REVERT: B 242 LEU cc_start: 0.6488 (mp) cc_final: 0.6281 (mm) REVERT: C 297 LEU cc_start: 0.5781 (mt) cc_final: 0.5570 (mt) REVERT: F 247 PRO cc_start: 0.2878 (Cg_exo) cc_final: 0.2190 (Cg_endo) outliers start: 24 outliers final: 3 residues processed: 507 average time/residue: 0.2995 time to fit residues: 209.5756 Evaluate side-chains 327 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 321 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 153 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 40.0000 chunk 142 optimal weight: 0.0980 chunk 55 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 ASN D 599 GLN D 624 GLN D 653 HIS 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 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 HIS F 110 GLN ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.250579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.211851 restraints weight = 20165.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.208663 restraints weight = 34456.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.204559 restraints weight = 29528.970| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4397 r_free = 0.4397 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4396 r_free = 0.4396 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 14655 Z= 0.316 Angle : 0.971 19.008 19949 Z= 0.470 Chirality : 0.054 0.425 2291 Planarity : 0.006 0.066 2510 Dihedral : 12.529 113.548 2440 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.76 % Favored : 96.02 % Rotamer: Outliers : 6.31 % Allowed : 26.58 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.19), residues: 1837 helix: -0.82 (0.15), residues: 1117 sheet: -0.41 (0.40), residues: 140 loop : -1.15 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 302 HIS 0.009 0.002 HIS D 529 PHE 0.032 0.003 PHE F 108 TYR 0.037 0.002 TYR D 282 ARG 0.009 0.001 ARG D 620 Details of bonding type rmsd link_NAG-ASN : bond 0.01370 ( 8) link_NAG-ASN : angle 8.08919 ( 24) link_ALPHA1-4 : bond 0.01046 ( 4) link_ALPHA1-4 : angle 4.30254 ( 12) link_ALPHA1-6 : bond 0.00888 ( 4) link_ALPHA1-6 : angle 2.34488 ( 12) link_BETA1-4 : bond 0.02230 ( 2) link_BETA1-4 : angle 9.12443 ( 6) link_ALPHA1-3 : bond 0.00615 ( 2) link_ALPHA1-3 : angle 4.76295 ( 6) hydrogen bonds : bond 0.05738 ( 799) hydrogen bonds : angle 5.26638 ( 2345) SS BOND : bond 0.00901 ( 10) SS BOND : angle 2.40514 ( 20) covalent geometry : bond 0.00710 (14625) covalent geometry : angle 0.90311 (19869) *********************** 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 437 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 353 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6394 (ttp) cc_final: 0.6086 (ttp) REVERT: A 43 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7531 (mmm) REVERT: A 82 TRP cc_start: 0.7684 (OUTLIER) cc_final: 0.5733 (t-100) REVERT: D 220 LYS cc_start: 0.7275 (tmtt) cc_final: 0.6932 (tmmt) REVERT: D 577 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7058 (mp10) REVERT: D 655 ARG cc_start: 0.7745 (ptt-90) cc_final: 0.7509 (ptt90) REVERT: B 12 LEU cc_start: 0.8661 (tp) cc_final: 0.8143 (mt) REVERT: B 48 ILE cc_start: 0.8847 (mm) cc_final: 0.8587 (mt) REVERT: B 163 ILE cc_start: 0.7473 (tp) cc_final: 0.7260 (tt) REVERT: B 242 LEU cc_start: 0.7028 (mp) cc_final: 0.6771 (mm) REVERT: C 528 MET cc_start: 0.6797 (ttt) cc_final: 0.6352 (ttm) REVERT: C 688 LYS cc_start: 0.6962 (tttm) cc_final: 0.6748 (tttm) REVERT: F 40 ASP cc_start: 0.4936 (t0) cc_final: 0.4683 (t0) REVERT: F 116 ARG cc_start: 0.4194 (ttt90) cc_final: 0.3749 (ttt180) outliers start: 84 outliers final: 37 residues processed: 408 average time/residue: 0.2691 time to fit residues: 156.3368 Evaluate side-chains 344 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 304 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU 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 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 238 ASN Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 535 VAL 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 685 HIS Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 150 TYR 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 19 VAL 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 549 VAL Chi-restraints excluded: chain C residue 555 TRP 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 215 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 72 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS D 294 HIS D 540 HIS E 257 ASN E 276 GLN B 158 HIS C 240 GLN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 HIS F 184 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.250270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.209856 restraints weight = 20676.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.209829 restraints weight = 32178.