Starting phenix.real_space_refine on Fri May 16 07:19:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kes_37166/05_2025/8kes_37166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kes_37166/05_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_37166/05_2025/8kes_37166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kes_37166/05_2025/8kes_37166.map" model { file = "/net/cci-nas-00/data/ceres_data/8kes_37166/05_2025/8kes_37166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kes_37166/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.94, per 1000 atoms: 0.77 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: 3.69 Conformation dependent library (CDL) restraints added in 2.4 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: 1.29 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: 3.93 Time building geometry restraints manager: 4.30 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.570 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.130 ------------------------------------------------------------------------------- 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 : 1.403 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: 0.2900 time to fit residues: 202.7975 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 : 1.387 ------------------------------------------------------------------------------- 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 = 0.211852 restraints weight = 20165.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.208671 restraints weight = 34451.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.204566 restraints weight = 29543.645| |-----------------------------------------------------------------------------| 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) = 0.204 | | 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: 0.6404 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 8.08918 ( 24) link_ALPHA1-4 : bond 0.01046 ( 4) link_ALPHA1-4 : angle 4.30255 ( 12) link_ALPHA1-6 : bond 0.00888 ( 4) link_ALPHA1-6 : angle 2.34489 ( 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 4.76303 ( 6) hydrogen bonds : bond 0.05738 ( 799) hydrogen bonds : angle 5.26638 ( 2345) SS BOND : bond 0.00901 ( 10) SS BOND : angle 2.40513 ( 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 : 1.500 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: 0.7530 (mmm) REVERT: A 82 TRP cc_start: 0.7684 (OUTLIER) cc_final: 0.5733 (t-100) REVERT: D 220 LYS cc_start: 0.7276 (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: 0.7746 (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: 0.4193 (ttt90) cc_final: 0.3749 (ttt180) outliers start: 84 outliers final: 37 residues processed: 408 average time/residue: 0.2633 time to fit residues: 153.3562 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 : 1.415 ------------------------------------------------------------------------------- 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: 20.0000 chunk 95 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.4808 r_free = 0.4808 target = 0.251015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.212422 restraints weight = 20767.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.211415 restraints weight = 30021.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.206364 restraints weight = 23998.668| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4409 r_free = 0.4409 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 = 0.4409 r_free = 0.4409 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14655 Z= 0.182 Angle : 0.837 18.405 19949 Z= 0.391 Chirality : 0.049 0.429 2291 Planarity : 0.005 0.065 2510 Dihedral : 11.396 115.044 2433 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.27 % Favored : 96.51 % Rotamer: Outliers : 5.27 % Allowed : 28.88 % Favored : 65.85 % 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: -0.67 (0.20), residues: 1837 helix: 0.05 (0.15), residues: 1113 sheet: -0.77 (0.38), residues: 160 loop : -1.09 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.011 0.001 HIS A 117 PHE 0.026 0.002 PHE E 269 TYR 0.023 0.002 TYR A 160 ARG 0.012 0.001 ARG F 250 Details of bonding type rmsd link_NAG-ASN : bond 0.01751 ( 8) link_NAG-ASN : angle 9.04573 ( 24) link_ALPHA1-4 : bond 0.01957 ( 4) link_ALPHA1-4 : angle 4.08348 ( 12) link_ALPHA1-6 : bond 0.01043 ( 4) link_ALPHA1-6 : angle 2.45587 ( 12) link_BETA1-4 : bond 0.02494 ( 2) link_BETA1-4 : angle 9.38470 ( 6) link_ALPHA1-3 : bond 0.02158 ( 2) link_ALPHA1-3 : angle 3.91352 ( 6) hydrogen bonds : bond 0.04555 ( 799) hydrogen bonds : angle 4.64776 ( 2345) SS BOND : bond 0.00556 ( 10) SS BOND : angle 1.72031 ( 