Starting phenix.real_space_refine on Thu Mar 5 01:22:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m4n_30079/03_2026/6m4n_30079.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m4n_30079/03_2026/6m4n_30079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m4n_30079/03_2026/6m4n_30079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m4n_30079/03_2026/6m4n_30079.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m4n_30079/03_2026/6m4n_30079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m4n_30079/03_2026/6m4n_30079.map" } resolution = 3.8 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 Anisotropic ADP refinement not supported. Converting 30 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 100 5.16 5 C 11492 2.51 5 N 3014 2.21 5 O 3228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17836 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3498 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3887 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "D" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 390 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3498 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3887 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "H" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 390 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C2 PLP B 601 " occ=0.80 ... (13 atoms not shown) pdb=" P PLP B 601 " occ=0.80 residue: pdb=" C2 PLP F 601 " occ=0.80 ... (13 atoms not shown) pdb=" P PLP F 601 " occ=0.80 Time building chain proxies: 3.22, per 1000 atoms: 0.18 Number of scatterers: 17836 At special positions: 0 Unit cell: (125.882, 157.074, 118.084, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 2 15.00 O 3228 8.00 N 3014 7.00 C 11492 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 648.6 milliseconds 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4172 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 14 sheets defined 47.4% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 3.683A pdb=" N LEU A 27 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 62 removed outlier: 3.692A pdb=" N GLU A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.563A pdb=" N ASP A 113 " --> pdb=" O GLY A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.547A pdb=" N GLY A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 194 through 202 removed outlier: 3.919A pdb=" N GLY A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 257 through 268 removed outlier: 4.279A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 361 through 374 removed outlier: 3.666A pdb=" N VAL A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.962A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 472 removed outlier: 3.707A pdb=" N LEU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 92 removed outlier: 3.740A pdb=" N LEU B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.751A pdb=" N ARG B 124 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 removed outlier: 4.546A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA B 192 " --> pdb=" O CYS B 188 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.516A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 4.096A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.717A pdb=" N VAL B 267 " --> pdb=" O HIS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 removed outlier: 3.838A pdb=" N ILE B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.517A pdb=" N LEU B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 335 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 removed outlier: 4.087A pdb=" N GLU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 399 Processing helix chain 'B' and resid 412 through 428 removed outlier: 3.536A pdb=" N VAL B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 456 removed outlier: 4.261A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.666A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 535 removed outlier: 3.720A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 533 " --> pdb=" O ASP B 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 39 removed outlier: 3.577A pdb=" N LEU C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 30 " --> pdb=" O TYR C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 63 removed outlier: 4.152A pdb=" N TRP C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.500A pdb=" N ARG C 81 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU C 82 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.681A pdb=" N TYR C 91 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 93 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 Proline residue: C 106 - end of helix removed outlier: 3.669A pdb=" N THR C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 120 removed outlier: 3.647A pdb=" N ASP C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 120' Processing helix chain 'C' and resid 121 through 136 removed outlier: 3.640A pdb=" N ASN C 127 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 129 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 131 " --> pdb=" O ASN C 127 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.698A pdb=" N SER D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE D 16 " --> pdb=" O GLN D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 30 through 53 removed outlier: 3.695A pdb=" N THR D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE D 44 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 40 removed outlier: 3.683A pdb=" N LEU E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 62 removed outlier: 3.693A pdb=" N GLU E 58 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 113 removed outlier: 3.562A pdb=" N ASP E 113 " --> pdb=" O GLY E 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 110 through 113' Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.547A pdb=" N GLY E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 157 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 194 through 202 removed outlier: 3.918A pdb=" N GLY E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 229 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 257 through 268 removed outlier: 4.278A pdb=" N LEU E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR E 265 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 294 Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 342 through 359 Processing helix chain 'E' and resid 361 through 374 removed outlier: 3.665A pdb=" N VAL E 365 " --> pdb=" O GLY E 361 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS E 367 " --> pdb=" O PHE E 363 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU E 368 " --> pdb=" O ALA E 364 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 373 " --> pdb=" O LYS E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 422 removed outlier: 3.962A pdb=" N ILE E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 472 removed outlier: 3.706A pdb=" N LEU E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG E 459 " --> pdb=" O GLU E 455 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 467 " --> pdb=" O THR E 463 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN E 469 " --> pdb=" O LYS E 465 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 470 " --> pdb=" O GLU E 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 92 removed outlier: 3.740A pdb=" N LEU F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.751A pdb=" N ARG F 124 " --> pdb=" O ASN F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 199 removed outlier: 4.546A pdb=" N GLN F 189 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA F 192 " --> pdb=" O CYS F 188 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA F 193 " --> pdb=" O GLN F 189 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.517A pdb=" N GLU F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA F 224 " --> pdb=" O GLU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 246 removed outlier: 4.097A pdb=" N ASN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 246 " --> pdb=" O ASN F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 263 through 273 removed outlier: 3.717A pdb=" N VAL F 267 " --> pdb=" O HIS F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.839A pdb=" N ILE F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 338 removed outlier: 3.517A pdb=" N LEU F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS F 335 " --> pdb=" O ILE F 331 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 336 " --> pdb=" O ALA F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 363 removed outlier: 4.087A pdb=" N GLU F 361 " --> pdb=" O ARG F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 399 Processing helix chain 'F' and resid 412 through 428 removed outlier: 3.537A pdb=" N VAL F 416 " --> pdb=" O SER F 412 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU F 417 " --> pdb=" O PRO F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 456 removed outlier: 4.261A pdb=" N GLN F 440 " --> pdb=" O LYS F 436 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG F 451 " --> pdb=" O ARG F 447 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS F 454 " --> pdb=" O ARG F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.666A pdb=" N GLY F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG F 484 " --> pdb=" O GLY F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 535 removed outlier: 3.720A pdb=" N GLU F 530 " --> pdb=" O LYS F 526 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 533 " --> pdb=" O ASP F 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 39 removed outlier: 3.577A pdb=" N LEU G 28 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 63 removed outlier: 4.152A pdb=" N TRP G 49 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN G 57 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR G 61 " --> pdb=" O ASN G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.500A pdb=" N ARG G 81 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU G 82 " --> pdb=" O LYS G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 93 removed outlier: 3.682A pdb=" N TYR G 91 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL G 93 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 116 Proline residue: G 106 - end of helix removed outlier: 3.669A pdb=" N THR G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 120 removed outlier: 3.647A pdb=" N ASP G 120 " --> pdb=" O THR G 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 120' Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.641A pdb=" N ASN G 127 " --> pdb=" O HIS G 123 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 129 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER G 130 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU G 131 " --> pdb=" O