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.205872 restraints weight = 23884.212| |-----------------------------------------------------------------------------| r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4404 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4404 r_free = 0.4404 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4404 r_free = 0.4404 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14655 Z= 0.196 Angle : 0.843 18.388 19949 Z= 0.395 Chirality : 0.049 0.423 2291 Planarity : 0.005 0.065 2510 Dihedral : 11.424 115.215 2433 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.38 % Favored : 96.40 % Rotamer: Outliers : 5.57 % Allowed : 28.95 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.19), residues: 1837 helix: 0.00 (0.15), residues: 1113 sheet: -0.58 (0.39), residues: 146 loop : -1.14 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.010 0.001 HIS A 117 PHE 0.025 0.002 PHE E 269 TYR 0.023 0.002 TYR A 160 ARG 0.008 0.001 ARG F 250 Details of bonding type rmsd link_NAG-ASN : bond 0.01683 ( 8) link_NAG-ASN : angle 9.02600 ( 24) link_ALPHA1-4 : bond 0.01930 ( 4) link_ALPHA1-4 : angle 4.13497 ( 12) link_ALPHA1-6 : bond 0.00974 ( 4) link_ALPHA1-6 : angle 2.48885 ( 12) link_BETA1-4 : bond 0.02626 ( 2) link_BETA1-4 : angle 9.34743 ( 6) link_ALPHA1-3 : bond 0.01951 ( 2) link_ALPHA1-3 : angle 3.76990 ( 6) hydrogen bonds : bond 0.04645 ( 799) hydrogen bonds : angle 4.68914 ( 2345) SS BOND : bond 0.00749 ( 10) SS BOND : angle 1.62860 ( 20) covalent geometry : bond 0.00433 (14625) covalent geometry : angle 0.75349 (19869) *********************** 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: 74 poor density : 336 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6257 (ttp) cc_final: 0.5915 (ttp) REVERT: A 43 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7518 (mmm) REVERT: A 77 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7406 (mp) REVERT: A 82 TRP cc_start: 0.7597 (OUTLIER) cc_final: 0.5850 (t-100) REVERT: A 92 PHE cc_start: 0.6174 (t80) cc_final: 0.5835 (t80) REVERT: A 234 MET cc_start: 0.7165 (mmt) cc_final: 0.6937 (mmt) REVERT: D 220 LYS cc_start: 0.7213 (tmtt) cc_final: 0.6858 (tmmt) REVERT: D 537 ARG cc_start: 0.6019 (ptm-80) cc_final: 0.5670 (ptt180) REVERT: D 577 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7095 (mp10) REVERT: D 655 ARG cc_start: 0.7701 (ptt-90) cc_final: 0.7414 (ptt90) REVERT: D 711 LYS cc_start: 0.8261 (tttp) cc_final: 0.7741 (ttmm) REVERT: E 193 MET cc_start: 0.6149 (ptp) cc_final: 0.5767 (ptp) REVERT: B 24 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.6172 (t80) REVERT: B 48 ILE cc_start: 0.8754 (mm) cc_final: 0.8520 (mt) REVERT: B 49 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7997 (mm110) REVERT: B 96 ARG cc_start: 0.5773 (mmm160) cc_final: 0.5267 (mmm160) REVERT: B 163 ILE cc_start: 0.7435 (tp) cc_final: 0.7176 (tt) REVERT: C 528 MET cc_start: 0.6762 (ttt) cc_final: 0.6350 (ttm) REVERT: C 722 ARG cc_start: 0.5534 (tpp-160) cc_final: 0.4979 (mpt180) REVERT: F 223 ILE cc_start: 0.2348 (OUTLIER) cc_final: 0.1893 (tt) outliers start: 74 outliers final: 46 residues processed: 380 average time/residue: 0.2696 time to fit residues: 147.2713 Evaluate side-chains 359 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 306 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 76 HIS Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 89 CYS 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 186 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 533 THR 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 24 TYR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 49 GLN 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 240 GLN Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 705 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 F residue 223 ILE 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 87 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 159 optimal weight: 0.0870 chunk 94 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN ** D 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 HIS E 130 HIS C 240 GLN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS F 184 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.252847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.220989 restraints weight = 29903.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.217828 restraints weight = 31934.