20) covalent geometry : bond 0.00399 (14625) covalent geometry : angle 0.74605 (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 409 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 339 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6329 (ttp) cc_final: 0.5991 (ttp) REVERT: A 43 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7542 (mmm) REVERT: A 77 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7377 (mp) REVERT: A 82 TRP cc_start: 0.7556 (OUTLIER) cc_final: 0.5816 (t-100) REVERT: A 92 PHE cc_start: 0.6159 (t80) cc_final: 0.5833 (t80) REVERT: A 234 MET cc_start: 0.7166 (mmt) cc_final: 0.6936 (mmt) REVERT: A 252 MET cc_start: 0.6817 (mmp) cc_final: 0.6585 (mmp) REVERT: D 220 LYS cc_start: 0.7169 (tmtt) cc_final: 0.6803 (tmmt) REVERT: D 537 ARG cc_start: 0.5976 (ptm-80) cc_final: 0.5701 (ptt180) REVERT: D 577 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: D 655 ARG cc_start: 0.7704 (ptt-90) cc_final: 0.7406 (ptt90) REVERT: D 711 LYS cc_start: 0.8241 (tttp) cc_final: 0.7709 (ttmm) REVERT: E 193 MET cc_start: 0.6217 (ptp) cc_final: 0.5834 (ptp) REVERT: B 24 TYR cc_start: 0.6613 (OUTLIER) cc_final: 0.6231 (t80) REVERT: B 48 ILE cc_start: 0.8765 (mm) cc_final: 0.8540 (mt) REVERT: B 49 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8027 (mm110) REVERT: B 96 ARG cc_start: 0.5782 (mmm160) cc_final: 0.5305 (mmm160) REVERT: B 163 ILE cc_start: 0.7423 (tp) cc_final: 0.7165 (tt) REVERT: C 528 MET cc_start: 0.6757 (ttt) cc_final: 0.6347 (ttm) REVERT: C 722 ARG cc_start: 0.5513 (tpp-160) cc_final: 0.4955 (mpt180) REVERT: F 223 ILE cc_start: 0.2320 (OUTLIER) cc_final: 0.1880 (tt) outliers start: 70 outliers final: 39 residues processed: 381 average time/residue: 0.2714 time to fit residues: 148.6070 Evaluate side-chains 352 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 306 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 330 SER 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 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 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 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: 0.9990 chunk 16 optimal weight: 8.9990 chunk 159 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 chunk 61 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 0.0670 chunk 109 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 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 = 0.4814 r_free = 0.4814 target = 0.252395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.218647 restraints weight = 29837.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.216050 restraints weight = 33624.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.212219 restraints weight = 23797.005| |-----------------------------------------------------------------------------| r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4451 r_free = 0.4451 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4451 r_free = 0.4451 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.5094 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= 0.146 Angle : 0.797 17.575 19949 Z= 0.368 Chirality : 0.047 0.401 2291 Planarity : 0.005 0.062 2510 Dihedral : 10.995 112.641 2433 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.49 % Favored : 96.29 % Rotamer: Outliers : 4.01 % Allowed : 30.14 % Favored : 65.85 % 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: -0.28 (0.20), residues: 1837 helix: 0.42 (0.16), residues: 1123 sheet: -0.57 (0.39), residues: 156 loop : -1.12 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 121 HIS 0.010 0.001 HIS A 117 PHE 0.037 0.002 PHE E 108 TYR 0.020 0.002 TYR A 160 ARG 0.006 0.000 ARG D 224 Details of bonding type rmsd link_NAG-ASN : bond 0.01531 ( 8) link_NAG-ASN : angle 8.35056 ( 24) link_ALPHA1-4 : bond 0.01439 ( 4) link_ALPHA1-4 : angle 3.87813 ( 12) link_ALPHA1-6 : bond 0.01216 ( 4) link_ALPHA1-6 : angle 2.36869 ( 12) link_BETA1-4 : bond 0.02393 ( 2) link_BETA1-4 : angle 9.31907 ( 6) link_ALPHA1-3 : bond 0.01736 ( 2) link_ALPHA1-3 : angle 3.74534 ( 6) hydrogen bonds : bond 0.03979 ( 799) hydrogen bonds : angle 4.42530 ( 2345) SS BOND : bond 0.00331 ( 10) SS BOND : angle 1.86996 ( 20) covalent geometry : bond 0.00313 (14625) covalent geometry : angle 0.71156 (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 381 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 328 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6189 (ttp) cc_final: 0.5850 (ttp) REVERT: A 43 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7516 (mmm) REVERT: A 55 PHE cc_start: 0.7600 (t80) cc_final: 0.7373 (t80) REVERT: A 57 LEU cc_start: 0.7984 (tt) cc_final: 0.7461 (tp) REVERT: A 