Starting phenix.real_space_refine on Thu Jul 31 19:15:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e1k_8956/07_2025/6e1k_8956_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e1k_8956/07_2025/6e1k_8956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6e1k_8956/07_2025/6e1k_8956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e1k_8956/07_2025/6e1k_8956.map" model { file = "/net/cci-nas-00/data/ceres_data/6e1k_8956/07_2025/6e1k_8956_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e1k_8956/07_2025/6e1k_8956_neut.cif" } resolution = 3.3 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2416 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 P 6 5.49 5 S 52 5.16 5 C 7652 2.51 5 N 1780 2.21 5 O 2144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11641 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4278 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 519} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4278 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 519} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 539 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 75, 539 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 541 Chain: "D" Number of atoms: 870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 867 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Conformer: "B" Number of residues, atoms: 114, 867 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 bond proxies already assigned to first conformer: 887 Chain: "E" Number of atoms: 542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 539 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 75, 539 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 541 Chain: "F" Number of atoms: 870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 114, 867 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Conformer: "B" Number of residues, atoms: 114, 867 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 bond proxies already assigned to first conformer: 887 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 148 Unusual residues: {' CA': 4, 'PLM': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 111 Unusual residues: {' CA': 3, 'PLM': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 8.31, per 1000 atoms: 0.71 Number of scatterers: 11641 At special positions: 0 Unit cell: (114.266, 115.482, 109.404, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 52 16.00 P 6 15.00 O 2144 8.00 N 1780 7.00 C 7652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.8 seconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 48.5% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 4.345A pdb=" N LEU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.636A pdb=" N ILE A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 67 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 69 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.616A pdb=" N ALA A 129 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 130 " --> pdb=" O THR A 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 126 through 130' Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 153 through 173 removed outlier: 3.792A pdb=" N VAL A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.693A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.524A pdb=" N VAL A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 208 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 239 removed outlier: 3.909A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 239 " --> pdb=" O PHE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.684A pdb=" N THR A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 removed outlier: 4.216A pdb=" N GLN A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.135A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.560A pdb=" N VAL A 289 " --> pdb=" O PHE A 285 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 293 " --> pdb=" O VAL A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 removed outlier: 4.297A pdb=" N VAL A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 323 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.885A pdb=" N ILE A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 335' Processing helix chain 'A' and resid 343 through 355 removed outlier: 4.330A pdb=" N LEU A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 355 " --> pdb=" O PHE A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 4.676A pdb=" N GLY A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.870A pdb=" N PHE A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 565 removed outlier: 3.768A pdb=" N ILE A 555 " --> pdb=" O TYR A 551 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 575 through 587 removed outlier: 4.234A pdb=" N SER A 581 " --> pdb=" O CYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.599A pdb=" N GLU