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.213260 restraints weight = 23149.512| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4465 r_free = 0.4465 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4465 r_free = 0.4465 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6243 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14655 Z= 0.141 Angle : 0.796 17.349 19949 Z= 0.368 Chirality : 0.046 0.394 2291 Planarity : 0.005 0.063 2510 Dihedral : 10.941 111.767 2433 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.54 % Favored : 96.24 % Rotamer: Outliers : 3.79 % Allowed : 30.51 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.20), residues: 1837 helix: 0.37 (0.16), residues: 1133 sheet: -0.57 (0.39), residues: 156 loop : -1.16 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 121 HIS 0.009 0.001 HIS A 117 PHE 0.022 0.002 PHE B 218 TYR 0.021 0.001 TYR C 523 ARG 0.006 0.001 ARG F 275 Details of bonding type rmsd link_NAG-ASN : bond 0.01537 ( 8) link_NAG-ASN : angle 8.28603 ( 24) link_ALPHA1-4 : bond 0.01655 ( 4) link_ALPHA1-4 : angle 3.84964 ( 12) link_ALPHA1-6 : bond 0.01247 ( 4) link_ALPHA1-6 : angle 2.35437 ( 12) link_BETA1-4 : bond 0.02230 ( 2) link_BETA1-4 : angle 9.27758 ( 6) link_ALPHA1-3 : bond 0.01846 ( 2) link_ALPHA1-3 : angle 3.77475 ( 6) hydrogen bonds : bond 0.03958 ( 799) hydrogen bonds : angle 4.39734 ( 2345) SS BOND : bond 0.00728 ( 10) SS BOND : angle 1.85465 ( 20) covalent geometry : bond 0.00298 (14625) covalent geometry : angle 0.71178 (19869) *********************** 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 379 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 329 time to evaluate : 1.677 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: 0.6145 (ttp) cc_final: 0.5840 (ttp) REVERT: A 43 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7476 (mmm) REVERT: A 55 PHE cc_start: 0.7566 (t80) cc_final: 0.7285 (t80) REVERT: A 57 LEU cc_start: 0.7950 (tt) cc_final: 0.7443 (tp) REVERT: A 82 TRP cc_start: 0.7479 (OUTLIER) cc_final: 0.5670 (t-100) REVERT: A 92 PHE cc_start: 0.6024 (t80) cc_final: 0.5815 (t80) REVERT: D 220 LYS cc_start: 0.7127 (tmtt) cc_final: 0.6812 (tmmt) REVERT: E 276 GLN cc_start: 0.7878 (tm130) cc_final: 0.7468 (tt0) REVERT: E 277 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7120 (mm) REVERT: B 12 LEU cc_start: 0.8757 (tp) cc_final: 0.8235 (mt) REVERT: B 24 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.6207 (t80) REVERT: B 48 ILE cc_start: 0.8754 (mm) cc_final: 0.8519 (mt) REVERT: B 96 ARG cc_start: 0.5849 (mmm160) cc_final: 0.5530 (mmm160) REVERT: B 163 ILE cc_start: 0.7338 (tp) cc_final: 0.7112 (tt) REVERT: C 295 MET cc_start: 0.7044 (tpp) cc_final: 0.6616 (tpt) REVERT: C 524 ASN cc_start: 0.6164 (m-40) cc_final: 0.5731 (t0) REVERT: C 528 MET cc_start: 0.6650 (ttt) cc_final: 0.6181 (ttm) REVERT: F 223 ILE cc_start: 0.2278 (OUTLIER) cc_final: 0.1685 (tt) outliers start: 50 outliers final: 26 residues processed: 357 average time/residue: 0.2792 time to fit residues: 141.7901 Evaluate side-chains 335 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 304 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 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 226 LEU Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 24 TYR Chi-restraints excluded: chain B residue 79 GLU 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 541 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 705 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 F residue 223 ILE 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 128 optimal weight: 7.9990 chunk 172 optimal weight: 0.0670 chunk 40 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 136 optimal weight: 0.3980 chunk 102 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN B 76 HIS ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.252632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.214714 restraints weight = 22495.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.212568 restraints weight = 29645.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.207238 restraints weight = 24980.496| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4417 r_free = 0.4417 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4417 r_free = 0.4417 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14655 Z= 0.140 Angle : 0.768 16.618 19949 Z= 0.355 Chirality : 0.046 0.379 2291 Planarity : 0.004 0.055 2510 Dihedral : 10.560 112.414 2429 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.16 % Favored : 96.62 % Rotamer: Outliers : 4.23 % Allowed : 30.59 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1837 helix: 0.63 (0.16), residues: 1133 sheet: -0.57 (0.39), residues: 156 loop : -1.12 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 118 HIS 0.009 0.001 HIS A 117 PHE 0.026 0.002 PHE E 269 TYR 0.020 0.001 TYR B 227 ARG 0.011 0.001 ARG B 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01418 ( 8) link_NAG-ASN : angle 7.90635 ( 24) link_ALPHA1-4 : bond 0.01510 ( 4) link_ALPHA1-4 : angle 3.62309 ( 12) link_ALPHA1-6 : bond 0.01213 ( 4) link_ALPHA1-6 : angle 2.31566 ( 12) link_BETA1-4 : bond 0.02296 ( 2) link_BETA1-4 : angle 8.94464 ( 6) link_ALPHA1-3 : bond 0.01757 ( 2) link_ALPHA1-3 : angle 3.76163 ( 6) hydrogen bonds : bond 0.03778 ( 799) hydrogen bonds : angle 4.24764 ( 2345) SS BOND : bond 0.00872 ( 10) SS BOND : angle 1.79992 ( 20) covalent geometry : bond 0.00298 (14625) covalent geometry : angle 