82 TRP cc_start: 0.7504 (OUTLIER) cc_final: 0.5698 (t-100) REVERT: A 92 PHE cc_start: 0.6102 (t80) cc_final: 0.5847 (t80) REVERT: D 220 LYS cc_start: 0.7219 (tmtt) cc_final: 0.6907 (tmmt) REVERT: D 537 ARG cc_start: 0.5944 (ptm-80) cc_final: 0.5650 (ptt180) REVERT: D 577 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6960 (mp10) REVERT: E 276 GLN cc_start: 0.7990 (tm130) cc_final: 0.7580 (tt0) REVERT: E 277 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7044 (mm) REVERT: B 24 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.6250 (t80) REVERT: B 48 ILE cc_start: 0.8773 (mm) cc_final: 0.8540 (mt) REVERT: B 49 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7833 (mm110) REVERT: B 96 ARG cc_start: 0.5902 (mmm160) cc_final: 0.5548 (mmm160) REVERT: B 163 ILE cc_start: 0.7338 (tp) cc_final: 0.7130 (tt) REVERT: C 295 MET cc_start: 0.7104 (tpp) cc_final: 0.6643 (tpt) REVERT: C 524 ASN cc_start: 0.6230 (m-40) cc_final: 0.5785 (t0) REVERT: C 528 MET cc_start: 0.6688 (ttt) cc_final: 0.6226 (ttm) REVERT: F 223 ILE cc_start: 0.2319 (OUTLIER) cc_final: 0.1539 (tt) outliers start: 53 outliers final: 30 residues processed: 358 average time/residue: 0.2652 time to fit residues: 135.0274 Evaluate side-chains 340 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 250 THR Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain E residue 37 LEU 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 277 LEU 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 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 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 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: 3.9990 chunk 172 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 237 GLN C 685 HIS ** F 184 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 = 0.4802 r_free = 0.4802 target = 0.250987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.213874 restraints weight = 22308.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.210904 restraints weight = 32681.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.205867 restraints weight = 25642.975| |-----------------------------------------------------------------------------| r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4403 r_free = 0.4403 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4403 r_free = 0.4403 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14655 Z= 0.159 Angle : 0.782 16.838 19949 Z= 0.363 Chirality : 0.046 0.383 2291 Planarity : 0.005 0.054 2510 Dihedral : 10.783 114.927 2433 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.49 % Favored : 96.29 % Rotamer: Outliers : 4.97 % Allowed : 29.99 % Favored : 65.03 % 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: 0.64 (0.16), residues: 1123 sheet: -0.57 (0.39), residues: 156 loop : -1.09 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 121 HIS 0.008 0.001 HIS A 117 PHE 0.035 0.002 PHE E 108 TYR 0.022 0.002 TYR B 227 ARG 0.015 0.001 ARG F 250 Details of bonding type rmsd link_NAG-ASN : bond 0.01417 ( 8) link_NAG-ASN : angle 7.95036 ( 24) link_ALPHA1-4 : bond 0.01553 ( 4) link_ALPHA1-4 : angle 3.79456 ( 12) link_ALPHA1-6 : bond 0.01189 ( 4) link_ALPHA1-6 : angle 2.32699 ( 12) link_BETA1-4 : bond 0.02044 ( 2) link_BETA1-4 : angle 8.93966 ( 6) link_ALPHA1-3 : bond 0.01435 ( 2) link_ALPHA1-3 : angle 3.70707 ( 6) hydrogen bonds : bond 0.03872 ( 799) hydrogen bonds : angle 4.30927 ( 2345) SS BOND : bond 0.00474 ( 10) SS BOND : angle 1.76212 ( 20) covalent geometry : bond 0.00350 (14625) covalent geometry : angle 0.70327 (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 380 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 314 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6357 (ttp) cc_final: 0.6045 (ttp) REVERT: A 43 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7473 (mmm) REVERT: A 55 PHE cc_start: 0.7665 (t80) cc_final: 0.7358 (t80) REVERT: A 57 LEU cc_start: 0.7990 (tt) cc_final: 0.7510 (tp) REVERT: A 82 TRP cc_start: 0.7578 (OUTLIER) cc_final: 0.5752 (t-100) REVERT: A 102 ARG cc_start: 0.6725 (tpt170) cc_final: 0.5537 (ptp-170) REVERT: A 246 ARG cc_start: 0.7636 (tmt-80) cc_final: 0.7371 (tmt170) REVERT: D 220 LYS cc_start: 0.7310 (tmtt) cc_final: 0.6993 (tmmt) REVERT: D 577 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6919 (mp10) REVERT: E 276 GLN cc_start: 0.7840 (tm130) cc_final: 0.7558 (tt0) REVERT: E 277 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7256 (mm) REVERT: B 12 LEU cc_start: 0.8753 (tp) cc_final: 0.8244 (mt) REVERT: B 24 TYR cc_start: 0.6627 (OUTLIER) cc_final: 0.6217 (t80) REVERT: B 48 ILE cc_start: 0.8827 (mm) cc_final: 0.8590 (mt) REVERT: B 