A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 629 removed outlier: 3.502A pdb=" N LEU A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 643 removed outlier: 4.397A pdb=" N TRP A 635 " --> pdb=" O ASN A 631 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 removed outlier: 3.988A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 676 removed outlier: 3.552A pdb=" N GLU A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 692 removed outlier: 4.386A pdb=" N GLU A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 692 " --> pdb=" O GLN A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 704 Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.886A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 45 No H-bonds generated for 'chain 'B' and resid 43 through 45' Processing helix chain 'B' and resid 51 through 57 removed outlier: 3.951A pdb=" N PHE B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.891A pdb=" N ILE B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 68 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 87 removed outlier: 3.555A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.580A pdb=" N ILE B 130 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 173 removed outlier: 3.646A pdb=" N VAL B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 199 removed outlier: 3.509A pdb=" N PHE B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.854A pdb=" N LEU B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 238 removed outlier: 3.916A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.701A pdb=" N THR B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 removed outlier: 4.176A pdb=" N GLN B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 removed outlier: 4.140A pdb=" N TRP B 271 " --> pdb=" O ASN B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'B' and resid 281 through 295 removed outlier: 3.754A pdb=" N PHE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 289 " --> pdb=" O PHE B 285 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 330 removed outlier: 4.292A pdb=" N VAL B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N MET B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 326 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.932A pdb=" N ILE B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 335' Processing helix chain 'B' and resid 343 through 350 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.560A pdb=" N LEU B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 371 removed outlier: 4.314A pdb=" N SER B 364 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU B 366 " --> pdb=" O LYS B 362 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY B 369 " --> pdb=" O LYS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 392 removed outlier: 3.642A pdb=" N ASP B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.744A pdb=" N ILE B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR B 557 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 562 " --> pdb=" O PHE B 558 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 578 through 587 Processing helix chain 'B' and resid 597 through 600 removed outlier: 4.043A pdb=" N GLU B 600 " --> pdb=" O LYS B 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 597 through 600' Processing helix chain 'B' and resid 601 through 606 removed outlier: 3.721A pdb=" N GLU B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 629 removed outlier: 3.534A pdb=" N PHE B 624 " --> pdb=" O MET B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 643 removed outlier: 3.741A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 663 removed outlier: 4.048A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR B 656 " --> pdb=" O PHE B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 676 removed outlier: 3.504A pdb=" N VAL B 671 " --> pdb=" O VAL B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 691 removed outlier: 4.440A pdb=" N GLU B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS B 687 " --> pdb=" O GLU B 683 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 707 removed outlier: 4.011A pdb=" N LYS B 705 " --> pdb=" O SER B 701 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 707 " --> pdb=" O GLY B 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 24 removed outlier: 3.684A pdb=" N PHE C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER C 63 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 removed outlier: 6.610A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AA4, first strand: chain 'D' and resid 46 through 50 removed outlier: 5.309A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 21 through 24 removed outlier: 3.592A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.562A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'F' and resid 46 through 50 removed outlier: 5.311A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1099 