0.68884 (19869) *********************** 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 370 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 314 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6202 (ttp) cc_final: 0.5888 (ttp) REVERT: A 43 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7444 (mmm) REVERT: A 55 PHE cc_start: 0.7589 (t80) cc_final: 0.7337 (t80) REVERT: A 57 LEU cc_start: 0.7879 (tt) cc_final: 0.7445 (tp) REVERT: A 82 TRP cc_start: 0.7478 (OUTLIER) cc_final: 0.5657 (t-100) REVERT: A 92 PHE cc_start: 0.6294 (t80) cc_final: 0.5915 (t80) REVERT: A 246 ARG cc_start: 0.7666 (tmt-80) cc_final: 0.7334 (tmt170) REVERT: D 220 LYS cc_start: 0.7248 (tmtt) cc_final: 0.6951 (tmmt) REVERT: E 188 TYR cc_start: 0.7410 (p90) cc_final: 0.7204 (p90) REVERT: E 276 GLN cc_start: 0.7783 (tm130) cc_final: 0.7446 (tt0) REVERT: B 24 TYR cc_start: 0.6594 (OUTLIER) cc_final: 0.6170 (t80) REVERT: B 48 ILE cc_start: 0.8761 (mm) cc_final: 0.8532 (mt) REVERT: B 49 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.8014 (mm110) REVERT: B 70 ARG cc_start: 0.4919 (ttm-80) cc_final: 0.4712 (ttm-80) REVERT: C 245 MET cc_start: 0.2572 (ppp) cc_final: 0.2268 (ppp) REVERT: C 295 MET cc_start: 0.7175 (tpp) cc_final: 0.6940 (tpp) REVERT: C 524 ASN cc_start: 0.6182 (m-40) cc_final: 0.5892 (t0) REVERT: C 528 MET cc_start: 0.6709 (ttt) cc_final: 0.6277 (ttm) REVERT: F 262 GLN cc_start: 0.5438 (tm-30) cc_final: 0.4453 (tm-30) outliers start: 56 outliers final: 33 residues processed: 346 average time/residue: 0.2711 time to fit residues: 134.4578 Evaluate side-chains 334 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 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 226 LEU Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 37 LEU 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 24 TYR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 541 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 193 MET 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 26 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 79 optimal weight: 0.0980 chunk 82 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 149 optimal weight: 4.9990 overall best weight: 1.8224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 599 GLN C 685 HIS C 719 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 = 0.4779 r_free = 0.4779 target = 0.248025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.209272 restraints weight = 22711.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.204979 restraints weight = 34287.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.200041 restraints weight = 28986.508| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4336 r_free = 0.4336 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4336 r_free = 0.4336 target_work(ls_wunit_k1) = 0.198 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14655 Z= 0.210 Angle : 0.825 18.251 19949 Z= 0.382 Chirality : 0.047 0.373 2291 Planarity : 0.005 0.066 2510 Dihedral : 10.577 118.219 2427 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.76 % Favored : 96.02 % Rotamer: Outliers : 4.75 % Allowed : 31.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.20), residues: 1837 helix: 0.74 (0.16), residues: 1121 sheet: -0.51 (0.40), residues: 146 loop : -1.18 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 118 HIS 0.011 0.001 HIS A 117 PHE 0.026 0.002 PHE A 153 TYR 0.029 0.002 TYR D 523 ARG 0.008 0.001 ARG B 80 Details of bonding type rmsd link_NAG-ASN : bond 0.01429 ( 8) link_NAG-ASN : angle 7.87559 ( 24) link_ALPHA1-4 : bond 0.01282 ( 4) link_ALPHA1-4 : angle 3.81033 ( 12) link_ALPHA1-6 : bond 0.01177 ( 4) link_ALPHA1-6 : angle 2.37485 ( 12) link_BETA1-4 : bond 0.02027 ( 2) link_BETA1-4 : angle 8.56453 ( 6) link_ALPHA1-3 : bond 0.01643 ( 2) link_ALPHA1-3 : angle 3.84549 ( 6) hydrogen bonds : bond 0.03994 ( 799) hydrogen bonds : angle 4.30032 ( 2345) SS BOND : bond 0.00488 ( 10) SS BOND : angle 1.82663 ( 20) covalent geometry : bond 0.00478 (14625) covalent geometry : angle 0.75212 (19869) *********************** 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 381 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 318 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7552 (mmm) REVERT: A 55 PHE cc_start: 0.7690 (t80) cc_final: 0.7407 (t80) REVERT: A 82 TRP cc_start: 0.7751 (OUTLIER) cc_final: 0.5837 (t-100) REVERT: A 121 GLU cc_start: 0.7506 (tt0) cc_final: 0.7275 (mt-10) REVERT: A 246 ARG cc_start: 0.7789 (tmt-80) cc_final: 0.7507 (tmt170) REVERT: A 249 TYR cc_start: 0.7922 (t80) cc_final: 0.7640 (t80) REVERT: D 220 LYS cc_start: 0.7396 (tmtt) cc_final: 0.7087 (tmmt) REVERT: E 77 TYR cc_start: 0.7975 (m-80) cc_final: 0.7748 (m-80) REVERT: B 12 LEU cc_start: 0.8683 (tp) cc_final: 0.8218 (mt) REVERT: B 48 ILE cc_start: 0.8865 (mm) cc_final: 0.8630 (mt) REVERT: B 246 ARG cc_start: 0.7525 (tmm160) cc_final: 0.6833 (tmm160) REVERT: C 524 ASN cc_start: 0.6316 (m-40) cc_final: 0.6015 (t0) REVERT: C 528 MET cc_start: 0.6879 (ttt) cc_final: 0.6424 (ttm) outliers start: 63 outliers final: 39 residues processed: 355 average time/residue: 0.2977 time to fit residues: 153.4442 Evaluate side-chains 338 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 297 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 125 ASP 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 226 LEU Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 575 VAL 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 115 TYR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 210 THR 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 32 THR Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 79 GLU 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 549 VAL Chi-restraints excluded: chain C residue 705 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 236 VAL Chi-restraints excluded: chain F residue 259 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 23 optimal weight: 3.9990 chunk 179 optimal weight: 30.0000 chunk 80 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 HIS D 685 HIS B 28 GLN B 76 HIS ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.244501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.209366 restraints weight = 28539.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.206236 restraints weight = 34598.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.200737 restraints weight = 25563.691| |-----------------------------------------------------------------------------| r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4349 r_free = 0.4349 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4349 r_free = 0.4349 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14655 Z= 0.279 Angle : 0.880 18.080 19949 Z= 0.415 Chirality : 0.051 0.369 2291 Planarity : 0.005 0.051 2510 Dihedral : 10.725 121.417 2427 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.31 % Favored : 95.47 % Rotamer: Outliers : 4.68 % Allowed : 30.96 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.20), residues: 1837 helix: 0.55 (0.16), residues: 1149 sheet: -0.30 (0.41), residues: 142 loop : -1.37 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP B 118 HIS 0.010 0.002 HIS A 117 PHE 0.029 0.002 PHE E 269 TYR 0.022 0.002 TYR D 523 ARG 0.012 0.001 ARG B 70 Details of bonding type rmsd link_NAG-ASN : bond 0.01424 ( 8) link_NAG-ASN : angle 8.58962 ( 24) link_ALPHA1-4 : bond 0.00974 ( 4) link_ALPHA1-4 : angle 4.08910 ( 12) link_ALPHA1-6 : bond 0.01307 ( 4) link_ALPHA1-6 : angle 2.46401 ( 12) link_BETA1-4 : bond 0.02264 ( 2) link_BETA1-4 : angle 7.70992 ( 6) link_ALPHA1-3 : bond 0.01271 ( 2) link_ALPHA1-3 : angle 3.88804 ( 6) hydrogen bonds : bond 0.04263 ( 799) hydrogen bonds : angle 4.47911 ( 2345) SS BOND : bond 0.00663 ( 10) SS BOND : angle 1.99536 ( 20) covalent geometry : bond 0.00637 (14625) covalent geometry : angle 0.80493 (19869) *********************** 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: 62 poor density : 301 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7630 (mmm) REVERT: A 82 TRP cc_start: 0.7995 (OUTLIER) cc_final: 0.6205 (t-100) REVERT: A 121 GLU cc_start: 0.7546 (tt0) cc_final: 0.7246 (mt-10) REVERT: A 234 MET cc_start: 0.7167 (mmt) cc_final: 0.6941 (mmt) REVERT: D 328 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6984 (t0) REVERT: D 673 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8760 (mmm) REVERT: B 12 LEU cc_start: 0.8730 (tp) cc_final: 0.8295 (mt) REVERT: B 70 ARG cc_start: 0.5470 (ttm110) cc_final: 0.4868 (ttm-80) REVERT: B 73 GLU cc_start: 0.7287 (pm20) cc_final: 0.6742 (mt-10) REVERT: B 246 ARG cc_start: 0.7418 (tmm160) cc_final: 0.6809 (tmm160) REVERT: C 245 MET cc_start: 0.2498 (ppp) cc_final: 0.2244 (ppp) REVERT: C 324 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6583 (t-90) REVERT: C 524 ASN cc_start: 0.6382 (m-40) cc_final: 0.6076 (t0) REVERT: C 528 MET cc_start: 0.6876 (ttt) cc_final: 0.6426 (ttm) REVERT: C 576 ILE cc_start: 0.7117 (mm) cc_final: 0.5905 (mt) REVERT: C 688 LYS cc_start: 0.7307 (tttm) cc_final: 0.7016 (tttm) outliers start: 62 outliers final: 46 residues processed: 337 average time/residue: 0.2866 time to fit residues: 137.4973 Evaluate side-chains 342 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 291 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR 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 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 226 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 328 ASP 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 575 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 115 TYR 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 160 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 555 TRP Chi-restraints excluded: chain C residue 705 VAL 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 28 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 87 optimal weight: 0.0470 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 49 GLN ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.245892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.207146 restraints weight = 19816.