49 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7918 (mm110) REVERT: B 70 ARG cc_start: 0.5177 (ttm-80) cc_final: 0.4966 (ttm-80) REVERT: C 240 GLN cc_start: 0.5094 (tp-100) cc_final: 0.4835 (tp-100) REVERT: C 245 MET cc_start: 0.2610 (ppp) cc_final: 0.2147 (ppp) REVERT: C 295 MET cc_start: 0.7236 (tpp) cc_final: 0.7025 (tpp) REVERT: C 524 ASN cc_start: 0.6284 (m-40) cc_final: 0.5953 (t0) REVERT: C 528 MET cc_start: 0.6790 (ttt) cc_final: 0.6346 (ttm) outliers start: 66 outliers final: 43 residues processed: 354 average time/residue: 0.2708 time to fit residues: 137.8699 Evaluate side-chains 343 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 294 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 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 238 ASN Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 115 TYR 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 E residue 277 LEU 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 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 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: 0.3980 chunk 98 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 180 optimal weight: 0.0870 chunk 129 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- 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 76 HIS ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 GLN ** F 184 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 = 0.4804 r_free = 0.4804 target = 0.251273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.214102 restraints weight = 23094.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.211141 restraints weight = 32765.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.206612 restraints weight = 25511.156| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4412 r_free = 0.4412 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4412 r_free = 0.4412 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14655 Z= 0.145 Angle : 0.772 16.086 19949 Z= 0.356 Chirality : 0.046 0.403 2291 Planarity : 0.005 0.072 2510 Dihedral : 10.475 113.798 2429 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.49 % Favored : 96.29 % Rotamer: Outliers : 4.23 % Allowed : 30.73 % Favored : 65.03 % 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: 0.06 (0.20), residues: 1837 helix: 0.77 (0.16), residues: 1129 sheet: -0.49 (0.41), residues: 142 loop : -1.18 (0.27), residues: 566 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 0.027 0.002 PHE E 108 TYR 0.022 0.001 TYR A 249 ARG 0.017 0.001 ARG B 246 Details of bonding type rmsd link_NAG-ASN : bond 0.01389 ( 8) link_NAG-ASN : angle 7.69162 ( 24) link_ALPHA1-4 : bond 0.01299 ( 4) link_ALPHA1-4 : angle 3.61251 ( 12) link_ALPHA1-6 : bond 0.01250 ( 4) link_ALPHA1-6 : angle 2.35443 ( 12) link_BETA1-4 : bond 0.02017 ( 2) link_BETA1-4 : angle 8.73822 ( 6) link_ALPHA1-3 : bond 0.01626 ( 2) link_ALPHA1-3 : angle 3.80184 ( 6) hydrogen bonds : bond 0.03689 ( 799) hydrogen bonds : angle 4.23070 ( 2345) SS BOND : bond 0.00509 ( 10) SS BOND : angle 1.50798 ( 20) covalent geometry : bond 0.00318 (14625) covalent geometry : angle 0.69678 (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 364 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 308 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7492 (mmm) REVERT: A 55 PHE cc_start: 0.7615 (t80) cc_final: 0.7365 (t80) REVERT: A 82 TRP cc_start: 0.7653 (OUTLIER) cc_final: 0.5734 (t-100) REVERT: A 246 ARG cc_start: 0.7762 (tmt-80) cc_final: 0.7453 (tmt170) REVERT: A 249 TYR cc_start: 0.7839 (t80) cc_final: 0.7557 (t80) REVERT: D 220 LYS cc_start: 0.7320 (tmtt) cc_final: 0.7052 (tmmt) REVERT: D 224 ARG cc_start: 0.7707 (tpp80) cc_final: 0.7307 (tpp80) REVERT: D 577 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: E 277 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6945 (mm) REVERT: B 12 LEU cc_start: 0.8673 (tp) cc_final: 0.8195 (mt) REVERT: B 24 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.6226 (t80) REVERT: B 49 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7915 (mm110) REVERT: C 524 ASN cc_start: 0.6198 (m-40) cc_final: 0.5932 (t0) REVERT: C 528 MET cc_start: 0.6803 (ttt) cc_final: 0.6373 (ttm) REVERT: C 576 ILE cc_start: 0.6122 (mm) cc_final: 0.5709 (mm) outliers start: 56 outliers final: 34 residues processed: 342 average time/residue: 0.2597 time to fit residues: 128.4609 Evaluate side-chains 337 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 297 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 125 ASP 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 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 575 VAL Chi-restraints excluded: chain D residue 577 GLN 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 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 E residue 277 LEU 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 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 549 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 23 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 145 optimal weight: 0.0010 chunk 94 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 624 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 = 0.4777 r_free = 0.4777 target = 0.247970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.213449 restraints weight = 28895.