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: 3.50 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1898 1.31 - 1.43: 3404 1.43 - 1.56: 6484 1.56 - 1.68: 28 1.68 - 1.81: 78 Bond restraints: 11892 Sorted by residual: bond pdb=" OG1 TPO A 29 " pdb=" P TPO A 29 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" OG1 TPO B 29 " pdb=" P TPO B 29 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO B 26 " pdb=" P TPO B 26 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" OG1 TPO A 26 " pdb=" P TPO A 26 " ideal model delta sigma weight residual 1.717 1.612 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" CA SER C 91 " pdb=" CB SER C 91 " ideal model delta sigma weight residual 1.532 1.468 0.063 1.45e-02 4.76e+03 1.92e+01 ... (remaining 11887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.77: 15938 6.77 - 13.54: 151 13.54 - 20.30: 7 20.30 - 27.07: 0 27.07 - 33.84: 2 Bond angle restraints: 16098 Sorted by residual: angle pdb=" CA LEU E 73 " pdb=" CB LEU E 73 " pdb=" CG LEU E 73 " ideal model delta sigma weight residual 116.30 150.14 -33.84 3.50e+00 8.16e-02 9.35e+01 angle pdb=" CA LEU C 73 " pdb=" CB LEU C 73 " pdb=" CG LEU C 73 " ideal model delta sigma weight residual 116.30 149.60 -33.30 3.50e+00 8.16e-02 9.05e+01 angle pdb=" N LEU A 610 " pdb=" CA LEU A 610 " pdb=" C LEU A 610 " ideal model delta sigma weight residual 110.80 91.21 19.59 2.13e+00 2.20e-01 8.46e+01 angle pdb=" C LEU A 609 " pdb=" N LEU A 610 " pdb=" CA LEU A 610 " ideal model delta sigma weight residual 121.54 135.37 -13.83 1.91e+00 2.74e-01 5.24e+01 angle pdb=" C VAL D 29 " pdb=" N TYR D 30 " pdb=" CA TYR D 30 " ideal model delta sigma weight residual 121.54 133.55 -12.01 1.91e+00 2.74e-01 3.96e+01 ... (remaining 16093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6406 17.94 - 35.89: 426 35.89 - 53.83: 74 53.83 - 71.77: 35 71.77 - 89.71: 5 Dihedral angle restraints: 6946 sinusoidal: 2688 harmonic: 4258 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual -86.00 -175.71 89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 96 " pdb=" CB CYS F 96 " ideal model delta sinusoidal sigma weight residual -86.00 -175.26 89.26 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CA ILE B 660 " pdb=" C ILE B 660 " pdb=" N LEU B 661 " pdb=" CA LEU B 661 " ideal model delta harmonic sigma weight residual 180.00 133.93 46.07 0 5.00e+00 4.00e-02 8.49e+01 ... (remaining 6943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1472 0.101 - 0.201: 293 0.201 - 0.302: 39 0.302 - 0.402: 5 0.402 - 0.502: 3 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CB THR D 107 " pdb=" CA THR D 107 " pdb=" OG1 THR D 107 " pdb=" CG2 THR D 107 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB ILE B 186 " pdb=" CA ILE B 186 " pdb=" CG1 ILE B 186 " pdb=" CG2 ILE B 186 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 1809 not shown) Planarity restraints: 1972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 107 " -0.050 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR A 107 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR A 107 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 107 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 107 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 107 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 107 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 107 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 107 " 0.044 2.00e-02 2.50e+03 2.51e-02 1.26e+01 pdb=" CG TYR B 107 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 107 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 107 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 107 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 107 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR B 107 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 107 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 36 " -0.046 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR E 36 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR E 36 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR E 36 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR E 36 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR E 36 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 36 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 36 " -0.031 2.00e-02 2.50e+03 ... (remaining 1969 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 220 2.62 - 3.19: 10056 3.19 - 3.76: 17696 3.76 - 4.33: 25148 4.33 - 4.90: 40119 Nonbonded interactions: 93239 Sorted by model distance: nonbonded pdb=" OH TYR A 114 " pdb=" OD2 ASP A 615 " model vdw 2.047 3.040 nonbonded pdb=" OD2 ASP B 606 " pdb=" O HOH B 901 " model vdw 2.080 3.040 nonbonded pdb=" OD2 ASP A 606 " pdb=" O HOH A 901 " model vdw 2.095 3.040 nonbonded pdb=" N LEU A 610 " pdb=" O LEU A 610 " model vdw 2.099 2.496 