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.203129 restraints weight = 32631.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.198838 restraints weight = 29302.035| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4333 r_free = 0.4333 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4333 r_free = 0.4333 target_work(ls_wunit_k1) = 0.197 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14655 Z= 0.211 Angle : 0.840 17.573 19949 Z= 0.394 Chirality : 0.048 0.355 2291 Planarity : 0.005 0.050 2510 Dihedral : 10.569 118.457 2427 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.87 % Favored : 95.91 % Rotamer: Outliers : 4.16 % Allowed : 31.48 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.20), residues: 1837 helix: 0.70 (0.16), residues: 1141 sheet: -0.41 (0.41), residues: 142 loop : -1.32 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 118 HIS 0.010 0.001 HIS A 117 PHE 0.028 0.002 PHE C 651 TYR 0.032 0.002 TYR B 83 ARG 0.010 0.001 ARG B 70 Details of bonding type rmsd link_NAG-ASN : bond 0.01497 ( 8) link_NAG-ASN : angle 7.67913 ( 24) link_ALPHA1-4 : bond 0.01344 ( 4) link_ALPHA1-4 : angle 3.88174 ( 12) link_ALPHA1-6 : bond 0.01139 ( 4) link_ALPHA1-6 : angle 2.40012 ( 12) link_BETA1-4 : bond 0.02426 ( 2) link_BETA1-4 : angle 7.38095 ( 6) link_ALPHA1-3 : bond 0.01714 ( 2) link_ALPHA1-3 : angle 3.90941 ( 6) hydrogen bonds : bond 0.04052 ( 799) hydrogen bonds : angle 4.34361 ( 2345) SS BOND : bond 0.00676 ( 10) SS BOND : angle 2.81903 ( 20) covalent geometry : bond 0.00476 (14625) covalent geometry : angle 0.77189 (19869) *********************** 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 361 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 306 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7523 (mmm) REVERT: A 80 ARG cc_start: 0.8572 (ttp-170) cc_final: 0.8133 (ttp-170) REVERT: A 82 TRP cc_start: 0.7937 (OUTLIER) cc_final: 0.6026 (t-100) REVERT: A 102 ARG cc_start: 0.6967 (tpt170) cc_final: 0.5765 (ptp-170) REVERT: A 121 GLU cc_start: 0.7469 (tt0) cc_final: 0.7174 (mt-10) REVERT: A 146 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6138 (t80) REVERT: A 177 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6933 (mm-30) REVERT: A 248 MET cc_start: 0.6457 (mmm) cc_final: 0.6180 (mmm) REVERT: E 35 PRO cc_start: 0.7730 (Cg_exo) cc_final: 0.7434 (Cg_endo) REVERT: E 184 GLN cc_start: 0.6115 (OUTLIER) cc_final: 0.5847 (tm-30) REVERT: E 269 PHE cc_start: 0.7387 (t80) cc_final: 0.7182 (t80) REVERT: B 12 LEU cc_start: 0.8716 (tp) cc_final: 0.8304 (mt) REVERT: B 70 ARG cc_start: 0.5522 (ttm110) cc_final: 0.5093 (ttm-80) REVERT: B 73 GLU cc_start: 0.7250 (pm20) cc_final: 0.6758 (mt-10) REVERT: C 524 ASN cc_start: 0.6307 (m-40) cc_final: 0.5988 (t0) REVERT: C 528 MET cc_start: 0.6833 (ttt) cc_final: 0.6376 (ttm) REVERT: C 576 ILE cc_start: 0.7248 (mm) cc_final: 0.6907 (mm) REVERT: C 688 LYS cc_start: 0.7299 (tttm) cc_final: 0.6987 (tttm) outliers start: 55 outliers final: 40 residues processed: 342 average time/residue: 0.2954 time to fit residues: 142.1703 Evaluate side-chains 341 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 297 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 82 TRP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 146 PHE 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 226 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 328 ASP 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 575 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 184 GLN 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 E residue 232 CYS 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 94 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 705 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 41 optimal weight: 0.0770 chunk 145 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 262 GLN B 76 HIS ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.248877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.211446 restraints weight = 22894.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.208116 restraints weight = 30542.