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.209385 restraints weight = 33956.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.203884 restraints weight = 27086.527| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4386 r_free = 0.4386 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4386 r_free = 0.4386 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14655 Z= 0.198 Angle : 0.842 17.997 19949 Z= 0.388 Chirality : 0.048 0.364 2291 Planarity : 0.005 0.059 2510 Dihedral : 10.462 118.676 2427 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.09 % Favored : 95.69 % Rotamer: Outliers : 4.31 % Allowed : 31.25 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (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: 0.09 (0.20), residues: 1837 helix: 0.81 (0.16), residues: 1131 sheet: -0.59 (0.41), residues: 146 loop : -1.18 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 118 HIS 0.009 0.001 HIS A 117 PHE 0.029 0.002 PHE E 269 TYR 0.023 0.002 TYR D 523 ARG 0.012 0.001 ARG B 70 Details of bonding type rmsd link_NAG-ASN : bond 0.01416 ( 8) link_NAG-ASN : angle 8.78876 ( 24) link_ALPHA1-4 : bond 0.01002 ( 4) link_ALPHA1-4 : angle 3.67807 ( 12) link_ALPHA1-6 : bond 0.01191 ( 4) link_ALPHA1-6 : angle 2.29348 ( 12) link_BETA1-4 : bond 0.02422 ( 2) link_BETA1-4 : angle 7.59210 ( 6) link_ALPHA1-3 : bond 0.01592 ( 2) link_ALPHA1-3 : angle 3.80686 ( 6) hydrogen bonds : bond 0.03934 ( 799) hydrogen bonds : angle 4.26966 ( 2345) SS BOND : bond 0.00433 ( 10) SS BOND : angle 1.75694 ( 20) covalent geometry : bond 0.00449 (14625) covalent geometry : angle 0.76266 (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 356 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 299 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7516 (mmm) REVERT: A 82 TRP cc_start: 0.7731 (OUTLIER) cc_final: 0.5843 (t-100) REVERT: A 102 ARG cc_start: 0.6679 (tpt170) cc_final: 0.5608 (ptp-170) REVERT: A 148 LEU cc_start: 0.7376 (mt) cc_final: 0.6595 (mt) REVERT: A 249 TYR cc_start: 0.7815 (t80) cc_final: 0.7606 (t80) REVERT: D 224 ARG cc_start: 0.7800 (tpp80) cc_final: 0.7480 (tpp80) REVERT: D 577 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6854 (mp10) REVERT: E 77 TYR cc_start: 0.8010 (m-80) cc_final: 0.7797 (m-80) REVERT: B 12 LEU cc_start: 0.8698 (tp) cc_final: 0.8312 (mt) REVERT: C 245 MET cc_start: 0.2450 (ppp) cc_final: 0.2237 (ppp) REVERT: C 524 ASN cc_start: 0.6328 (m-40) cc_final: 0.6043 (t0) REVERT: C 528 MET cc_start: 0.6876 (ttt) cc_final: 0.6461 (ttm) REVERT: C 576 ILE cc_start: 0.6293 (mm) cc_final: 0.6088 (mm) REVERT: C 688 LYS cc_start: 0.7186 (tttm) cc_final: 0.6890 (tttm) REVERT: F 148 GLU cc_start: 0.4257 (tp30) cc_final: 0.4054 (tp30) outliers start: 57 outliers final: 43 residues processed: 336 average time/residue: 0.2713 time to fit residues: 131.0317 Evaluate side-chains 334 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 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 238 ASN Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain E residue 37 LEU 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 549 VAL 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: 8.9990 chunk 12 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 161 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 87 optimal weight: 0.0370 overall best weight: 2.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS D 294 HIS D 685 HIS B 76 HIS ** C 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 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 = 0.4751 r_free = 0.4751 target = 0.245232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.204072 restraints weight = 19823.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.200655 restraints weight = 33117.