nonbonded pdb=" O THR D 105 " pdb=" OG1 THR D 105 " model vdw 2.124 3.040 ... (remaining 93234 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' and (resid 22 through 707 or resid 801 through 803 or resid 805 throu \ gh 809)) selection = (chain 'B' and (resid 22 through 707 or resid 801 through 803 or resid 805 throu \ gh 809)) } ncs_group { reference = (chain 'C' and (resid 4 through 64 or resid 66 through 100)) selection = (chain 'E' and (resid 4 through 64 or resid 66 through 100)) } ncs_group { reference = (chain 'D' and (resid 2 through 16 or resid 18 through 120)) selection = (chain 'F' and (resid 2 through 16 or resid 18 through 120)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.880 Find NCS groups from input model: 0.570 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 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 : 0.019 0.180 11899 Z= 0.799 Angle : 1.757 33.840 16106 Z= 0.882 Chirality : 0.084 0.502 1812 Planarity : 0.009 0.076 1972 Dihedral : 13.485 75.250 4198 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.39 % Favored : 88.32 % Rotamer: Outliers : 1.50 % Allowed : 2.59 % Favored : 95.91 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 1.14 % 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: -6.12 (0.15), residues: 1400 helix: -4.20 (0.10), residues: 684 sheet: -4.08 (0.31), residues: 152 loop : -3.62 (0.21), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.007 TRP B 271 HIS 0.007 0.003 HIS B 134 PHE 0.040 0.006 PHE A 587 TYR 0.055 0.007 TYR A 107 ARG 0.010 0.001 ARG F 98 Details of bonding type rmsd hydrogen bonds : bond 0.30055 ( 387) hydrogen bonds : angle 11.45697 ( 1099) SS BOND : bond 0.00369 ( 4) SS BOND : angle 2.11665 ( 8) covalent geometry : bond 0.01863 (11892) covalent geometry : angle 1.75710 (16098) Misc. bond : bond 0.00440 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 248 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.2877 (p90) cc_final: 0.2490 (p90) REVERT: A 77 ASN cc_start: 0.7794 (m-40) cc_final: 0.6635 (t0) REVERT: A 84 LEU cc_start: 0.7166 (tp) cc_final: 0.6919 (tp) REVERT: A 189 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6953 (m-10) REVERT: A 200 ARG cc_start: 0.7105 (ttp80) cc_final: 0.6633 (ttp-110) REVERT: A 204 ASP cc_start: 0.7315 (m-30) cc_final: 0.6908 (m-30) REVERT: A 229 PHE cc_start: 0.7723 (t80) cc_final: 0.7455 (t80) REVERT: A 319 MET cc_start: 0.6986 (tpt) cc_final: 0.6460 (tpt) REVERT: A 596 LYS cc_start: 0.8305 (mmtm) cc_final: 0.8009 (mmtm) REVERT: B 77 ASN cc_start: 0.7792 (m-40) cc_final: 0.6701 (t0) REVERT: B 189 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: B 200 ARG cc_start: 0.7070 (ttp80) cc_final: 0.6625 (ttp-110) REVERT: B 204 ASP cc_start: 0.7336 (m-30) cc_final: 0.6942 (m-30) REVERT: B 229 PHE cc_start: 0.7682 (t80) cc_final: 0.7404 (t80) REVERT: B 246 THR cc_start: 0.8259 (m) cc_final: 0.7850 (p) REVERT: B 319 MET cc_start: 0.7340 (tpt) cc_final: 0.7046 (tpt) REVERT: B 596 LYS cc_start: 0.8380 (mptt) cc_final: 0.8134 (mmtm) REVERT: B 651 TYR cc_start: 0.8146 (t80) cc_final: 0.7714 (t80) REVERT: C 49 TYR cc_start: 0.6435 (p90) cc_final: 0.5763 (p90) REVERT: D 59 SER cc_start: 0.7587 (t) cc_final: 0.7374 (m) REVERT: E 49 TYR cc_start: 0.6579 (p90) cc_final: 0.5736 (p90) REVERT: F 32 TYR cc_start: 0.6632 (t80) cc_final: 0.6252 (t80) REVERT: F 59 SER cc_start: 0.7559 (t) cc_final: 0.7331 (m) REVERT: F 108 LEU cc_start: 0.5705 (pt) cc_final: 0.4097 (tp) outliers start: 14 outliers final: 7 residues processed: 262 average time/residue: 0.2533 time to fit residues: 91.8052 Evaluate side-chains 179 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 612 ASN B 89 GLN B 242 GLN ** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.262567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.234846 restraints weight = 19244.280| |-----------------------------------------------------------------------------| r_work (start): 0.4644 rms_B_bonded: 2.65 r_work (final): 0.4644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4644 r_free = 0.4644 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4644 r_free = 0.4644 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11899 Z= 0.197 Angle : 0.814 12.263 16106 Z= 0.421 Chirality : 0.046 0.179 1812 Planarity : 0.005 0.061 1972 Dihedral : 12.883 59.930 1790 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.42 % Allowed : 6.84 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -4.80 (0.18), residues: 1400 helix: -3.06 (0.15), residues: 676 sheet: -3.80 (0.33), residues: 144 loop : -2.97 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 114 HIS 0.003 0.001 HIS B 27 PHE 0.019 0.002 PHE B 624 TYR 0.028 0.002 TYR A 305 ARG 0.004 0.000 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 387) hydrogen bonds : angle 6.37546 ( 1099) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.76944 ( 8) covalent