Starting phenix.real_space_refine on Tue Nov 18 11:33:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e1k_8956/11_2025/6e1k_8956_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e1k_8956/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/6e1k_8956/11_2025/6e1k_8956_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e1k_8956/11_2025/6e1k_8956_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6e1k_8956/11_2025/6e1k_8956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e1k_8956/11_2025/6e1k_8956.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'TPO:plan-1': 2, 'PHE:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} 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: {'TPO:plan-1': 2, 'PHE:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASP:plan': 3, 'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1} 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: {'ARG:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 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: {'ARG:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 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, 'ARG:plan': 1, 'GLU: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, 'ARG:plan': 1, 'GLU: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: {'ARG:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 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: {'ARG:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 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, 'ARG:plan': 1, 'GLU: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, 'ARG:plan': 1, 'GLU: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: 3.35, per 1000 atoms: 0.29 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: 1.04 Conformation dependent library (CDL) restraints added in 655.8 milliseconds 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: 0.39 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: 1.75 Time building geometry restraints manager: 1.36 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 803 or resid 805 through 809)) selection = (chain 'B' and (resid 22 through 803 or resid 805 through 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.520 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.530 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.010 0.001 ARG F 98 TYR 0.055 0.007 TYR A 107 PHE 0.040 0.006 PHE A 587 TRP 0.033 0.007 TRP B 271 HIS 0.007 0.003 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.01863 (11892) covalent geometry : angle 1.75710 (16098) SS BOND : bond 0.00369 ( 4) SS BOND : angle 2.11665 ( 8) hydrogen bonds : bond 0.30055 ( 387) hydrogen bonds : angle 11.45697 ( 1099) 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 : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.2877 (p90) cc_final: 0.2491 (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: 0.6952 (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: 0.7456 (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: 0.8010 (mmtm) REVERT: B 77 ASN cc_start: 0.7792 (m-40) cc_final: 0.6700 (t0) REVERT: B 189 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.7025 (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: 0.6943 (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: 0.7713 (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: 0.6253 (t80) REVERT: F 59 SER cc_start: 0.7559 (t) cc_final: 0.7330 (m) REVERT: F 108 LEU cc_start: 0.5705 (pt) cc_final: 0.4096 (tp) outliers start: 14 outliers final: 7 residues processed: 262 average time/residue: 0.1216 time to fit residues: 44.3072 Evaluate side-chains 178 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 242 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4878 r_free = 0.4878 target = 0.265016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.244817 restraints weight = 28130.708| |-----------------------------------------------------------------------------| r_work (start): 0.4723 rms_B_bonded: 2.83 r_work (final): 0.4723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4723 r_free = 0.4723 target_work(ls_wunit_k1) = 0.246 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4723 r_free = 0.4723 target_work(ls_wunit_k1) = 0.246 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11899 Z= 0.172 Angle : 0.778 11.274 16106 Z= 0.404 Chirality : 0.045 0.178 1812 Planarity : 0.005 0.058 1972 Dihedral : 12.654 59.939 1790 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.50 % Allowed : 6.68 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.75 (0.18), residues: 1400 helix: -3.01 (0.15), residues: 674 sheet: -3.74 (0.34), residues: 144 loop : -2.96 (0.23), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 279 TYR 0.027 0.002 TYR A 305 PHE 0.020 0.002 PHE B 624 TRP 0.016 0.002 TRP D 114 HIS 0.002 0.001 HIS B 27 Details of bonding type rmsd covalent geometry : bond 0.00396 (11892) covalent geometry : angle 0.77790 (16098) SS BOND : bond 0.00139 ( 4) SS BOND : angle 0.51344 ( 8) hydrogen bonds : bond 0.04779 ( 387) hydrogen bonds : angle 6.27452 ( 