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.195983 restraints weight = 27446.905| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4307 r_free = 0.4307 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4307 r_free = 0.4307 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14655 Z= 0.245 Angle : 0.842 17.754 19949 Z= 0.396 Chirality : 0.049 0.356 2291 Planarity : 0.005 0.051 2510 Dihedral : 10.566 120.030 2427 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.20 % Favored : 95.58 % Rotamer: Outliers : 3.93 % Allowed : 30.66 % Favored : 65.40 % 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: 1151 sheet: -0.61 (0.40), residues: 146 loop : -1.29 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 118 HIS 0.010 0.001 HIS A 117 PHE 0.027 0.002 PHE C 651 TYR 0.023 0.002 TYR B 227 ARG 0.021 0.001 ARG A 70 Details of bonding type rmsd link_NAG-ASN : bond 0.01369 ( 8) link_NAG-ASN : angle 7.52396 ( 24) link_ALPHA1-4 : bond 0.01194 ( 4) link_ALPHA1-4 : angle 3.95984 ( 12) link_ALPHA1-6 : bond 0.01144 ( 4) link_ALPHA1-6 : angle 2.48931 ( 12) link_BETA1-4 : bond 0.02246 ( 2) link_BETA1-4 : angle 6.72532 ( 6) link_ALPHA1-3 : bond 0.01528 ( 2) link_ALPHA1-3 : angle 4.02275 ( 6) hydrogen bonds : bond 0.04100 ( 799) hydrogen bonds : angle 4.40482 ( 2345) SS BOND : bond 0.00487 ( 10) SS BOND : angle 2.00560 ( 20) covalent geometry : bond 0.00561 (14625) covalent geometry : angle 0.77897 (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 353 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7548 (mmm) REVERT: A 82 TRP cc_start: 0.7892 (OUTLIER) cc_final: 0.6156 (t-100) REVERT: A 102 ARG cc_start: 0.6952 (tpt170) cc_final: 0.5739 (ptp-170) REVERT: A 146 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6180 (t80) REVERT: A 249 TYR cc_start: 0.8156 (t80) cc_final: 0.7914 (t80) REVERT: D 224 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7568 (tpp80) REVERT: D 577 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6930 (mp10) REVERT: E 35 PRO cc_start: 0.7697 (Cg_exo) cc_final: 0.7410 (Cg_endo) REVERT: E 77 TYR cc_start: 0.8089 (m-80) cc_final: 0.7875 (m-80) REVERT: E 184 GLN cc_start: 0.6239 (OUTLIER) cc_final: 0.5911 (tm-30) REVERT: B 12 LEU cc_start: 0.8777 (tp) cc_final: 0.8246 (mt) REVERT: B 49 GLN cc_start: 0.8180 (tp40) cc_final: 0.7764 (tp40) REVERT: C 240 GLN cc_start: 0.5522 (tp-100) cc_final: 0.5292 (tp-100) REVERT: C 324 HIS cc_start: 0.7128 (OUTLIER) cc_final: 0.6649 (t-90) REVERT: C 524 ASN cc_start: 0.6431 (m-40) cc_final: 0.6066 (t0) REVERT: C 528 MET cc_start: 0.6944 (ttt) cc_final: 0.6507 (ttm) REVERT: C 688 LYS cc_start: 0.7345 (tttm) cc_final: 0.7049 (tttm) REVERT: F 185 MET cc_start: 0.7166 (tpp) cc_final: 0.6833 (mpp) outliers start: 52 outliers final: 44 residues processed: 336 average time/residue: 0.2830 time to fit residues: 135.1625 Evaluate side-chains 332 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 282 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 A residue 255 PHE Chi-restraints excluded: chain D residue 238 ASN 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 330 SER Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 605 VAL 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 184 GLN 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 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 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 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: 0.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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** B 76 HIS ** C 624 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 660 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.248481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.210815 restraints weight = 22772.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.205765 restraints weight = 32599.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.203741 restraints weight = 27938.350| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4380 r_free = 0.4380 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4380 r_free = 0.4380 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.6594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14655 Z= 0.150 Angle : 0.816 16.884 19949 Z= 0.376 Chirality : 0.046 0.342 2291 Planarity : 0.005 0.056 2510 Dihedral : 10.239 114.790 2427 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.65 % Favored : 96.13 % Rotamer: Outliers : 3.64 % Allowed : 31.18 % 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: 0.13 (0.20), residues: 1837 helix: 0.87 (0.16), residues: 1141 sheet: -0.62 (0.41), residues: 142 loop : -1.25 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 118 HIS 0.023 0.001 HIS D 685 PHE 0.025 0.002 PHE E 269 TYR 0.029 0.002 TYR C 563 ARG 0.014 0.001 ARG B 70 Details of bonding type rmsd link_NAG-ASN : bond 0.01381 ( 8) link_NAG-ASN : angle 7.28382 ( 