Starting phenix.real_space_refine on Sun Sep 13 05:59:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6c1d_7329/09_2026/6c1d_7329.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c1d_7329/09_2026/6c1d_7329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6c1d_7329/09_2026/6c1d_7329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c1d_7329/09_2026/6c1d_7329.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6c1d_7329/09_2026/6c1d_7329.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6c1d_7329/09_2026/6c1d_7329.cif" model { file = "/net/cci-nas-00/data/ceres_data/6c1d_7329/09_2026/6c1d_7329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c1d_7329/09_2026/6c1d_7329.cif" } resolution = 3.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 127 5.16 5 C 13150 2.51 5 N 3638 2.21 5 O 4116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21049 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "B" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "C" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "D" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "E" Number of atoms: 2933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2933 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "P" Number of atoms: 5570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5570 Classifications: {'peptide': 729} Incomplete info: {'backbone_only': 71, 'n_c_alpha_c_only': 1} Link IDs: {'CIS': 4, 'PCIS': 3, 'PTRANS': 20, 'TRANS': 701} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 521 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 92 Planarities with less than four sites: {'TYR:plan': 4, 'GLU:plan': 8, 'ARG:plan': 6, 'GLN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 185 Chain: "R" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 591 Classifications: {'peptide': 148} Incomplete info: {'backbone_only': 136, 'n_c_alpha_c_only': 1} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 143} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 587 Unresolved non-hydrogen angles: 842 Unresolved non-hydrogen dihedrals: 357 Unresolved non-hydrogen chiralities: 173 Planarities with less than four sites: {'ASP:plan': 17, 'GLN:plan1': 6, 'GLU:plan': 21, 'PHE:plan': 8, 'ARG:plan': 6, 'ASN:plan1': 6, 'TYR:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 308 Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2TL:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'DCY:plan-1': 1, 'HYP:plan-1': 1, 'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.81, per 1000 atoms: 0.23 Number of scatterers: 21049 At special positions: 0 Unit cell: (202.8, 104, 193.7, 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) S 127 16.00 P 12 15.00 Mg 6 11.99 O 4116 8.00 N 3638 7.00 C 13150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.3 seconds 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 2TL F 2 " Input residue name is d-peptide pdb=" CB DCY F 3 " Number of C-beta restraints generated: 4724 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 32 sheets defined 49.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.677A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.589A pdb=" N LEU A 65 " --> pdb=" O ARG A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.812A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.529A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.820A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.031A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.678A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.588A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.811A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 181 through 197 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.529A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.819A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.031A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.678A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.588A pdb=" N LEU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.810A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 Processing helix chain 'C' and resid 181 through 197 Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.529A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.819A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 351 through 355 removed outlier: 4.031A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.678A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.588A pdb=" N LEU D 65 " --> pdb=" O ARG D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.811A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 181 through 197 Processing helix chain 'D' and resid 202 through 216 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.529A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.820A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.031A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.677A pdb=" N GLN E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.588A pdb=" N LEU E 65 " --> pdb=" O ARG E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.811A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 144 Processing helix chain 'E' and resid 181 through 197 Processing helix chain 'E' and resid 202 through 216 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.529A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 264 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.820A pdb=" N ALA E 319 " --> pdb=" O LYS E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 351 through 355 removed outlier: 4.031A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'P' and