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.203253 restraints weight = 25559.584| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4357 r_free = 0.4357 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4357 r_free = 0.4357 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.6668 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 : 0.791 17.171 19949 Z= 0.366 Chirality : 0.046 0.335 2291 Planarity : 0.004 0.055 2510 Dihedral : 10.093 113.225 2427 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.76 % Favored : 96.02 % Rotamer: Outliers : 3.04 % Allowed : 33.33 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1837 helix: 0.91 (0.16), residues: 1141 sheet: -0.33 (0.42), residues: 136 loop : -1.30 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 118 HIS 0.008 0.001 HIS A 117 PHE 0.025 0.001 PHE C 651 TYR 0.035 0.001 TYR B 83 ARG 0.010 0.001 ARG B 70 Details of bonding type rmsd link_NAG-ASN : bond 0.01404 ( 8) link_NAG-ASN : angle 7.29343 ( 24) link_ALPHA1-4 : bond 0.01287 ( 4) link_ALPHA1-4 : angle 3.20203 ( 12) link_ALPHA1-6 : bond 0.01381 ( 4) link_ALPHA1-6 : angle 2.26762 ( 12) link_BETA1-4 : bond 0.02304 ( 2) link_BETA1-4 : angle 7.81479 ( 6) link_ALPHA1-3 : bond 0.01898 ( 2) link_ALPHA1-3 : angle 4.00090 ( 6) hydrogen bonds : bond 0.03656 ( 799) hydrogen bonds : angle 4.12786 ( 2345) SS BOND : bond 0.00408 ( 10) SS BOND : angle 1.99886 ( 20) covalent geometry : bond 0.00313 (14625) covalent geometry : angle 0.72658 (19869) *********************** 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 349 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 309 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7504 (mmm) REVERT: A 55 PHE cc_start: 0.7561 (t80) cc_final: 0.7314 (t80) REVERT: A 80 ARG cc_start: 0.8529 (ttp-170) cc_final: 0.8007 (ttp-170) REVERT: A 82 TRP cc_start: 0.7842 (OUTLIER) cc_final: 0.5917 (t-100) REVERT: A 121 GLU cc_start: 0.7516 (tt0) cc_final: 0.7198 (mt-10) REVERT: A 234 MET cc_start: 0.7293 (mmt) cc_final: 0.7015 (mmt) REVERT: A 246 ARG cc_start: 0.7728 (tmt-80) cc_final: 0.7450 (tmt170) REVERT: D 220 LYS cc_start: 0.7382 (tmtt) cc_final: 0.7008 (tmmt) REVERT: E 35 PRO cc_start: 0.7524 (Cg_exo) cc_final: 0.7252 (Cg_endo) REVERT: E 184 GLN cc_start: 0.6342 (OUTLIER) cc_final: 0.5996 (tm-30) REVERT: E 262 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.6969 (mp-120) REVERT: E 269 PHE cc_start: 0.7443 (t80) cc_final: 0.7236 (t80) REVERT: B 70 ARG cc_start: 0.5338 (ttm110) cc_final: 0.4988 (ttm-80) REVERT: B 73 GLU cc_start: 0.7215 (pm20) cc_final: 0.6698 (mt-10) REVERT: B 246 ARG cc_start: 0.7485 (tmm160) cc_final: 0.7127 (tmt170) REVERT: C 240 GLN cc_start: 0.5345 (tp-100) cc_final: 0.5100 (tp-100) REVERT: C 324 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6659 (t-90) REVERT: C 524 ASN cc_start: 0.6331 (m-40) cc_final: 0.6009 (t0) REVERT: C 528 MET cc_start: 0.6898 (ttt) cc_final: 0.6480 (ttm) REVERT: C 576 ILE cc_start: 0.7262 (mm) cc_final: 0.6885 (mm) REVERT: C 688 LYS cc_start: 0.7313 (tttm) cc_final: 0.7015 (tttm) REVERT: F 148 GLU cc_start: 0.4254 (tp30) cc_final: 0.4050 (tp30) outliers start: 40 outliers final: 27 residues processed: 336 average time/residue: 0.3181 time to fit residues: 153.6143 Evaluate side-chains 332 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 1.758 ------------------------------------------------------------------------------- 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 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 226 LEU Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 605 VAL Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 718 LEU 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 E residue 232 CYS Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 705 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 41 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 71 optimal weight: 0.0030 chunk 28 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.6994 ------------------------------------------------------------------------------- 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** D 599 GLN E 262 GLN B 49 GLN ** C 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.246115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.211977 restraints weight = 22286.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.205983 restraints weight = 26796.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.201086 restraints weight = 27720.825| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4360 r_free = 0.4360 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4360 r_free = 0.4360 target_work(ls_wunit_k1) = 0.200 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.6848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14655 Z= 0.200 Angle : 0.839 16.958 19949 Z= 0.391 Chirality : 0.047 0.338 2291 Planarity : 0.005 0.067 2510 Dihedral : 10.198 118.740 2427 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.93 % Favored : 95.86 % Rotamer: Outliers : 3.19 % Allowed : 31.92 % Favored : 64.