geometry : bond 0.00458 (11892) covalent geometry : angle 0.81413 (16098) Misc. bond : bond 0.00114 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ARG cc_start: 0.5410 (mmm160) cc_final: 0.5185 (mmm160) REVERT: A 189 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.6643 (m-10) REVERT: A 319 MET cc_start: 0.6139 (tpt) cc_final: 0.5657 (tpt) REVERT: A 607 ASP cc_start: 0.7433 (t70) cc_final: 0.7221 (t70) REVERT: A 651 TYR cc_start: 0.8082 (t80) cc_final: 0.7642 (t80) REVERT: B 189 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.6719 (m-10) REVERT: B 242 GLN cc_start: 0.7382 (tp-100) cc_final: 0.6566 (tt0) REVERT: B 620 MET cc_start: 0.7723 (tpt) cc_final: 0.7459 (tpt) REVERT: B 651 TYR cc_start: 0.8170 (t80) cc_final: 0.7590 (t80) REVERT: F 28 ASN cc_start: 0.6371 (OUTLIER) cc_final: 0.6044 (t0) REVERT: F 108 LEU cc_start: 0.3833 (pt) cc_final: 0.3293 (mt) outliers start: 25 outliers final: 7 residues processed: 197 average time/residue: 0.2286 time to fit residues: 65.5995 Evaluate side-chains 164 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 3 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN ** D 28 ASN ** 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 = 0.4839 r_free = 0.4839 target = 0.259914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.239823 restraints weight = 27782.591| |-----------------------------------------------------------------------------| r_work (start): 0.4683 rms_B_bonded: 2.80 r_work (final): 0.4683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4683 r_free = 0.4683 target_work(ls_wunit_k1) = 0.241 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4683 r_free = 0.4683 target_work(ls_wunit_k1) = 0.241 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11899 Z= 0.202 Angle : 0.770 12.285 16106 Z= 0.392 Chirality : 0.045 0.164 1812 Planarity : 0.005 0.057 1972 Dihedral : 11.937 59.800 1784 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.50 % Allowed : 8.18 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -4.27 (0.19), residues: 1400 helix: -2.57 (0.16), residues: 706 sheet: -3.51 (0.35), residues: 146 loop : -2.75 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 114 HIS 0.004 0.001 HIS A 27 PHE 0.026 0.002 PHE E 71 TYR 0.036 0.002 TYR D 32 ARG 0.002 0.000 ARG D 98 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 387) hydrogen bonds : angle 5.71914 ( 1099) SS BOND : bond 0.00262 ( 4) SS BOND : angle 0.62025 ( 8) covalent geometry : bond 0.00475 (11892) covalent geometry : angle 0.76982 (16098) Misc. bond : bond 0.00141 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6707 (m-10) REVERT: B 189 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6867 (m-10) REVERT: B 242 GLN cc_start: 0.7443 (tp-100) cc_final: 0.6430 (tt0) REVERT: F 28 ASN cc_start: 0.6476 (OUTLIER) cc_final: 0.6088 (t0) REVERT: F 108 LEU cc_start: 0.3988 (pt) cc_final: 0.3230 (mt) outliers start: 26 outliers final: 16 residues processed: 187 average time/residue: 0.2145 time to fit residues: 59.3629 Evaluate side-chains 174 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 189 TYR Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 56 optimal weight: 0.4980 chunk 94 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 108 optimal weight: 0.0970 chunk 65 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 15 optimal weight: 0.0570 chunk 7 optimal weight: 0.0980 chunk 68 optimal weight: 4.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** 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 = 0.4907 r_free = 0.4907 target = 0.268894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.248553 restraints weight = 25220.167| |-----------------------------------------------------------------------------| r_work (start): 0.4752 rms_B_bonded: 2.59 r_work (final): 0.4752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4751 r_free = 0.4751 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4751 r_free = 0.4751 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11899 Z= 0.111 Angle : 0.624 8.059 16106 Z= 0.318 Chirality : 0.041 0.154 1812 Planarity : 0.004 0.085 1972 Dihedral : 10.320 59.552 1784 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.67 % Allowed : 10.27 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.32 (0.21), residues: 1400 helix: -1.77 (0.18), residues: 708 sheet: -2.99 (0.42), residues: 140 loop : -2.37 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 223 HIS 0.002 0.001 HIS F 35 PHE 0.022 0.001 PHE C 71 TYR 0.015 0.001 TYR B 216 ARG 0.009 0.000 ARG F 104 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 387) hydrogen bonds : angle 5.15405 ( 1099) SS BOND : bond 0.00294 ( 4) SS BOND : angle 1.31997 ( 8) covalent geometry : bond 0.00244 (11892) covalent geometry : angle 0.62380 (16098) Misc. bond : bond 0.00023 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 242 GLN