ASN G 127 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU G 135 " --> pdb=" O LEU G 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 23 removed outlier: 3.697A pdb=" N SER H 14 " --> pdb=" O TRP H 10 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP H 15 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE H 16 " --> pdb=" O GLN H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 26 No H-bonds generated for 'chain 'H' and resid 24 through 26' Processing helix chain 'H' and resid 30 through 53 removed outlier: 3.695A pdb=" N THR H 35 " --> pdb=" O PRO H 31 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL H 36 " --> pdb=" O TRP H 32 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE H 44 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL H 45 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR H 50 " --> pdb=" O GLY H 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 95 removed outlier: 6.943A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.581A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE A 186 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.530A pdb=" N VAL A 446 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 152 removed outlier: 5.321A pdb=" N VAL B 146 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY B 169 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN B 165 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N GLN B 152 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 163 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.847A pdb=" N GLY B 375 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR B 376 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.762A pdb=" N SER B 323 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 471 removed outlier: 3.794A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 92 through 95 removed outlier: 6.942A pdb=" N ALA E 425 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE E 101 " --> pdb=" O ALA E 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 160 through 164 removed outlier: 6.581A pdb=" N ILE E 242 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE E 186 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 393 through 395 removed outlier: 3.529A pdb=" N VAL E 446 " --> pdb=" O PHE E 394 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 145 through 152 removed outlier: 5.320A pdb=" N VAL F 146 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY F 169 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN F 165 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLN F 152 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR F 163 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N GLY F 492 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE F 171 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.847A pdb=" N GLY F 375 " --> pdb=" O TYR F 387 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR F 376 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR F 342 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE F 312 " --> pdb=" O TYR F 342 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP F 344 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL F 314 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 317 through 318 removed outlier: 3.762A pdb=" N SER F 323 " --> pdb=" O TYR F 318 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 468 through 471 removed outlier: 3.795A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1920 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: 2.73 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5613 1.34 - 1.45: 3574 1.45 - 1.57: 8871 1.57 - 1.69: 2 1.69 - 1.81: 164 Bond restraints: 18224 Sorted by residual: bond pdb=" CA ILE E 175 " pdb=" CB ILE E 175 " ideal model delta sigma weight residual 1.539 1.524 0.015 5.40e-03 3.43e+04 7.78e+00 bond pdb=" CA ILE A 175 " pdb=" CB ILE A 175 " ideal model delta sigma weight residual 1.539 1.524 0.015 5.40e-03 3.43e+04 7.49e+00 bond pdb=" CA TYR F 342 " pdb=" CB TYR F 342 " ideal model delta sigma weight residual 1.531 1.497 0.034 1.52e-02 4.33e+03 4.94e+00 bond pdb=" CA TYR B 342 " pdb=" CB TYR B 342 " ideal model delta sigma weight residual 1.531 1.498 0.033 1.52e-02 4.33e+03 4.69e+00 bond pdb=" C HIS G 65 " pdb=" N THR G 66 " ideal model delta sigma weight residual 1.331 1.303 0.029 1.40e-02 5.10e+03 4.21e+00 ... (remaining 18219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 22987 2.05 - 4.11: 1385 4.11 - 6.16: 170 6.16 - 8.21: 91 8.21 - 10.27: 23 Bond angle restraints: 24656 Sorted by residual: angle pdb=" C PRO E 72 " pdb=" N VAL E 73 " pdb=" CA VAL E 73 " ideal model delta sigma weight residual 120.43 127.18 -6.75 9.60e-01 1.09e+00 4.95e+01 angle pdb=" C PRO A 72 " pdb=" N VAL A 73 " pdb=" CA VAL A 73 " ideal model delta sigma weight residual 120.43 127.15 -6.72 9.60e-01 1.09e+00 4.90e+01 angle pdb=" N VAL F 406 " pdb=" CA VAL F 406 " pdb=" C VAL F 406 " ideal model delta sigma weight residual 113.53 107.70 5.83 9.80e-01 1.04e+00 3.54e+01 angle pdb=" N VAL B 406 " pdb=" CA VAL B 406 " pdb=" C VAL B 406 " ideal model delta sigma weight residual 113.53 107.73 5.80 9.80e-01 1.04e+00 3.50e+01 angle pdb=" C LYS F 538 " pdb=" N TYR F 539 " pdb=" CA TYR F 539 " ideal model delta sigma weight residual 120.28 127.24 -6.96 1.44e+00 4.82e-01 2.33e+01 ... (remaining 24651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 