24) link_ALPHA1-4 : bond 0.01214 ( 4) link_ALPHA1-4 : angle 3.43452 ( 12) link_ALPHA1-6 : bond 0.01276 ( 4) link_ALPHA1-6 : angle 2.30361 ( 12) link_BETA1-4 : bond 0.02189 ( 2) link_BETA1-4 : angle 7.63760 ( 6) link_ALPHA1-3 : bond 0.01749 ( 2) link_ALPHA1-3 : angle 3.84976 ( 6) hydrogen bonds : bond 0.03759 ( 799) hydrogen bonds : angle 4.20372 ( 2345) SS BOND : bond 0.00698 ( 10) SS BOND : angle 2.23969 ( 20) covalent geometry : bond 0.00329 (14625) covalent geometry : angle 0.75330 (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 344 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 296 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7412 (mmm) REVERT: A 55 PHE cc_start: 0.7907 (t80) cc_final: 0.7443 (t80) REVERT: A 82 TRP cc_start: 0.7819 (OUTLIER) cc_final: 0.6174 (t-100) REVERT: A 90 LEU cc_start: 0.8576 (tt) cc_final: 0.8363 (tp) REVERT: A 246 ARG cc_start: 0.7990 (tmt-80) cc_final: 0.7702 (tmt170) REVERT: A 249 TYR cc_start: 0.8194 (t80) cc_final: 0.7844 (t80) REVERT: D 220 LYS cc_start: 0.7452 (tmtt) cc_final: 0.7117 (tmmt) REVERT: D 224 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7516 (tpp80) REVERT: D 576 ILE cc_start: 0.8880 (mm) cc_final: 0.8538 (mt) REVERT: D 577 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6994 (mp10) REVERT: E 35 PRO cc_start: 0.7654 (Cg_exo) cc_final: 0.7362 (Cg_endo) REVERT: E 184 GLN cc_start: 0.6360 (OUTLIER) cc_final: 0.6031 (tm-30) REVERT: B 12 LEU cc_start: 0.8744 (tp) cc_final: 0.8245 (mt) REVERT: B 49 GLN cc_start: 0.8212 (tp40) cc_final: 0.7817 (tp40) REVERT: C 245 MET cc_start: 0.2044 (ppp) cc_final: 0.1826 (ppp) REVERT: C 524 ASN cc_start: 0.6332 (m-40) cc_final: 0.6000 (t0) REVERT: C 528 MET cc_start: 0.6853 (ttt) cc_final: 0.6447 (ttm) REVERT: C 654 TYR cc_start: 0.6753 (m-80) cc_final: 0.6311 (m-80) REVERT: C 688 LYS cc_start: 0.7264 (tttm) cc_final: 0.6937 (tttm) REVERT: F 185 MET cc_start: 0.7051 (tpp) cc_final: 0.6712 (mpp) outliers start: 48 outliers final: 39 residues processed: 326 average time/residue: 0.2715 time to fit residues: 125.3801 Evaluate side-chains 328 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 32 THR 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 A residue 255 PHE Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 698 SER 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 199 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 232 CYS 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 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: 6.9990 chunk 133 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 120 optimal weight: 30.0000 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 126 optimal weight: 0.0270 chunk 119 optimal weight: 7.9990 chunk 160 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- 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** B 76 HIS C 624 GLN ** 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 = 0.4770 r_free = 0.4770 target = 0.247699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.209679 restraints weight = 22261.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.205527 restraints weight = 29797.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.200004 restraints weight = 26229.063| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4347 r_free = 0.4347 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4347 r_free = 0.4347 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.6833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14655 Z= 0.168 Angle : 0.810 16.435 19949 Z= 0.374 Chirality : 0.046 0.336 2291 Planarity : 0.004 0.056 2510 Dihedral : 10.075 117.210 2427 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.93 % Favored : 95.86 % Rotamer: Outliers : 3.41 % Allowed : 30.73 % Favored : 65.85 % 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: 0.21 (0.20), residues: 1837 helix: 0.94 (0.16), residues: 1143 sheet: -0.52 (0.43), residues: 138 loop : -1.26 (0.27), residues: 556 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 0.030 0.002 PHE A 153 TYR 0.036 0.002 TYR B 83 ARG 0.010 0.001 ARG F 250 Details of bonding type rmsd link_NAG-ASN : bond 0.01342 ( 8) link_NAG-ASN : angle 7.03682 ( 24) link_ALPHA1-4 : bond 0.01264 ( 4) link_ALPHA1-4 : angle 3.40837 ( 12) link_ALPHA1-6 : bond 0.01281 ( 4) link_ALPHA1-6 : angle 2.33460 ( 12) link_BETA1-4 : bond 0.02102 ( 2) link_BETA1-4 : angle 7.74336 ( 6) link_ALPHA1-3 : bond 0.01702 ( 2) link_ALPHA1-3 : angle 3.82891 ( 6) hydrogen bonds : bond 0.03709 ( 799) hydrogen bonds : angle 4.18161 ( 2345) SS BOND : bond 0.00413 ( 10) SS BOND : angle 2.23275 ( 20) covalent geometry : bond 0.00379 (14625) covalent geometry : angle 