resid 28 through 41 removed outlier: 3.709A pdb=" N ASN P 34 " --> pdb=" O THR P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 72 Processing helix chain 'P' and resid 83 through 97 removed outlier: 3.890A pdb=" N LEU P 87 " --> pdb=" O HIS P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 113 through 128 Processing helix chain 'P' and resid 134 through 153 removed outlier: 4.184A pdb=" N VAL P 138 " --> pdb=" O GLU P 134 " (cutoff:3.500A) Proline residue: P 147 - end of helix Processing helix chain 'P' and resid 206 through 214 Processing helix chain 'P' and resid 216 through 223 Processing helix chain 'P' and resid 249 through 262 Processing helix chain 'P' and resid 264 through 281 Processing helix chain 'P' and resid 282 through 284 No H-bonds generated for 'chain 'P' and resid 282 through 284' Processing helix chain 'P' and resid 303 through 314 Processing helix chain 'P' and resid 316 through 325 removed outlier: 3.821A pdb=" N SER P 325 " --> pdb=" O GLU P 321 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 370 Processing helix chain 'P' and resid 398 through 417 Processing helix chain 'P' and resid 417 through 430 Processing helix chain 'P' and resid 442 through 450 Processing helix chain 'P' and resid 455 through 466 removed outlier: 3.668A pdb=" N MET P 459 " --> pdb=" O GLY P 455 " (cutoff:3.500A) Processing helix chain 'P' and resid 471 through 482 Processing helix chain 'P' and resid 525 through 531 removed outlier: 4.016A pdb=" N ASN P 531 " --> pdb=" O VAL P 527 " (cutoff:3.500A) Processing helix chain 'P' and resid 535 through 543 removed outlier: 3.517A pdb=" N SER P 539 " --> pdb=" O TYR P 535 " (cutoff:3.500A) Processing helix chain 'P' and resid 549 through 554 Processing helix chain 'P' and resid 555 through 558 Processing helix chain 'P' and resid 570 through 584 Processing helix chain 'P' and resid 608 through 620 removed outlier: 3.602A pdb=" N VAL P 612 " --> pdb=" O SER P 608 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY P 620 " --> pdb=" O ILE P 616 " (cutoff:3.500A) Processing helix chain 'P' and resid 620 through 629 Processing helix chain 'P' and resid 638 through 646 Processing helix chain 'P' and resid 647 through 649 No H-bonds generated for 'chain 'P' and resid 647 through 649' Processing helix chain 'P' and resid 659 through 671 removed outlier: 3.691A pdb=" N LEU P 671 " --> pdb=" O LEU P 667 " (cutoff:3.500A) Processing helix chain 'P' and resid 689 through 730 removed outlier: 3.772A pdb=" N LEU P 693 " --> pdb=" O ASN P 689 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP P 706 " --> pdb=" O GLN P 702 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 20 Processing helix chain 'R' and resid 31 through 40 Processing helix chain 'R' and resid 44 through 56 Processing helix chain 'R' and resid 64 through 75 Processing helix chain 'R' and resid 81 through 93 removed outlier: 3.598A pdb=" N ILE R 85 " --> pdb=" O SER R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 112 Processing helix chain 'R' and resid 117 through 128 removed outlier: 3.663A pdb=" N VAL R 121 " --> pdb=" O THR R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 146 removed outlier: 3.732A pdb=" N GLN R 143 " --> pdb=" O GLU R 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.800A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.800A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.800A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.799A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.801A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'P' and resid 45 through 47 removed outlier: 6.212A pdb=" N VAL P 52 " --> pdb=" O ARG P 594 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE P 596 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER P 54 " --> pdb=" O ILE P 596 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLN P 102 " --> pdb=" O GLY P 384 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N LEU P 386 " --> pdb=" O GLN P 102 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE P 104 " --> pdb=" O LEU P 386 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY P 182 " --> pdb=" O GLU P 173 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP P 175 " --> pdb=" O PRO P 180 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 154 through 155 Processing sheet with id=AD1, first strand: chain 'P' and resid 286 through 289 Processing sheet with id=AD2, first strand: chain 'P' and resid 326 through 329 Processing sheet with id=AD3, first strand: chain 'P' and resid 489 through 490 Processing sheet with id=AD4, first strand: chain 'P' and resid 634 through 637 removed outlier: 3.541A pdb=" N PHE P 686 " --> pdb=" O SER P 679 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 99 through 101 1013 hydrogen bonds defined for protein. 