cc_start: 0.7267 (tp-100) cc_final: 0.6361 (tt0) REVERT: B 651 TYR cc_start: 0.8173 (t80) cc_final: 0.7908 (t80) REVERT: F 60 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5662 (p90) REVERT: F 108 LEU cc_start: 0.3522 (pt) cc_final: 0.3139 (mt) outliers start: 16 outliers final: 6 residues processed: 198 average time/residue: 0.2167 time to fit residues: 63.7942 Evaluate side-chains 168 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 39 optimal weight: 0.0770 chunk 74 optimal weight: 0.0060 chunk 53 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 overall best weight: 0.6956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS C 6 GLN ** D 28 ASN ** 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 = 0.4882 r_free = 0.4882 target = 0.265479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.244485 restraints weight = 21210.782| |-----------------------------------------------------------------------------| r_work (start): 0.4726 rms_B_bonded: 2.29 r_work (final): 0.4726 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4726 r_free = 0.4726 target_work(ls_wunit_k1) = 0.246 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4726 r_free = 0.4726 target_work(ls_wunit_k1) = 0.246 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11899 Z= 0.136 Angle : 0.657 10.923 16106 Z= 0.326 Chirality : 0.042 0.151 1812 Planarity : 0.004 0.051 1972 Dihedral : 10.186 59.921 1780 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.25 % Allowed : 12.27 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.22), residues: 1400 helix: -1.43 (0.18), residues: 716 sheet: -2.68 (0.43), residues: 136 loop : -2.25 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 271 HIS 0.002 0.001 HIS A 27 PHE 0.027 0.001 PHE A 284 TYR 0.019 0.002 TYR D 32 ARG 0.005 0.000 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 387) hydrogen bonds : angle 4.96079 ( 1099) SS BOND : bond 0.00221 ( 4) SS BOND : angle 1.04642 ( 8) covalent geometry : bond 0.00319 (11892) covalent geometry : angle 0.65722 (16098) Misc. bond : bond 0.00077 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 242 GLN cc_start: 0.7776 (tp-100) cc_final: 0.6849 (tt0) REVERT: B 651 TYR cc_start: 0.8186 (t80) cc_final: 0.7902 (t80) REVERT: E 87 TYR cc_start: 0.7905 (m-10) cc_final: 0.7595 (m-80) REVERT: F 60 TYR cc_start: 0.6310 (OUTLIER) cc_final: 0.5988 (p90) REVERT: F 104 ARG cc_start: 0.6584 (ttm-80) cc_final: 0.6360 (ttm-80) REVERT: F 108 LEU cc_start: 0.3608 (pt) cc_final: 0.2976 (mt) outliers start: 23 outliers final: 16 residues processed: 194 average time/residue: 0.2447 time to fit residues: 68.5075 Evaluate side-chains 176 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 129 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN D 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.264115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.236389 restraints weight = 24682.176| |-----------------------------------------------------------------------------| r_work (start): 0.4658 rms_B_bonded: 1.93 r_work: 0.4290 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4296 r_free = 0.4296 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4296 r_free = 0.4296 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11899 Z= 0.142 Angle : 0.643 7.846 16106 Z= 0.322 Chirality : 0.042 0.148 1812 Planarity : 0.004 0.043 1972 Dihedral : 9.907 58.777 1778 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.75 % Allowed : 12.27 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.70 (0.22), residues: 1400 helix: -1.19 (0.19), residues: 724 sheet: -2.56 (0.44), residues: 136 loop : -2.25 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 103 HIS 0.001 0.000 HIS F 35 PHE 0.024 0.001 PHE C 71 TYR 0.018 0.002 TYR D 32 ARG 0.004 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 387) hydrogen bonds : angle 4.87041 ( 1099) SS BOND : bond 0.00186 ( 4) SS BOND : angle 0.94566 ( 8) covalent geometry : bond 0.00333 (11892) covalent geometry : angle 0.64329 (16098) Misc. bond : bond 0.00088 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 ASP cc_start: 0.7264 (t0) cc_final: 0.7061 (t0) REVERT: B 166 ASP cc_start: 0.7944 (t0) cc_final: 0.7456 (t0) REVERT: B 651 TYR cc_start: 0.8189 (t80) cc_final: 0.7828 (t80) REVERT: E 87 TYR cc_start: 0.8376 (m-10) cc_final: 0.8103 (m-80) REVERT: F 60 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6704 (p90) REVERT: F 104 ARG cc_start: 0.7382 (ttm-80) cc_final: 0.6962 (ttm-80) REVERT: F 108 LEU cc_start: 0.4073 (pt) cc_final: 0.3200 (mt) outliers start: 29 outliers final: 23 residues processed: 184 average time/residue: 0.2273 time to fit residues: 60.7229 Evaluate side-chains 184 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 92 optimal weight: 0.0870 chunk 138 optimal weight: 8.9990 chunk 93 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.268598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.231887 