1099) Misc. bond : bond 0.00090 ( 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 218 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LEU cc_start: 0.7045 (mt) cc_final: 0.6835 (mt) REVERT: A 189 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6815 (m-10) REVERT: A 319 MET cc_start: 0.6127 (tpt) cc_final: 0.5669 (tpt) REVERT: A 651 TYR cc_start: 0.8028 (t80) cc_final: 0.7534 (t80) REVERT: B 189 TYR cc_start: 0.7461 (OUTLIER) cc_final: 0.6959 (m-10) REVERT: B 212 MET cc_start: 0.7366 (mtm) cc_final: 0.7160 (mtp) REVERT: B 242 GLN cc_start: 0.7161 (tp-100) cc_final: 0.6224 (tt0) REVERT: B 620 MET cc_start: 0.7592 (tpt) cc_final: 0.7260 (tpt) REVERT: B 651 TYR cc_start: 0.8141 (t80) cc_final: 0.7606 (t80) REVERT: F 28 ASN cc_start: 0.6276 (OUTLIER) cc_final: 0.5953 (t0) REVERT: F 108 LEU cc_start: 0.3551 (pt) cc_final: 0.3172 (mt) outliers start: 26 outliers final: 8 residues processed: 206 average time/residue: 0.1088 time to fit residues: 31.8367 Evaluate side-chains 167 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 TYR Chi-restraints excluded: chain A residue 612 ASN 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 105 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 1 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 GLN A 612 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.265086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.244244 restraints weight = 28642.419| |-----------------------------------------------------------------------------| r_work (start): 0.4716 rms_B_bonded: 2.88 r_work (final): 0.4716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4716 r_free = 0.4716 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4716 r_free = 0.4716 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.3307 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= 0.143 Angle : 0.682 9.197 16106 Z= 0.351 Chirality : 0.043 0.156 1812 Planarity : 0.004 0.052 1972 Dihedral : 11.564 59.712 1786 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.84 % Allowed : 8.68 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.94 (0.20), residues: 1400 helix: -2.29 (0.17), residues: 694 sheet: -3.30 (0.39), residues: 134 loop : -2.67 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 145 TYR 0.029 0.002 TYR D 32 PHE 0.026 0.002 PHE E 71 TRP 0.021 0.001 TRP D 114 HIS 0.003 0.001 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00327 (11892) covalent geometry : angle 0.68229 (16098) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.48386 ( 8) hydrogen bonds : bond 0.04004 ( 387) hydrogen bonds : angle 5.45714 ( 1099) Misc. bond : bond 0.00080 ( 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 197 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 242 GLN cc_start: 0.7278 (tp-100) cc_final: 0.6449 (tt0) REVERT: B 620 MET cc_start: 0.7573 (tpt) cc_final: 0.6867 (tpt) REVERT: F 28 ASN cc_start: 0.6538 (m-40) cc_final: 0.5947 (t0) outliers start: 18 outliers final: 10 residues processed: 190 average time/residue: 0.1120 time to fit residues: 30.6907 Evaluate side-chains 176 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASN 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 194 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 105 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 128 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 117 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 57 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 585 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 = 0.266559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.246292 restraints weight = 25240.703| |-----------------------------------------------------------------------------| r_work (start): 0.4736 rms_B_bonded: 2.64 r_work (final): 0.4736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4736 r_free = 0.4736 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4736 r_free = 0.4736 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11899 Z= 0.126 Angle : 0.638 9.356 16106 Z= 0.324 Chirality : 0.042 0.146 1812 Planarity : 0.004 0.096 1972 Dihedral : 10.711 59.181 1780 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.25 % Allowed : 9.35 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.21), residues: 1400 helix: -1.79 (0.18), residues: 714 sheet: -2.84 (0.43), residues: 138 loop : -2.45 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 104 TYR 0.015 0.002 TYR A 305 PHE 0.019 0.001 PHE C 71 TRP 0.012 0.001 TRP D 114 HIS 0.001 0.000 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00292 (11892) covalent geometry : angle 0.63821 (16098) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.31620 ( 8) hydrogen bonds : bond 0.03579 ( 387) hydrogen bonds : angle 5.09540 ( 1099) Misc. bond : bond 0.00069 ( 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 211 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 242 GLN cc_start: 0.7346 (tp-100) cc_final: 0.6456 (tt0) REVERT: B 620 MET cc_start: 0.7650 (tpt) cc_final: 0.7087 (tpt) REVERT: B 651 TYR cc_start: 0.8152 (t80) cc_final: 0.7865 (t80) REVERT: F 60 TYR cc_start: 0.5974 (OUTLIER) cc_final: 0.5680 (p90) REVERT: F 108 LEU cc_start: 0.3379 (pt) cc_final: 0.2975 (mt) outliers start: 23 outliers final: 11 residues processed: 199 average time/residue: 0.1092 time to fit residues: 31.1749 Evaluate side-chains 173 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 110 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 47 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 257 GLN A 585 GLN ** B 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4810 r_free = 0.4810 target = 0.255866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.233438 restraints weight = 24376.486| |-----------------------------------------------------------------------------| r_work (start): 0.4639 rms_B_bonded: 1.52 r_work: 0.4366 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4375 r_free = 0.4375 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4375 r_free = 0.4375 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11899 Z= 0.258 Angle : 0.788 11.317 16106 Z= 0.397 Chirality : 0.047 0.181 1812 Planarity : 0.005 0.056 1972 Dihedral : 11.246 59.989 1780 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.01 % Allowed : 10.60 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.21), residues: 1400 helix: -1.78 (0.18), residues: 716 sheet: -2.90 (0.43), residues: 140 loop : -2.62 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 104 TYR 0.030 0.003 TYR D 32 PHE 0.027 0.002 PHE E 71 TRP 0.021 0.002 TRP F 101 HIS 0.001 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00618 (11892) covalent geometry : angle 0.78843 (16098) SS BOND : bond 0.00392 ( 4) SS BOND : angle 0.89309 ( 8) hydrogen bonds : bond 0.04352 ( 387) hydrogen bonds : angle 5.35483 ( 1099) Misc. bond : bond 0.00197 ( 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 208 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 176 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ARG cc_start: 0.6942 (ttp-110) cc_final: 0.6153 (ttp-110) REVERT: A 607 ASP cc_start: 0.7867 (t0) cc_final: 0.7639 (t0) REVERT: F 28 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6442 (t0) REVERT: F 104 ARG cc_start: 0.7348 (ttm-80) cc_final: 0.7085 (ttm-80) REVERT: F 108 LEU cc_start: 0.4831 (pt) cc_final: 0.3565 (mt) outliers start: 32 outliers final: 17 residues processed: 194 average time/residue: 0.1100 time to fit residues: 30.6520 Evaluate side-chains 174 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 210 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 620 MET 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 342 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain B residue 663 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 11 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.259167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.239272 restraints weight = 25951.541| |-----------------------------------------------------------------------------| r_work (start): 0.4684 rms_B_bonded: 2.63 r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4684 r_free = 0.4684 target_work(ls_wunit_k1) = 0.240 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4684 r_free = 0.4684 target_work(ls_wunit_k1) = 0.240 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11899 Z= 0.173 Angle : 0.703 9.389 16106 Z= 0.354 Chirality : 0.043 0.152 1812 Planarity : 0.004 0.054 1972 Dihedral : 10.736 59.841 1778 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.84 % Allowed : 12.35 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.21), residues: 1400 helix: -1.57 (0.18), residues: 714 sheet: -2.67 (0.43), residues: 136 loop : -2.48 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 104 TYR 0.020 0.002 TYR D 32 PHE 0.027 0.002 PHE E 71 TRP 0.014 0.002 TRP F 101 HIS 0.001 0.000 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00415 (11892) covalent geometry : angle 0.70128 (16098) SS BOND : bond 0.00193 ( 4) SS BOND : angle 2.36767 ( 8) hydrogen bonds : bond 0.03823 ( 387) hydrogen bonds : angle 5.23803 ( 1099) Misc. bond : bond 0.00112 ( 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 195 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 675 PHE cc_start: 0.8375 (t80) cc_final: 0.8147 (t80) REVERT: B 151 ARG cc_start: 0.6628 (tpm170) cc_final: 0.6379 (tpp-160) REVERT: C 48 ILE cc_start: 0.6192 (mm) cc_final: 0.5805 (mt) REVERT: F 104 ARG cc_start: 0.6657 (ttm-80) cc_final: 0.6379 (ttm-80) REVERT: F 108 LEU cc_start: 0.4070 (pt) cc_final: 0.3221 (mt) outliers start: 30 outliers final: 22 residues processed: 185 average time/residue: 0.1117 time to fit residues: 29.4412 Evaluate side-chains 179 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 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 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 264 THR Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 105 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 126 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 53 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4835 