2811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 3628 1.28 - 1.42: 5365 1.42 - 1.56: 12233 1.56 - 1.69: 24 1.69 - 1.83: 217 Bond restraints: 21467 Sorted by residual: bond pdb=" CA ALA F 1 " pdb=" C ALA F 1 " ideal model delta sigma weight residual 1.525 1.318 0.207 2.10e-02 2.27e+03 9.67e+01 bond pdb=" NE1 TRP F 6 " pdb=" CE2 TRP F 6 " ideal model delta sigma weight residual 1.370 1.294 0.076 1.10e-02 8.26e+03 4.82e+01 bond pdb=" CA TRP F 6 " pdb=" C TRP F 6 " ideal model delta sigma weight residual 1.525 1.384 0.141 2.10e-02 2.27e+03 4.53e+01 bond pdb=" CA ALA F 5 " pdb=" C ALA F 5 " ideal model delta sigma weight residual 1.525 1.386 0.139 2.10e-02 2.27e+03 4.38e+01 bond pdb=" CD1 TRP F 6 " pdb=" NE1 TRP F 6 " ideal model delta sigma weight residual 1.374 1.236 0.138 2.10e-02 2.27e+03 4.35e+01 ... (remaining 21462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.06: 28777 5.06 - 10.13: 208 10.13 - 15.19: 8 15.19 - 20.26: 2 20.26 - 25.32: 2 Bond angle restraints: 28997 Sorted by residual: angle pdb=" CA DCY F 3 " pdb=" C DCY F 3 " pdb=" N HYP F 4 " ideal model delta sigma weight residual 116.20 141.52 -25.32 2.00e+00 2.50e-01 1.60e+02 angle pdb=" CA DCY F 3 " pdb=" C DCY F 3 " pdb=" O DCY F 3 " ideal model delta sigma weight residual 120.80 104.70 16.10 1.70e+00 3.46e-01 8.97e+01 angle pdb=" CA DCY F 3 " pdb=" CB DCY F 3 " pdb=" SG DCY F 3 " ideal model delta sigma weight residual 109.00 130.36 -21.36 3.00e+00 1.11e-01 5.07e+01 angle pdb=" N TRP F 6 " pdb=" CA TRP F 6 " pdb=" CB TRP F 6 " ideal model delta sigma weight residual 110.50 98.65 11.85 1.70e+00 3.46e-01 4.86e+01 angle pdb=" N DCY F 3 " pdb=" CA DCY F 3 " pdb=" CB DCY F 3 " ideal model delta sigma weight residual 110.40 120.41 -10.01 1.50e+00 4.44e-01 4.46e+01 ... (remaining 28992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.93: 12355 26.93 - 53.86: 250 53.86 - 80.78: 25 80.78 - 107.71: 1 107.71 - 134.64: 5 Dihedral angle restraints: 12636 sinusoidal: 5056 harmonic: 7580 Sorted by residual: dihedral pdb=" CA DCY F 3 " pdb=" C DCY F 3 " pdb=" N HYP F 4 " pdb=" CA HYP F 4 " ideal model delta harmonic sigma weight residual -180.00 -112.33 -67.67 0 5.00e+00 4.00e-02 1.83e+02 dihedral pdb=" CA HIS P 436 " pdb=" C HIS P 436 " pdb=" N ILE P 437 " pdb=" CA ILE P 437 " ideal model delta harmonic sigma weight residual -180.00 -145.76 -34.24 0 5.00e+00 4.00e-02 4.69e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 74.64 -134.64 1 2.00e+01 2.50e-03 4.09e+01 ... (remaining 12633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.319: 3076 0.319 - 0.638: 10 0.638 - 0.956: 0 0.956 - 1.275: 0 1.275 - 1.594: 1 Chirality restraints: 3087 Sorted by residual: chirality pdb=" CA DCY F 3 " pdb=" N DCY F 3 " pdb=" C DCY F 3 " pdb=" CB DCY F 3 " both_signs ideal model delta sigma weight residual False -2.48 -0.89 -1.59 2.00e-01 2.50e+01 6.35e+01 chirality pdb=" CA 2TL F 2 " pdb=" N 2TL F 2 " pdb=" C 2TL F 2 " pdb=" CB 2TL F 2 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" CA ALA F 5 " pdb=" N ALA F 5 " pdb=" C ALA F 5 " pdb=" CB ALA F 5 " both_signs ideal model delta sigma weight residual False 2.48 1.98 0.50 2.00e-01 2.50e+01 6.26e+00 ... (remaining 3084 not shown) Planarity restraints: 3809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 6 " -0.148 2.00e-02 2.50e+03 1.26e-01 3.96e+02 pdb=" CG TRP F 6 " 0.166 2.00e-02 2.50e+03 pdb=" CD1 TRP F 6 " -0.193 2.00e-02 2.50e+03 pdb=" CD2 TRP F 6 " 0.071 2.00e-02 2.50e+03 pdb=" NE1 TRP F 6 " 0.097 2.00e-02 2.50e+03 pdb=" CE2 TRP F 6 " 0.137 2.00e-02 2.50e+03 pdb=" CE3 TRP F 6 " 0.081 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 6 " -0.045 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 6 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 6 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 332 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C PRO E 332 " -0.047 2.00e-02 2.50e+03 pdb=" O PRO E 332 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO E 333 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 332 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C PRO B 332 " 0.046 2.00e-02 2.50e+03 pdb=" O PRO B 332 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO B 333 " -0.016 2.00e-02 2.50e+03 ... (remaining 3806 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 5 2.26 - 2.92: 8503 2.92 - 3.58: 30094 3.58 - 4.24: 52309 4.24 - 4.90: 86034 Nonbonded interactions: 176945 Sorted by model distance: nonbonded pdb=" SG DCY F 3 " pdb=" CD1 TRP F 6 " model vdw 1.605 3.620 nonbonded pdb=" SG DCY F 3 " pdb=" NE1 TRP F 6 " model vdw 2.078 3.480 nonbonded pdb=" NH2 ARG P 231 " pdb=" OE2 GLU P 305 " model vdw 2.093 3.120 nonbonded pdb=" CG ARG E 183 " pdb=" NH2 ARG E 206 " model vdw 2.191 3.520 nonbonded pdb=" OG1 THR P 115 " pdb="MG MG P 801 " model vdw 2.234 2.170 ... (remaining 176940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=1.00 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: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.590 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 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 : 0.011 0.394 21471 Z= 0.596 Angle : 1.216 25.321 28997 Z= 0.668 Chirality : 0.077 1.594 3087 Planarity : 0.008 0.126 3809 Dihedral : 11.447 134.637 7912 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.06 % Allowed : 4.24 % Favored : 94.71 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.37 (0.12), residues: 2738 helix: -2.91 (0.10), residues: 1215 sheet: -2.84 (0.21), residues: 400 loop : -2.67 (0.15), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 335 TYR 0.026 0.003 TYR P 389 PHE 0.041 0.004 PHE P 415 TRP 0.193 0.010 TRP F 6 HIS 0.029 0.004 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.01020 / 0.44 (21467) covalent geometry : angle 1.21584 / 0.67 (28997) hydrogen bonds : bond 0.15481 / 10.44 ( 1013) hydrogen bonds : angle 9.62527 / 6.72 ( 2811) Misc. bond : bond 0.29265 / 14.68 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 351 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 47 MET cc_start: 0.7555 (tpt) cc_final: 0.7215 (tpt) REVERT: D 263 GLN cc_start: 0.7984 (tt0) cc_final: 0.7723 (tt0) REVERT: D 325 MET cc_start: 0.7639 (mmp) cc_final: 0.7281 (mmt) outliers start: 23 outliers final: 4 residues processed: 373 average time/residue: 0.1899 time to fit residues: 104.0357 Evaluate side-chains 165 