0.74862 (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 342 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7478 (mmm) REVERT: A 55 PHE cc_start: 0.7901 (t80) cc_final: 0.7436 (t80) REVERT: A 82 TRP cc_start: 0.7947 (OUTLIER) cc_final: 0.6484 (t-100) REVERT: A 102 ARG cc_start: 0.6803 (tpt170) cc_final: 0.5628 (ptp-170) REVERT: A 246 ARG cc_start: 0.7889 (tmt-80) cc_final: 0.7592 (tmt170) REVERT: A 249 TYR cc_start: 0.8209 (t80) cc_final: 0.7759 (t80) REVERT: D 224 ARG cc_start: 0.7901 (tpp80) cc_final: 0.7602 (tpp80) REVERT: D 554 ARG cc_start: 0.7482 (ptp-170) cc_final: 0.7248 (ptp-170) REVERT: D 577 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: E 35 PRO cc_start: 0.7599 (Cg_exo) cc_final: 0.7294 (Cg_endo) REVERT: E 184 GLN cc_start: 0.6389 (OUTLIER) cc_final: 0.6086 (tm-30) REVERT: B 12 LEU cc_start: 0.8841 (tp) cc_final: 0.8381 (mt) REVERT: B 49 GLN cc_start: 0.8211 (tp40) cc_final: 0.7846 (tp40) REVERT: B 73 GLU cc_start: 0.7188 (pm20) cc_final: 0.6846 (mt-10) REVERT: C 245 MET cc_start: 0.2131 (ppp) cc_final: 0.1874 (ppp) REVERT: C 324 HIS cc_start: 0.7001 (OUTLIER) cc_final: 0.6512 (t-90) REVERT: C 524 ASN cc_start: 0.6288 (m-40) cc_final: 0.5972 (t0) REVERT: C 528 MET cc_start: 0.6881 (ttt) cc_final: 0.6459 (ttm) REVERT: C 654 TYR cc_start: 0.6960 (m-80) cc_final: 0.6595 (m-80) REVERT: C 688 LYS cc_start: 0.7262 (tttm) cc_final: 0.6943 (tttm) REVERT: F 185 MET cc_start: 0.7116 (tpp) cc_final: 0.6837 (mpp) outliers start: 45 outliers final: 36 residues processed: 324 average time/residue: 0.2973 time to fit residues: 139.6110 Evaluate side-chains 325 residues out of total 1585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 284 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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 32 THR 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 A residue 255 PHE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 295 MET Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 555 TRP Chi-restraints excluded: chain D residue 575 VAL Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 587 GLU Chi-restraints excluded: chain D residue 673 MET Chi-restraints excluded: chain D residue 698 SER 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 199 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 216 HIS Chi-restraints excluded: chain E residue 232 CYS 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 259 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 92 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 176 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN B 76 HIS ** C 660 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 = 0.4777 r_free = 0.4777 target = 0.248602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.213392 restraints weight = 28249.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.210558 restraints weight = 32089.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.205436 restraints weight = 22651.757| |-----------------------------------------------------------------------------| r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4400 r_free = 0.4400 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4399 r_free = 0.4399 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.6952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14655 Z= 0.152 Angle : 0.804 16.076 19949 Z= 0.372 Chirality : 0.045 0.328 2291 Planarity : 0.005 0.071 2510 Dihedral : 9.903 115.021 2427 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.98 % Favored : 95.80 % Rotamer: Outliers : 3.12 % Allowed : 32.22 % Favored : 64.66 % 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: 0.29 (0.20), residues: 1837 helix: 1.00 (0.16), residues: 1143 sheet: -0.40 (0.44), residues: 136 loop : -1.26 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 118 HIS 0.010 0.001 HIS A 117 PHE 0.021 0.001 PHE C 651 TYR 0.038 0.002 TYR B 83 ARG 0.015 0.001 ARG B 70 Details of bonding type rmsd link_NAG-ASN : bond 0.01328 ( 8) link_NAG-ASN : angle 6.92425 ( 24) link_ALPHA1-4 : bond 0.01225 ( 4) link_ALPHA1-4 : angle 3.39728 ( 12) link_ALPHA1-6 : bond 0.01326 ( 4) link_ALPHA1-6 : angle 2.32448 ( 12) link_BETA1-4 : bond 0.02064 ( 2) link_BETA1-4 : angle 7.83313 ( 6) link_ALPHA1-3 : bond 0.01747 ( 2) link_ALPHA1-3 : angle 3.81096 ( 6) hydrogen bonds : bond 0.03621 ( 799) hydrogen bonds : angle 4.15041 ( 2345) SS BOND : bond 0.00341 ( 10) SS BOND : angle 1.95742 ( 20) covalent geometry : bond 0.00340 (14625) covalent geometry : angle 0.74484 (19869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5416.99 seconds wall clock time: 95 minutes 19.87 seconds (5719.87 seconds total)