10684 30.03 - 60.06: 190 60.06 - 90.09: 18 90.09 - 120.12: 0 120.12 - 150.15: 2 Dihedral angle restraints: 10894 sinusoidal: 4378 harmonic: 6516 Sorted by residual: dihedral pdb=" CA ALA A 20 " pdb=" C ALA A 20 " pdb=" N PRO A 21 " pdb=" CA PRO A 21 " ideal model delta harmonic sigma weight residual 180.00 143.16 36.84 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CA ALA E 20 " pdb=" C ALA E 20 " pdb=" N PRO E 21 " pdb=" CA PRO E 21 " ideal model delta harmonic sigma weight residual 180.00 143.16 36.84 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" C5A PLP F 601 " pdb=" O4P PLP F 601 " pdb=" P PLP F 601 " pdb=" O1P PLP F 601 " ideal model delta sinusoidal sigma weight residual 76.43 -133.43 -150.15 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 10891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1873 0.059 - 0.117: 718 0.117 - 0.176: 147 0.176 - 0.234: 12 0.234 - 0.293: 10 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CB ILE B 459 " pdb=" CA ILE B 459 " pdb=" CG1 ILE B 459 " pdb=" CG2 ILE B 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE F 459 " pdb=" CA ILE F 459 " pdb=" CG1 ILE F 459 " pdb=" CG2 ILE F 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB VAL E 237 " pdb=" CA VAL E 237 " pdb=" CG1 VAL E 237 " pdb=" CG2 VAL E 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2757 not shown) Planarity restraints: 3124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 501 " 0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO F 502 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO F 502 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 502 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO B 502 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 20 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO E 21 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 21 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 21 " 0.039 5.00e-02 4.00e+02 ... (remaining 3121 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1063 2.71 - 3.26: 17785 3.26 - 3.81: 29960 3.81 - 4.35: 36183 4.35 - 4.90: 60112 Nonbonded interactions: 145103 Sorted by model distance: nonbonded pdb=" OG1 THR A 427 " pdb=" OE1 GLU B 209 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR E 427 " pdb=" OE1 GLU F 209 " model vdw 2.250 3.040 nonbonded pdb=" OD2 ASP E 188 " pdb=" OH TYR E 248 " model vdw 2.276 3.040 nonbonded pdb=" OD2 ASP A 188 " pdb=" OH TYR A 248 " model vdw 2.276 3.040 nonbonded pdb=" OE1 GLN C 121 " pdb=" OH TYR E 23 " model vdw 2.294 3.040 ... (remaining 145098 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 14.390 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.009 0.084 18226 Z= 0.445 Angle : 1.175 10.267 24656 Z= 0.647 Chirality : 0.062 0.293 2760 Planarity : 0.008 0.084 3124 Dihedral : 11.939 150.149 6722 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.87 % Favored : 88.95 % Rotamer: Outliers : 0.73 % Allowed : 8.06 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.09 % 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: -4.50 (0.14), residues: 2226 helix: -3.26 (0.11), residues: 932 sheet: -1.78 (0.35), residues: 230 loop : -2.96 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG F 131 TYR 0.028 0.003 TYR B 176 PHE 0.027 0.003 PHE A 209 TRP 0.029 0.003 TRP E 64 HIS 0.016 0.003 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00931 (18224) covalent geometry : angle 1.17482 (24656) hydrogen bonds : bond 0.29686 ( 670) hydrogen bonds : angle 9.32049 ( 1920) Misc. bond : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 362 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.9194 (mp) cc_final: 0.8801 (tt) REVERT: C 34 HIS cc_start: 0.8253 (t-90) cc_final: 0.7985 (t70) REVERT: C 89 MET cc_start: 0.8611 (mtt) cc_final: 0.8319 (mtt) REVERT: C 118 LYS cc_start: 0.8009 (mptt) cc_final: 0.7606 (mmtm) REVERT: D 13 MET cc_start: 0.8742 (tpt) cc_final: 0.8026 (tmm) REVERT: D 19 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8479 (tm-30) REVERT: D 44 ILE cc_start: 0.9247 (mm) cc_final: 0.8972 (pt) REVERT: F 126 LEU cc_start: 0.9130 (mp) cc_final: 0.8733 (tt) REVERT: F 128 MET cc_start: 0.8574 (tpt) cc_final: 0.8356 (tpp) REVERT: F 131 ARG cc_start: 0.9192 (ptm-80) cc_final: 0.8719 (ptt180) REVERT: G 34 HIS cc_start: 0.8457 (t-90) cc_final: 0.8131 (t70) REVERT: G 58 MET cc_start: 0.8430 (tpt) cc_final: 0.8222 (tpp) REVERT: H 13 MET cc_start: 0.8642 (tpt) cc_final: 0.8202 (tmm) REVERT: H 19 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8427 (tm-30) REVERT: H 44 ILE cc_start: 0.9232 (mm) cc_final: 0.8982 (pt) outliers start: 14 outliers final: 4 residues processed: 374 average time/residue: 0.1395 time to fit residues: 77.5001 Evaluate side-chains 192 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain F residue 372 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0020 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 114 ASN A 224 GLN A 231 ASN A 309 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 242 ASN B 263 HIS B 282 HIS B 284 ASN B 403 HIS B 490 ASN E 114 ASN E 224 GLN E 231 ASN E 309 ASN ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 GLN F 50 GLN F 242 ASN F 245 ASN F 263 HIS F 282 HIS F 284 ASN F 403 HIS F 490 ASN G 94 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.061139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.050040 restraints weight = 91423.