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 244 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 0.0020 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 40 HIS A 73 HIS ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN A 246 GLN B 12 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 246 GLN C 12 ASN C 59 GLN C 73 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN D 12 ASN D 73 HIS D 87 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN D 275 HIS D 314 GLN E 12 ASN E 73 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 ASN P 42 ASN P 83 HIS P 137 GLN P 293 ASN P 375 GLN ** P 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 442 ASN P 454 ASN ** P 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 584 ASN ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 614 HIS P 624 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.065495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.049255 restraints weight = 79777.922| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.33 r_work: 0.2832 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21471 Z= 0.142 Angle : 0.690 7.510 28997 Z= 0.355 Chirality : 0.045 0.166 3087 Planarity : 0.005 0.056 3809 Dihedral : 8.486 127.685 3061 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.98 % Allowed : 8.70 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.15), residues: 2738 helix: -0.56 (0.14), residues: 1249 sheet: -2.33 (0.23), residues: 381 loop : -2.10 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 254 TYR 0.012 0.001 TYR A 143 PHE 0.014 0.001 PHE E 90 TRP 0.026 0.002 TRP P 434 HIS 0.009 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (21467) covalent geometry : angle 0.69009 / 0.36 (28997) hydrogen bonds : bond 0.03424 / 2.30 ( 1013) hydrogen bonds : angle 5.89820 / 4.03 ( 2811) Misc. bond : bond 0.00159 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 CYS cc_start: 0.9334 (m) cc_final: 0.9095 (m) REVERT: B 176 MET cc_start: 0.8543 (tpp) cc_final: 0.7996 (mpp) REVERT: B 211 ASP cc_start: 0.9308 (t0) cc_final: 0.9017 (t0) REVERT: B 274 ILE cc_start: 0.9015 (tp) cc_final: 0.8727 (tp) REVERT: B 326 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8723 (tppt) REVERT: C 132 MET cc_start: 0.9112 (ttp) cc_final: 0.8891 (ttp) REVERT: C 325 MET cc_start: 0.8494 (mmm) cc_final: 0.8285 (mmt) REVERT: D 78 ASN cc_start: 0.9400 (OUTLIER) cc_final: 0.9197 (t0) REVERT: D 132 MET cc_start: 0.8876 (ttp) cc_final: 0.8653 (ttp) REVERT: D 176 MET cc_start: 0.7838 (tpp) cc_final: 0.7515 (mpp) REVERT: D 224 GLU cc_start: 0.8681 (pm20) cc_final: 0.8457 (pm20) REVERT: D 246 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8274 (pm20) REVERT: D 299 MET cc_start: 0.8857 (tmm) cc_final: 0.8303 (tmm) REVERT: E 176 MET cc_start: 0.7800 (tpp) cc_final: 0.7123 (mmp) REVERT: E 227 MET cc_start: 0.9284 (tpt) cc_final: 0.8964 (mmm) REVERT: E 299 MET cc_start: 0.8521 (tmm) cc_final: 0.8220 (tmm) REVERT: E 355 MET cc_start: 0.9139 (mtm) cc_final: 0.8215 (mtm) REVERT: P 193 SER cc_start: 0.9031 (m) cc_final: 0.8779 (p) REVERT: P 221 HIS cc_start: 0.8797 (m90) cc_final: 0.8236 (m90) REVERT: P 477 GLU cc_start: 0.9401 (mt-10) cc_final: 0.9074 (mt-10) REVERT: P 482 VAL cc_start: 0.8300 (m) cc_final: 0.8045 (m) REVERT: P 493 MET cc_start: 0.9189 (mmm) cc_final: 0.8827 (mmt) REVERT: P 542 MET cc_start: 0.9091 (mmm) cc_final: 0.8624 (mmm) outliers start: 43 outliers final: 20 residues processed: 235 average time/residue: 0.1493 time to fit residues: 55.4057 Evaluate side-chains 174 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 12 ASN Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 526 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 227 optimal weight: 0.0000 chunk 107 optimal weight: 4.9990 chunk 185 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 186 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 115 ASN B 128 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 115 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS P 408 ASN ** P 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 454 ASN ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.061889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.045679 restraints weight = 81147.420| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.24 r_work: 0.2723 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21471 Z= 0.209 Angle : 0.671 7.223 28997 Z= 0.343 Chirality : 0.046 0.200 3087 Planarity : 0.004 0.064 3809 Dihedral : 7.979 121.627 3058 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.62 % Allowed : 9.85 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.16), residues: 2738 helix: 0.38 (0.15), residues: 1258 sheet: -2.22 (0.23), residues: 391 loop : -1.73 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 254 TYR 0.012 0.001 TYR A 143 PHE 0.014 0.002 PHE P 176 TRP 0.029 0.002 TRP P 434 HIS 0.018 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (21467) covalent geometry : angle 0.67134 / 0.34 (28997) hydrogen bonds : bond 0.03413 / 2.32 ( 1013) hydrogen bonds : angle 5.44575 / 3.74 ( 2811) Misc. bond : bond 0.00112 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 150 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8301 (tpp) cc_final: 0.8097 (tpp) REVERT: A 305 MET cc_start: 0.7993 (mpp) cc_final: 0.7772 (mmm) REVERT: B 326 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8754 (tppt) REVERT: D 44 MET cc_start: 0.9174 (mmm) cc_final: 0.8676 (mmp) REVERT: D 176 MET cc_start: 0.8393 (tpp) cc_final: 0.7696 (mpp) REVERT: D 299 MET cc_start: 0.8910 (tmm) cc_final: 0.8336 (tmm) REVERT: D 313 MET