restraints weight = 28295.090| |-----------------------------------------------------------------------------| r_work (start): 0.4609 rms_B_bonded: 6.39 r_work (final): 0.4609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4609 r_free = 0.4609 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4609 r_free = 0.4609 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 11899 Z= 0.106 Angle : 0.597 8.369 16106 Z= 0.297 Chirality : 0.040 0.146 1812 Planarity : 0.003 0.050 1972 Dihedral : 9.140 59.427 1778 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.59 % Allowed : 12.85 % Favored : 84.56 % 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: -2.46 (0.22), residues: 1400 helix: -0.94 (0.19), residues: 734 sheet: -2.40 (0.44), residues: 138 loop : -2.27 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 223 HIS 0.001 0.000 HIS A 27 PHE 0.022 0.001 PHE C 71 TYR 0.013 0.001 TYR D 32 ARG 0.004 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 387) hydrogen bonds : angle 4.66256 ( 1099) SS BOND : bond 0.00089 ( 4) SS BOND : angle 0.64520 ( 8) covalent geometry : bond 0.00247 (11892) covalent geometry : angle 0.59667 (16098) Misc. bond : bond 0.00042 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 ASP cc_start: 0.7523 (t0) cc_final: 0.6931 (t0) REVERT: B 651 TYR cc_start: 0.8088 (t80) cc_final: 0.7795 (t80) REVERT: C 4 MET cc_start: 0.5525 (ptp) cc_final: 0.5324 (ptp) REVERT: C 86 TYR cc_start: 0.6623 (m-80) cc_final: 0.6319 (m-80) REVERT: E 87 TYR cc_start: 0.7893 (m-10) cc_final: 0.7638 (m-80) REVERT: F 104 ARG cc_start: 0.6650 (ttm-80) cc_final: 0.6206 (ttm-80) REVERT: F 108 LEU cc_start: 0.3183 (pt) cc_final: 0.2829 (mt) outliers start: 27 outliers final: 21 residues processed: 178 average time/residue: 0.2340 time to fit residues: 60.9062 Evaluate side-chains 176 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 136 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 93 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** D 28 ASN ** 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 = 0.4892 r_free = 0.4892 target = 0.266552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.245854 restraints weight = 24871.288| |-----------------------------------------------------------------------------| r_work (start): 0.4734 rms_B_bonded: 2.59 r_work (final): 0.4734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4734 r_free = 0.4734 target_work(ls_wunit_k1) = 0.246 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4734 r_free = 0.4734 target_work(ls_wunit_k1) = 0.246 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11899 Z= 0.122 Angle : 0.613 8.938 16106 Z= 0.305 Chirality : 0.041 0.148 1812 Planarity : 0.003 0.042 1972 Dihedral : 9.177 59.274 1778 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.92 % Allowed : 12.85 % Favored : 84.22 % 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: -2.27 (0.22), residues: 1400 helix: -0.76 (0.19), residues: 734 sheet: -2.24 (0.44), residues: 138 loop : -2.23 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 103 HIS 0.001 0.000 HIS F 35 PHE 0.021 0.001 PHE C 71 TYR 0.016 0.001 TYR D 32 ARG 0.006 0.000 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.03315 ( 387) hydrogen bonds : angle 4.63063 ( 1099) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.63370 ( 8) covalent geometry : bond 0.00290 (11892) covalent geometry : angle 0.61283 (16098) Misc. bond : bond 0.00073 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 651 TYR cc_start: 0.8155 (t80) cc_final: 0.7867 (t80) REVERT: C 4 MET cc_start: 0.5472 (ptp) cc_final: 0.5114 (ptp) REVERT: E 87 TYR cc_start: 0.7946 (m-10) cc_final: 0.7667 (m-80) REVERT: F 104 ARG cc_start: 0.6530 (ttm-80) cc_final: 0.6148 (ttm-80) REVERT: F 108 LEU cc_start: 0.3413 (pt) cc_final: 0.2901 (mt) outliers start: 31 outliers final: 22 residues processed: 182 average time/residue: 0.2346 time to fit residues: 62.2883 Evaluate side-chains 182 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 96 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 0.0980 chunk 75 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 GLN ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.268389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.248064 restraints weight = 28087.113| |-----------------------------------------------------------------------------| r_work (start): 0.4753 rms_B_bonded: 2.78 r_work (final): 0.4753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4753 r_free = 0.4753 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4753 r_free = 0.4753 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11899 Z= 0.113 Angle : 0.604 9.727 16106 Z= 0.300 Chirality : 0.041 0.146 1812 Planarity : 0.003 0.038 1972 Dihedral : 8.909 58.373 1778 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.67 % Allowed : 13.44 % Favored : 83.89 % 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: -2.05 (0.22), residues: 1400 helix: -0.56 (0.19), residues: 734 sheet: -2.10 (0.45), residues: 138 loop : -2.18 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 632 HIS 0.000 0.000 HIS A 27 PHE 0.021 0.001 PHE C 71 TYR 0.015 0.001 TYR B 639 ARG 0.004 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03226 ( 387) hydrogen bonds : angle 4.56077 ( 1099) SS BOND : bond 0.00141 ( 4) SS BOND : angle 0.55288 ( 8) covalent geometry : bond 0.00266 (11892) covalent geometry : angle 0.60379 (16098) Misc. bond : bond 0.00057 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 TYR cc_start: 0.8148 (t80) cc_final: 0.7890 (t80) REVERT: B 651 TYR cc_start: 0.8186 (t80) cc_final: 0.7815 (t80) REVERT: C 4 MET cc_start: 0.5369 (ptp) cc_final: 0.5144 (ptp) REVERT: C 86 TYR cc_start: 0.6681 (m-80) cc_final: 0.6389 (m-80) REVERT: E 87 TYR cc_start: 0.8135 (m-10) cc_final: 0.7868 (m-80) REVERT: F 108 LEU cc_start: 0.3272 (pt) cc_final: 0.2902 (mt) outliers start: 28 outliers final: 23 residues processed: 182 average time/residue: 0.2249 time to fit residues: 60.8889 Evaluate side-chains 182 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 35 optimal weight: 0.0030 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN F 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.267411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.240725 restraints weight = 28848.648| |-----------------------------------------------------------------------------| r_work (start): 0.4683 rms_B_bonded: 3.93 r_work (final): 0.4683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4683 r_free = 0.4683 target_work(ls_wunit_k1) = 0.240 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4683 r_free = 0.4683 target_work(ls_wunit_k1) = 0.240 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11899 Z= 0.124 Angle : 0.613 9.903 16106 Z= 0.305 Chirality : 0.041 0.156 1812 Planarity : 0.004 0.061 1972 Dihedral : 8.961 58.476 1778 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.34 % Allowed : 14.02 % Favored : 83.64 % 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: -1.96 (0.22), residues: 1400 helix: -0.48 (0.19), residues: 736 sheet: -2.00 (0.45), residues: 138 loop : -2.18 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 632 HIS 0.001 0.000 HIS F 35 PHE 0.020 0.001 PHE C 71 TYR 0.016 0.001 TYR D 32 ARG 0.009 0.000 ARG B 398 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 387) hydrogen bonds : angle 4.54559 ( 1099) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.58816 ( 8) covalent geometry : bond 0.00295 (11892) covalent geometry : angle 0.61329 (16098) Misc. bond : bond 0.00073 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 TYR cc_start: 0.8130 (t80) cc_final: 0.7884 (t80) REVERT: B 651 TYR cc_start: 0.8139 (t80) cc_final: 0.7785 (t80) REVERT: E 87 TYR cc_start: 0.8030 (m-10) cc_final: 0.7751 (m-80) REVERT: F 108 LEU cc_start: 0.3423 (pt) cc_final: 0.2936 (mt) outliers start: 24 outliers final: 22 residues processed: 178 average time/residue: 0.2281 time to fit residues: 59.9487 Evaluate side-chains 178 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain B residue 96 ASN Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 105 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 137 optimal weight: 0.0670 chunk 134 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 108 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.267623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.236156 restraints weight = 26368.796| |-----------------------------------------------------------------------------| r_work (start): 0.4652 rms_B_bonded: 5.00 r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4652 r_free = 0.4652 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4652 r_free = 0.4652 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11899 Z= 0.118 Angle : 0.613 9.954 16106 Z= 0.305 Chirality : 0.041 0.155 1812 Planarity : 0.003 0.054 1972 Dihedral : 8.862 58.118 1778 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.75 % Allowed : 13.61 % Favored : 83.64 % 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: -1.78 (0.22), residues: 1400 helix: -0.35 (0.19), residues: 734 sheet: -1.85 (0.46), residues: 138 loop : -2.08 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 632 HIS 0.001 0.000 HIS F 35 PHE 0.020 0.001 PHE C 71 TYR 0.015 0.001 TYR D 32 ARG 0.003 0.000 ARG B 325 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 387) hydrogen bonds : angle 4.51215 ( 1099) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.53959 ( 8) covalent geometry : bond 0.00281 (11892) covalent geometry : angle 0.61262 (16098) Misc. bond : bond 0.00068 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4550.98 seconds wall clock time: 79 minutes 25.87 seconds (4765.87 seconds total)