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1837 helix: 0.86 (0.16), residues: 1141 sheet: -0.37 (0.43), residues: 140 loop : -1.34 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 118 HIS 0.010 0.001 HIS A 117 PHE 0.026 0.002 PHE A 153 TYR 0.038 0.002 TYR B 83 ARG 0.019 0.001 ARG A 70 Details of bonding type rmsd link_NAG-ASN : bond 0.01366 ( 8) link_NAG-ASN : angle 7.15955 ( 24) link_ALPHA1-4 : bond 0.01183 ( 4) link_ALPHA1-4 : angle 3.60766 ( 12) link_ALPHA1-6 : bond 0.01234 ( 4) link_ALPHA1-6 : angle 2.38484 ( 12) link_BETA1-4 : bond 0.02063 ( 2) link_BETA1-4 : angle 7.74354 ( 6) link_ALPHA1-3 : bond 0.01569 ( 2) link_ALPHA1-3 : angle 3.87003 ( 6) hydrogen bonds : bond 0.03881 ( 799) hydrogen bonds : angle 4.24267 ( 2345) SS BOND : bond 0.00562 ( 10) SS BOND : angle 2.78803 ( 20) covalent geometry : bond 0.00457 (14625) covalent geometry : angle 0.77705 (19869) ********************** 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 338 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 296 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7520 (mmm) REVERT: A 80 ARG cc_start: 0.8502 (ttp-170) cc_final: 0.7980 (ttp-170) REVERT: A 82 TRP cc_start: 0.7815 (OUTLIER) cc_final: 0.5875 (t-100) REVERT: A 96 ARG cc_start: 0.6621 (tpp-160) cc_final: 0.6398 (ttt180) REVERT: A 102 ARG cc_start: 0.6706 (tpt170) cc_final: 0.5579 (ptp-170) REVERT: A 121 GLU cc_start: 0.7401 (tt0) cc_final: 0.7082 (mt-10) REVERT: A 246 ARG cc_start: 0.7738 (tmt-80) cc_final: 0.7503 (tmt170) REVERT: E 35 PRO cc_start: 0.7557 (Cg_exo) cc_final: 0.7271 (Cg_endo) REVERT: E 184 GLN cc_start: 0.6514 (OUTLIER) cc_final: 0.6237 (tm-30) REVERT: E 193 MET cc_start: 0.4098 (OUTLIER) cc_final: 0.3676 (ptt) REVERT: E 262 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.6814 (mp-120) REVERT: B 12 LEU cc_start: 0.8570 (tp) cc_final: 0.8261 (mt) REVERT: B 70 ARG cc_start: 0.5321 (ttm110) cc_final: 0.4994 (ttm-80) REVERT: B 73 GLU cc_start: 0.7097 (pm20) cc_final: 0.6651 (mt-10) REVERT: B 246 ARG cc_start: 0.7536 (tmm160) cc_final: 0.7182 (tmt170) REVERT: C 240 GLN cc_start: 0.5257 (tp-100) cc_final: 0.5005 (tp-100) REVERT: C 324 HIS cc_start: 0.7002 (OUTLIER) cc_final: 0.6527 (t-90) REVERT: C 528 MET cc_start: 0.6878 (ttt) cc_final: 0.6435 (ttm) REVERT: C 688 LYS cc_start: 0.7203 (tttm) cc_final: 0.6924 (tttm) REVERT: F 148 GLU cc_start: 0.4158 (tp30) cc_final: 0.3941 (tp30) outliers start: 42 outliers final: 34 residues processed: 322 average time/residue: 0.3202 time to fit residues: 149.7636 Evaluate side-chains 335 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 295 time to evaluate : 1.457 ------------------------------------------------------------------------------- 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 92 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 226 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 328 ASP 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 575 VAL Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 718 LEU 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 186 THR 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 E residue 232 CYS Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain C residue 324 HIS Chi-restraints excluded: chain C residue 705 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 92 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 176 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.246319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.211105 restraints weight = 28243.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.208477 restraints weight = 32359.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.203936 restraints weight = 23957.460| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4385 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4385 r_free = 0.4385 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 = 0.4385 r_free = 0.4385 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.208 14655 Z= 0.249 Angle : 1.115 59.186 19949 Z= 0.606 Chirality : 0.047 0.338 2291 Planarity : 0.005 0.118 2510 Dihedral : 10.204 119.092 2427 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.98 % Favored : 95.80 % Rotamer: Outliers : 3.71 % Allowed : 31.85 % Favored : 64.44 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.20), residues: 1837 helix: 0.85 (0.16), residues: 1141 sheet: -0.49 (0.43), residues: 148 loop : -1.32 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 118 HIS 0.009 0.001 HIS A 117 PHE 0.031 0.002 PHE D 595 TYR 0.033 0.002 TYR B 83 ARG 0.016 0.001 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.01355 ( 8) link_NAG-ASN : angle 7.15793 ( 24) link_ALPHA1-4 : bond 0.01146 ( 4) link_ALPHA1-4 : angle 3.58565 ( 12) link_ALPHA1-6 : bond 0.01322 ( 4) link_ALPHA1-6 : angle 2.48230 ( 12) link_BETA1-4 : bond 0.01947 ( 2) link_BETA1-4 : angle 7.79058 ( 6) link_ALPHA1-3 : bond 0.01545 ( 2) link_ALPHA1-3 : angle 3.89048 ( 6) hydrogen bonds : bond 0.03933 ( 799) hydrogen bonds : angle 4.23953 ( 2345) SS BOND : bond 0.00451 ( 10) SS BOND : angle 2.78966 ( 20) covalent geometry : bond 0.00555 (14625) covalent geometry : angle 1.07008 (19869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6118.80 seconds wall clock time: 108 minutes 26.25 seconds (6506.25 seconds total)