cc_start: 0.9565 (tpp) cc_final: 0.9195 (tpp) REVERT: E 82 MET cc_start: 0.9702 (tpt) cc_final: 0.9415 (tpt) REVERT: E 175 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8458 (mt) REVERT: E 176 MET cc_start: 0.8042 (tpp) cc_final: 0.7512 (mmm) REVERT: E 299 MET cc_start: 0.8544 (tmm) cc_final: 0.8156 (tmm) REVERT: E 355 MET cc_start: 0.9293 (mtm) cc_final: 0.8456 (mtm) REVERT: P 477 GLU cc_start: 0.9439 (mt-10) cc_final: 0.9039 (mt-10) REVERT: P 493 MET cc_start: 0.9208 (mmm) cc_final: 0.8808 (mmt) REVERT: P 542 MET cc_start: 0.9219 (mmm) cc_final: 0.8838 (mmm) outliers start: 57 outliers final: 23 residues processed: 200 average time/residue: 0.1290 time to fit residues: 42.9874 Evaluate side-chains 163 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 526 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 254 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 249 optimal weight: 0.0470 chunk 185 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** P 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 405 ASN P 413 GLN P 424 GLN ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.062648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.046469 restraints weight = 80494.433| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.24 r_work: 0.2750 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21471 Z= 0.139 Angle : 0.616 6.994 28997 Z= 0.311 Chirality : 0.044 0.196 3087 Planarity : 0.004 0.048 3809 Dihedral : 7.318 107.751 3058 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 2.49 % Allowed : 9.58 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.16), residues: 2738 helix: 0.74 (0.15), residues: 1288 sheet: -1.87 (0.23), residues: 406 loop : -1.46 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 254 TYR 0.012 0.001 TYR B 143 PHE 0.011 0.001 PHE P 176 TRP 0.032 0.002 TRP P 434 HIS 0.005 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (21467) covalent geometry : angle 0.61594 / 0.31 (28997) hydrogen bonds : bond 0.02989 / 2.02 ( 1013) hydrogen bonds : angle 5.12251 / 3.51 ( 2811) Misc. bond : bond 0.00132 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.8886 (p) REVERT: A 305 MET cc_start: 0.7858 (mpp) cc_final: 0.7553 (mmm) REVERT: B 202 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.8877 (p) REVERT: B 326 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8723 (tppt) REVERT: D 176 MET cc_start: 0.8522 (tpp) cc_final: 0.8066 (mpp) REVERT: D 227 MET cc_start: 0.9406 (mmm) cc_final: 0.9177 (mmm) REVERT: D 299 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8368 (tmm) REVERT: D 313 MET cc_start: 0.9574 (tpp) cc_final: 0.9128 (tpp) REVERT: E 82 MET cc_start: 0.9680 (tpt) cc_final: 0.9471 (tpt) REVERT: E 202 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9195 (p) REVERT: E 227 MET cc_start: 0.9189 (mmm) cc_final: 0.8798 (mmm) REVERT: E 244 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.6496 (m-30) REVERT: E 283 MET cc_start: 0.9254 (mmm) cc_final: 0.9033 (mmp) REVERT: E 299 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8167 (tmm) REVERT: E 355 MET cc_start: 0.9284 (mtm) cc_final: 0.8362 (mtm) REVERT: P 477 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9025 (mt-10) REVERT: P 493 MET cc_start: 0.9139 (mmm) cc_final: 0.8810 (mmt) REVERT: P 542 MET cc_start: 0.9105 (mmm) cc_final: 0.8604 (mmm) REVERT: P 595 CYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7417 (t) outliers start: 54 outliers final: 25 residues processed: 195 average time/residue: 0.1229 time to fit residues: 40.3350 Evaluate side-chains 171 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 595 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 113 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 246 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 253 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 HIS ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.061372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.045187 restraints weight = 80844.928| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.20 r_work: 0.2712 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21471 Z= 0.187 Angle : 0.636 8.021 28997 Z= 0.320 Chirality : 0.045 0.210 3087 Planarity : 0.004 0.070 3809 Dihedral : 7.255 107.870 3058 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.16 % Allowed : 10.87 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2738 helix: 1.00 (0.15), residues: 1288 sheet: -1.74 (0.24), residues: 366 loop : -1.26 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 254 TYR 0.016 0.001 TYR C 143 PHE 0.012 0.001 PHE P 176 TRP 0.033 0.002 TRP P 434 HIS 0.014 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (21467) covalent geometry : angle 0.63639 / 0.32 (28997) hydrogen bonds : bond 0.03059 / 2.07 ( 1013) hydrogen bonds : angle 5.06592 / 3.49 ( 2811) Misc. bond : bond 0.00445 / 0.