r_free = 0.4835 target = 0.258880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.237832 restraints weight = 28330.137| |-----------------------------------------------------------------------------| r_work (start): 0.4667 rms_B_bonded: 2.88 r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4667 r_free = 0.4667 target_work(ls_wunit_k1) = 0.238 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4667 r_free = 0.4667 target_work(ls_wunit_k1) = 0.238 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11899 Z= 0.180 Angle : 0.701 9.710 16106 Z= 0.352 Chirality : 0.043 0.151 1812 Planarity : 0.004 0.055 1972 Dihedral : 10.454 59.410 1778 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.01 % Allowed : 12.77 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.21), residues: 1400 helix: -1.38 (0.18), residues: 722 sheet: -2.68 (0.43), residues: 138 loop : -2.36 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.020 0.002 TYR F 32 PHE 0.022 0.002 PHE C 71 TRP 0.021 0.002 TRP A 632 HIS 0.001 0.000 HIS A 27 Details of bonding type rmsd covalent geometry : bond 0.00433 (11892) covalent geometry : angle 0.69902 (16098) SS BOND : bond 0.00261 ( 4) SS BOND : angle 2.26419 ( 8) hydrogen bonds : bond 0.03766 ( 387) hydrogen bonds : angle 5.17137 ( 1099) Misc. bond : bond 0.00124 ( 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 200 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.7708 (t0) cc_final: 0.7229 (t0) REVERT: B 151 ARG cc_start: 0.6592 (tpm170) cc_final: 0.6359 (tpp-160) REVERT: F 104 ARG cc_start: 0.6738 (ttm-80) cc_final: 0.6214 (ttm-80) REVERT: F 108 LEU cc_start: 0.4148 (pt) cc_final: 0.3296 (mt) outliers start: 32 outliers final: 24 residues processed: 186 average time/residue: 0.1105 time to fit residues: 29.6831 Evaluate side-chains 183 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 122 ILE Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 206 LEU 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 B residue 620 MET Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 29 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 96 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 63 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 135 optimal weight: 0.6980 chunk 122 optimal weight: 0.0270 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.264792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.232633 restraints weight = 17094.329| |-----------------------------------------------------------------------------| r_work (start): 0.4630 rms_B_bonded: 2.38 r_work (final): 0.4630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4630 r_free = 0.4630 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4630 r_free = 0.4630 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.4539 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= 0.116 Angle : 0.620 8.081 16106 Z= 0.312 Chirality : 0.041 0.145 1812 Planarity : 0.003 0.048 1972 Dihedral : 9.396 59.711 1778 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.34 % Allowed : 13.61 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.22), residues: 1400 helix: -1.09 (0.19), residues: 728 sheet: -2.36 (0.45), residues: 136 loop : -2.33 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 398 TYR 0.015 0.001 TYR D 32 PHE 0.020 0.001 PHE C 71 TRP 0.014 0.001 TRP B 632 HIS 0.001 0.000 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00269 (11892) covalent geometry : angle 0.61943 (16098) SS BOND : bond 0.00093 ( 4) SS BOND : angle 1.53662 ( 8) hydrogen bonds : bond 0.03329 ( 387) hydrogen bonds : angle 4.88797 ( 1099) Misc. bond : bond 0.00059 ( 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 193 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.7365 (tp) cc_final: 0.7147 (tp) REVERT: F 104 ARG cc_start: 0.6606 (ttm-80) cc_final: 0.6188 (ttm-80) REVERT: F 108 LEU cc_start: 0.3422 (pt) cc_final: 0.2856 (mt) outliers start: 24 outliers final: 18 residues processed: 184 average time/residue: 0.0973 time to fit residues: 26.7354 Evaluate side-chains 176 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 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 A residue 660 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain D residue 29 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 F residue 60 TYR 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 17 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 141 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 127 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.263813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.242749 restraints weight = 21921.482| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 2.39 r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4711 r_free = 0.4711 target_work(ls_wunit_k1) = 0.243 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4711 r_free = 0.4711 target_work(ls_wunit_k1) = 0.243 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11899 Z= 0.130 Angle : 0.636 7.881 16106 Z= 0.319 Chirality : 0.042 0.145 1812 Planarity : 0.003 0.044 1972 Dihedral : 9.217 59.069 1778 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.84 % Allowed : 14.69 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.22), residues: 1400 helix: -0.91 (0.19), residues: 728 sheet: -2.13 (0.47), residues: 130 loop : -2.32 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 398 TYR 0.017 0.002 TYR F 32 PHE 0.019 0.001 PHE C 71 TRP 0.015 0.001 TRP A 632 HIS 0.001 0.000 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00310 (11892) covalent geometry : angle 0.63506 (16098) SS BOND : bond 0.00177 ( 4) SS BOND : angle 1.37391 ( 8) hydrogen bonds : bond 0.03426 ( 387) hydrogen bonds : angle 4.87064 ( 1099) Misc. bond : bond 0.00075 ( 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 174 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 651 TYR cc_start: 0.8089 (t80) cc_final: 0.7803 (t80) REVERT: F 108 LEU cc_start: 0.3501 (pt) cc_final: 0.2919 (mt) outliers start: 18 outliers final: 15 residues processed: 168 average time/residue: 0.0970 time to fit residues: 24.4061 Evaluate side-chains 168 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 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 B residue 215 THR Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 659 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 F residue 60 TYR 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 74 optimal weight: 0.0050 chunk 91 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.262802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.240889 restraints weight = 26584.802| |-----------------------------------------------------------------------------| r_work (start): 0.4680 rms_B_bonded: 2.91 r_work (final): 0.4680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4680 r_free = 0.4680 target_work(ls_wunit_k1) = 0.239 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4680 r_free = 0.4680 target_work(ls_wunit_k1) = 0.239 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11899 Z= 0.154 Angle : 0.659 8.676 16106 Z= 0.331 Chirality : 0.043 0.157 1812 Planarity : 0.004 0.045 1972 Dihedral : 9.326 58.575 1778 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.92 % Allowed : 14.44 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.22), residues: 1400 helix: -0.85 (0.19), residues: 728 sheet: -2.11 (0.47), residues: 130 loop : -2.31 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 398 TYR 0.019 0.002 TYR D 32 PHE 0.020 0.001 PHE C 71 TRP 0.022 0.002 TRP B 632 HIS 0.001 0.000 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00369 (11892) covalent geometry : angle 0.65833 (16098) SS BOND : bond 0.00223 ( 4) SS BOND : angle 1.48881 ( 8) hydrogen bonds : bond 0.03538 ( 387) hydrogen bonds : angle 4.86864 ( 1099) Misc. bond : bond 0.00103 ( 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 172 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 104 ARG cc_start: 0.6472 (ttm-80) cc_final: 0.6005 (ttm-80) REVERT: F 108 LEU cc_start: 0.3956 (pt) cc_final: 0.3099 (mt) outliers start: 19 outliers final: 15 residues processed: 166 average time/residue: 0.1036 time to fit residues: 25.8548 Evaluate side-chains 164 residues out of total 1268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 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 B residue 215 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 659 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 60 TYR 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 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 0.0370 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.267001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4721 r_free = 0.4721 target = 0.245265 restraints weight = 25015.561| |-----------------------------------------------------------------------------| r_work (start): 0.4724 rms_B_bonded: 2.90 r_work (final): 0.4724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4714 r_free = 0.4714 target_work(ls_wunit_k1) = 0.243 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4714 r_free = 0.4714 target_work(ls_wunit_k1) = 0.243 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11899 Z= 0.125 Angle : 0.622 7.875 16106 Z= 0.313 Chirality : 0.041 0.153 1812 Planarity : 0.003 0.045 1972 Dihedral : 8.962 59.855 1778 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.25 % Allowed : 14.02 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.22), residues: 1400 helix: -0.67 (0.19), residues: 728 sheet: -2.17 (0.44), residues: 142 loop : -2.23 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 398 TYR 0.016 0.002 TYR A 639 PHE 0.019 0.001 PHE C 71 TRP 0.017 0.001 TRP B 632 HIS 0.001 0.000 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00297 (11892) covalent geometry : angle 0.62117 (16098) SS BOND : bond 0.00134 ( 4) SS BOND : angle 1.24385 ( 8) hydrogen bonds : bond 0.03345 ( 387) hydrogen bonds : angle 4.77164 ( 1099) Misc. bond : bond 0.00071 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.14 seconds wall clock time: 36 minutes 45.75 seconds (2205.75 seconds total)