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7720 (tpp) REVERT: A 202 THR cc_start: 0.9364 (OUTLIER) cc_final: 0.8883 (p) REVERT: A 305 MET cc_start: 0.7893 (mpp) cc_final: 0.7634 (mmm) REVERT: A 360 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8211 (pp30) REVERT: B 202 THR cc_start: 0.9361 (OUTLIER) cc_final: 0.8900 (p) REVERT: B 326 LYS cc_start: 0.8936 (mmmt) cc_final: 0.8726 (tppt) REVERT: D 176 MET cc_start: 0.8888 (tpp) cc_final: 0.8392 (mpp) REVERT: D 227 MET cc_start: 0.9353 (mmm) cc_final: 0.8896 (mmm) REVERT: D 299 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8418 (tmm) REVERT: D 313 MET cc_start: 0.9579 (tpp) cc_final: 0.9037 (tpp) REVERT: E 82 MET cc_start: 0.9697 (tpt) cc_final: 0.9407 (tpt) REVERT: E 202 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9255 (p) REVERT: E 227 MET cc_start: 0.9158 (mmm) cc_final: 0.8932 (tpt) REVERT: E 244 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6563 (m-30) REVERT: E 283 MET cc_start: 0.9322 (mmm) cc_final: 0.9115 (mmp) REVERT: E 299 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8184 (tmm) REVERT: P 477 GLU cc_start: 0.9456 (mt-10) cc_final: 0.9183 (mt-10) REVERT: P 493 MET cc_start: 0.9153 (mmm) cc_final: 0.8859 (mmt) REVERT: P 542 MET cc_start: 0.9249 (mmm) cc_final: 0.8837 (mmm) REVERT: P 595 CYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7487 (t) outliers start: 47 outliers final: 25 residues processed: 179 average time/residue: 0.1273 time to fit residues: 39.1786 Evaluate side-chains 169 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 595 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 163 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 256 optimal weight: 50.0000 chunk 185 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 46 optimal weight: 0.0570 chunk 140 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS D 40 HIS D 115 ASN D 371 HIS E 40 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.061246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.045095 restraints weight = 80630.372| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.19 r_work: 0.2709 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21471 Z= 0.175 Angle : 0.624 7.838 28997 Z= 0.315 Chirality : 0.045 0.193 3087 Planarity : 0.004 0.086 3809 Dihedral : 7.093 106.735 3058 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.21 % Allowed : 11.05 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.16), residues: 2738 helix: 1.17 (0.15), residues: 1291 sheet: -1.50 (0.25), residues: 366 loop : -1.12 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 254 TYR 0.014 0.001 TYR C 143 PHE 0.012 0.001 PHE P 176 TRP 0.040 0.002 TRP P 434 HIS 0.011 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (21467) covalent geometry : angle 0.62422 / 0.31 (28997) hydrogen bonds : bond 0.03000 / 2.03 ( 1013) hydrogen bonds : angle 4.98369 / 3.43 ( 2811) Misc. bond : bond 0.00321 / 0.15 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 136 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7698 (tpp) REVERT: A 202 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.8850 (p) REVERT: A 305 MET cc_start: 0.7907 (mpp) cc_final: 0.7599 (mmm) REVERT: B 202 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.8905 (p) REVERT: C 140 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9066 (mt) REVERT: D 176 MET cc_start: 0.8917 (tpp) cc_final: 0.8434 (mpp) REVERT: D 299 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8437 (tmm) REVERT: D 313 MET cc_start: 0.9583 (tpp) cc_final: 0.8994 (tpp) REVERT: E 82 MET cc_start: 0.9705 (tpt) cc_final: 0.9443 (tpt) REVERT: E 202 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.9244 (p) REVERT: E 244 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6565 (m-30) REVERT: E 283 MET cc_start: 0.9246 (mmm) cc_final: 0.9010 (mmp) REVERT: E 299 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8155 (tmm) REVERT: E 355 MET cc_start: 0.9212 (mtm) cc_final: 0.8709 (mtm) REVERT: P 477 GLU cc_start: 0.9437 (mt-10) cc_final: 0.9033 (mt-10) REVERT: P 493 MET cc_start: 0.9135 (mmm) cc_final: 0.8841 (mmt) REVERT: P 542 MET cc_start: 0.9265 (mmm) cc_final: 0.8844 (mmm) REVERT: P 595 CYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7489 (t) outliers start: 48 outliers final: 25 residues processed: 175 average time/residue: 0.1280 time to fit residues: 38.7157 Evaluate side-chains 166 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 595 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 165 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 193 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 116 optimal weight: 0.2980 chunk 233 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 HIS ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 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 = 0.3314 r_free = 0.3314 target = 0.061808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.045654 restraints weight = 80665.103| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.21 r_work: 0.2727 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21471 Z= 0.137 Angle : 0.611 10.710 28997 Z= 0.304 Chirality : 0.044 0.186 3087 Planarity : 0.003 0.047 3809 Dihedral : 6.957 105.302 3058 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.03 % Allowed : 11.51 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.17), residues: 2738 helix: 1.34 (0.15), residues: 1291 sheet: -1.40 (0.24), residues: 396 loop : -1.12 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 254 TYR 0.014 0.001 TYR C 143 PHE 0.011 0.001 PHE P 176 TRP 0.011 0.001 TRP E 79 HIS 0.012 0.001 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (21467) covalent geometry : angle 0.61121 / 0.30 (28997) hydrogen bonds : bond 0.02845 / 1.92 ( 1013) hydrogen bonds : angle 4.86764 / 3.35 ( 2811) Misc. bond : bond 0.00278 / 0.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7703 (tpp) REVERT: A 202 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.8857 (p) REVERT: A 305 MET cc_start: 0.7933 (mpp) cc_final: 0.7685 (mmm) REVERT: B 202 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.8890 (p) REVERT: C 140 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9035 (mt) REVERT: D 176 MET cc_start: 0.8887 (tpp) cc_final: 0.8429 (mpp) REVERT: D 299 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8434 (tmm) REVERT: D 313 MET cc_start: 0.9601 (tpp) cc_final: 0.9388 (tpt) REVERT: E 82 MET cc_start: 0.9704 (tpt) cc_final: 0.9433 (tpt) REVERT: E 202 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9247 (p) REVERT: E 227 MET cc_start: 0.9174 (tpt) cc_final: 0.8832 (mmm) REVERT: E 244 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6709 (m-30) REVERT: E 299 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8148 (tmm) REVERT: E 355 MET cc_start: 0.9246 (mtm) cc_final: 0.8630 (mtm) REVERT: P 477 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9063 (mt-10) REVERT: P 493 MET cc_start: 0.9042 (mmm) cc_final: 0.8745 (mmt) REVERT: P 542 MET cc_start: 0.9203 (mmm) cc_final: 0.8745 (mmm) REVERT: P 595 CYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7488 (t) outliers start: 44 outliers final: 25 residues processed: 171 average time/residue: 0.1221 time to fit residues: 36.1327 Evaluate side-chains 169 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 324 PHE Chi-restraints excluded: chain P residue 376 THR Chi-restraints excluded: chain P residue 595 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 8 optimal weight: 0.5980 chunk 259 optimal weight: 0.0270 chunk 78 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 chunk 255 optimal weight: 40.0000 chunk 184 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 HIS B 101 HIS ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** 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 = 0.3332 r_free = 0.3332 target = 0.062503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.046428 restraints weight = 80313.510| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 3.22 r_work: 0.2753 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21471 Z= 0.113 Angle : 0.596 10.325 28997 Z= 0.295 Chirality : 0.044 0.186 3087 Planarity : 0.003 0.034 3809 Dihedral : 6.734 100.901 3058 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.84 % Allowed : 11.88 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2738 helix: 1.51 (0.15), residues: 1285 sheet: -1.26 (0.24), residues: 396 loop : -1.00 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 39 TYR 0.013 0.001 TYR C 143 PHE 0.010 0.001 PHE P 176 TRP 0.015 0.001 TRP P 434 HIS 0.008 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (21467) covalent geometry : angle 0.59609 / 0.29 (28997) hydrogen bonds : bond 0.02701 / 1.82 ( 1013) hydrogen bonds : angle 4.73993 / 3.26 ( 2811) Misc. bond : bond 0.00237 / 0.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7716 (tpp) REVERT: A 202 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 305 MET cc_start: 0.7896 (mpp) cc_final: 0.7586 (mmm) REVERT: B 202 THR cc_start: 0.9321 (OUTLIER) cc_final: 0.8871 (p) REVERT: D 137 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8652 (mt0) REVERT: D 299 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8358 (tmm) REVERT: D 313 MET cc_start: 0.9596 (tpp) cc_final: 0.9387 (tpt) REVERT: E 82 MET cc_start: 0.9718 (tpt) cc_final: 0.9481 (tpt) REVERT: E 202 THR cc_start: 0.9501 (OUTLIER) cc_final: 0.9257 (p) REVERT: E 283 MET cc_start: 0.9276 (mmm) cc_final: 0.8846 (mmp) REVERT: E 299 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8139 (tmm) REVERT: E 355 MET cc_start: 0.9277 (mtm) cc_final: 0.8682 (mtm) REVERT: P 312 LEU cc_start: 0.9440 (tt) cc_final: 0.9057 (pp) REVERT: P 389 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.8146 (p90) REVERT: P 414 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.9001 (tp) REVERT: P 477 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9042 (mt-10) REVERT: P 493 MET cc_start: 0.9021 (mmm) cc_final: 0.8682 (mmt) REVERT: P 542 MET cc_start: 0.9090 (mmm) cc_final: 0.8533 (mmm) REVERT: P 595 CYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7508 (t) outliers start: 40 outliers final: 19 residues processed: 172 average time/residue: 0.1257 time to fit residues: 36.9882 Evaluate side-chains 162 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 HIS Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 389 TYR Chi-restraints excluded: chain P residue 414 ILE Chi-restraints excluded: chain P residue 595 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 67 optimal weight: 0.9990 chunk 206 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 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 = 0.3334 r_free = 0.3334 target = 0.062578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.046527 restraints weight = 80556.931| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.22 r_work: 0.2757 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21471 Z= 0.115 Angle : 0.594 9.952 28997 Z= 0.294 Chirality : 0.044 0.187 3087 Planarity : 0.003 0.035 3809 Dihedral : 6.628 98.580 3058 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.75 % Allowed : 11.97 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2738 helix: 1.58 (0.15), residues: 1285 sheet: -1.17 (0.25), residues: 396 loop : -0.99 (0.20), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 254 TYR 0.013 0.001 TYR C 143 PHE 0.010 0.001 PHE P 176 TRP 0.012 0.001 TRP P 434 HIS 0.006 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (21467) covalent geometry : angle 0.59414 / 0.29 (28997) hydrogen bonds : bond 0.02674 / 1.81 ( 1013) hydrogen bonds : angle 4.68692 / 3.22 ( 2811) Misc. bond : bond 0.00241 / 0.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.8860 (p) REVERT: A 305 MET cc_start: 0.7881 (mpp) cc_final: 0.7612 (mmm) REVERT: B 202 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.8904 (p) REVERT: D 137 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8664 (mt0) REVERT: D 299 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8410 (tmm) REVERT: D 313 MET cc_start: 0.9601 (tpp) cc_final: 0.9399 (tpt) REVERT: E 202 THR cc_start: 0.9508 (OUTLIER) cc_final: 0.9263 (p) REVERT: E 283 MET cc_start: 0.9262 (mmm) cc_final: 0.8825 (mmp) REVERT: E 299 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8149 (tmm) REVERT: E 355 MET cc_start: 0.9277 (mtm) cc_final: 0.8601 (mtm) REVERT: P 389 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.8182 (p90) REVERT: P 477 GLU cc_start: 0.9465 (mt-10) cc_final: 0.9079 (mt-10) REVERT: P 493 MET cc_start: 0.9003 (mmm) cc_final: 0.8665 (mmt) REVERT: P 542 MET cc_start: 0.9127 (mmm) cc_final: 0.8593 (mmm) REVERT: P 595 CYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7533 (t) outliers start: 38 outliers final: 19 residues processed: 165 average time/residue: 0.1305 time to fit residues: 36.7783 Evaluate side-chains 158 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 324 PHE Chi-restraints excluded: chain P residue 389 TYR Chi-restraints excluded: chain P residue 595 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 180 optimal weight: 9.9990 chunk 219 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 118 optimal weight: 0.0980 chunk 174 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 HIS E 40 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.061940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.045834 restraints weight = 81211.225| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.21 r_work: 0.2735 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21471 Z= 0.144 Angle : 0.619 12.862 28997 Z= 0.304 Chirality : 0.044 0.217 3087 Planarity : 0.003 0.045 3809 Dihedral : 6.637 99.733 3058 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.61 % Allowed : 12.20 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2738 helix: 1.58 (0.15), residues: 1293 sheet: -1.15 (0.25), residues: 396 loop : -1.00 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 39 TYR 0.013 0.001 TYR C 143 PHE 0.010 0.001 PHE P 176 TRP 0.011 0.001 TRP E 79 HIS 0.013 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (21467) covalent geometry : angle 0.61904 / 0.30 (28997) hydrogen bonds : bond 0.02762 / 1.87 ( 1013) hydrogen bonds : angle 4.71962 / 3.25 ( 2811) Misc. bond : bond 0.00264 / 0.13 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5476 Ramachandran restraints generated. 2738 Oldfield, 0 Emsley, 2738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.8857 (p) REVERT: A 305 MET cc_start: 0.7909 (mpp) cc_final: 0.7619 (mmm) REVERT: B 202 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.8919 (p) REVERT: D 137 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8646 (mt0) REVERT: D 299 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8394 (tmm) REVERT: D 313 MET cc_start: 0.9585 (tpp) cc_final: 0.9371 (tpt) REVERT: E 202 THR cc_start: 0.9512 (OUTLIER) cc_final: 0.9272 (p) REVERT: E 283 MET cc_start: 0.9269 (mmm) cc_final: 0.8840 (mmp) REVERT: E 299 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.8119 (tmm) REVERT: E 355 MET cc_start: 0.9298 (mtm) cc_final: 0.8470 (mtm) REVERT: P 383 MET cc_start: 0.9087 (tpp) cc_final: 0.8784 (tpp) REVERT: P 389 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8332 (p90) REVERT: P 414 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8988 (tp) REVERT: P 477 GLU cc_start: 0.9456 (mt-10) cc_final: 0.9080 (mt-10) REVERT: P 542 MET cc_start: 0.9134 (mmm) cc_final: 0.8561 (mmm) REVERT: P 595 CYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7530 (t) outliers start: 35 outliers final: 21 residues processed: 162 average time/residue: 0.1277 time to fit residues: 35.7619 Evaluate side-chains 159 residues out of total 2368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 137 GLN Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 40 HIS Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain P residue 206 HIS Chi-restraints excluded: chain P residue 324 PHE Chi-restraints excluded: chain P residue 389 TYR Chi-restraints excluded: chain P residue 414 ILE Chi-restraints excluded: chain P residue 595 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 102 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 270 optimal weight: 30.0000 chunk 12 optimal weight: 0.6980 chunk 218 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 599 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 = 0.3329 r_free = 0.3329 target = 0.062332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.046280 restraints weight = 80838.241| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.21 r_work: 0.2749 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21471 Z= 0.123 Angle : 0.611 12.142 28997 Z= 0.298 Chirality : 0.044 0.208 3087 Planarity : 0.003 0.038 3809 Dihedral : 6.573 99.782 3058 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.52 % Allowed : 12.29 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.17), residues: 2738 helix: 1.64 (0.15), residues: 1287 sheet: -1.10 (0.25), residues: 396 loop : -0.92 (0.20), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 254 TYR 0.012 0.001 TYR C 143 PHE 0.010 0.001 PHE P 176 TRP 0.013 0.001 TRP P 434 HIS 0.008 0.001 HIS E 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (21467) covalent geometry : angle 0.61087 / 0.30 (28997) hydrogen bonds : bond 0.02690 / 1.82 ( 1013) hydrogen bonds : angle 4.66674 / 3.21 ( 2811) Misc. bond : bond 0.00246 / 0.12 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4764.82 seconds wall clock time: 83 minutes 13.94 seconds (4993.94 seconds total)