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.051505 restraints weight = 50134.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.052484 restraints weight = 33680.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.053095 restraints weight = 25885.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.053522 restraints weight = 21837.017| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18226 Z= 0.147 Angle : 0.764 10.946 24656 Z= 0.388 Chirality : 0.046 0.179 2760 Planarity : 0.006 0.074 3124 Dihedral : 8.222 168.274 2470 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.77 % Allowed : 11.05 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -2.81 (0.17), residues: 2226 helix: -1.23 (0.15), residues: 966 sheet: -1.74 (0.33), residues: 240 loop : -2.51 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 236 TYR 0.012 0.001 TYR G 116 PHE 0.029 0.002 PHE F 59 TRP 0.019 0.001 TRP H 15 HIS 0.004 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00307 (18224) covalent geometry : angle 0.76448 (24656) hydrogen bonds : bond 0.06105 ( 670) hydrogen bonds : angle 5.38435 ( 1920) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 261 time to evaluate : 0.682 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: A 183 ASP cc_start: 0.7032 (m-30) cc_final: 0.6332 (m-30) REVERT: A 214 MET cc_start: 0.7935 (mmp) cc_final: 0.7364 (mmm) REVERT: A 275 GLU cc_start: 0.8322 (pt0) cc_final: 0.7743 (pp20) REVERT: A 307 MET cc_start: 0.8544 (mpp) cc_final: 0.8268 (mpp) REVERT: B 126 LEU cc_start: 0.9113 (mp) cc_final: 0.8849 (tt) REVERT: B 128 MET cc_start: 0.9015 (mmm) cc_final: 0.8620 (tpt) REVERT: B 472 MET cc_start: 0.8674 (tpp) cc_final: 0.8408 (tpp) REVERT: C 34 HIS cc_start: 0.8462 (t-90) cc_final: 0.8066 (t70) REVERT: C 118 LYS cc_start: 0.8089 (mptt) cc_final: 0.7545 (mmtm) REVERT: D 13 MET cc_start: 0.8335 (tpt) cc_final: 0.7823 (tmm) REVERT: D 28 MET cc_start: 0.8483 (pmt) cc_final: 0.8139 (pmt) REVERT: D 55 PHE cc_start: 0.7144 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: E 183 ASP cc_start: 0.7260 (m-30) cc_final: 0.6443 (m-30) REVERT: E 228 ASP cc_start: 0.7967 (m-30) cc_final: 0.7515 (m-30) REVERT: E 275 GLU cc_start: 0.8312 (pt0) cc_final: 0.7704 (pp20) REVERT: E 307 MET cc_start: 0.8533 (mpp) cc_final: 0.8215 (mpp) REVERT: F 126 LEU cc_start: 0.9088 (mp) cc_final: 0.8784 (tt) REVERT: F 131 ARG cc_start: 0.9158 (ptm-80) cc_final: 0.8891 (ptt90) REVERT: F 173 MET cc_start: 0.8968 (mmm) cc_final: 0.8736 (mmm) REVERT: F 503 ILE cc_start: 0.8917 (tp) cc_final: 0.8681 (tp) REVERT: F 504 ILE cc_start: 0.9367 (OUTLIER) cc_final: 0.9058 (mp) REVERT: G 34 HIS cc_start: 0.8516 (t-90) cc_final: 0.8000 (t70) REVERT: G 58 MET cc_start: 0.8362 (tpt) cc_final: 0.8130 (tpp) REVERT: H 13 MET cc_start: 0.8137 (tpt) cc_final: 0.7873 (tmm) REVERT: H 19 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8035 (tm-30) REVERT: H 40 MET cc_start: 0.8418 (mmp) cc_final: 0.8104 (mmp) REVERT: H 44 ILE cc_start: 0.9105 (mm) cc_final: 0.8884 (pt) outliers start: 72 outliers final: 32 residues processed: 311 average time/residue: 0.1128 time to fit residues: 55.6032 Evaluate side-chains 221 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 94 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 66 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 219 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 HIS B 157 ASN B 245 ASN C 123 HIS E 292 HIS ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 HIS F 245 ASN F 516 HIS G 77 GLN ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.058379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.047312 restraints weight = 95651.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048735 restraints weight = 51228.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.049673 restraints weight = 34062.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.050280 restraints weight = 26175.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050665 restraints weight = 22010.821| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18226 Z= 0.248 Angle : 0.777 9.926 24656 Z= 0.395 Chirality : 0.048 0.265 2760 Planarity : 0.005 0.074 3124 Dihedral : 7.945 166.087 2470 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 3.93 % Allowed : 13.87 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -2.11 (0.17), residues: 2226 helix: -0.43 (0.16), residues: 964 sheet: -1.58 (0.34), residues: 234 loop : -2.30 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 271 TYR 0.020 0.002 TYR A 248 PHE 0.017 0.002 PHE B 59 TRP 0.021 0.002 TRP H 15 HIS 0.006 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00538 (18224) covalent geometry : angle 0.77704 (24656) hydrogen bonds : bond 0.04930 ( 670) hydrogen bonds : angle 5.09219 ( 1920) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 191 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: A 274 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7433 (tm-30) REVERT: A 275 GLU cc_start: 0.8376 (pt0) cc_final: 0.8143 (pt0) REVERT: A 307 MET cc_start: 0.8743 (mpp) cc_final: 0.8115 (mpp) REVERT: B 126 LEU cc_start: 0.9232 (mp) cc_final: 0.8945 (tt) REVERT: B 472 MET cc_start: 0.8740 (tpp) cc_final: 0.8487 (tpp) REVERT: C 34 HIS cc_start: 0.8549 (t-90) cc_final: 0.8010 (t70) REVERT: C 118 LYS cc_start: 0.8101 (mptt) cc_final: 0.7710 (mmtm) REVERT: D 13 MET cc_start: 0.8424 (tpt) cc_final: 0.7955 (tmm) REVERT: D 19 GLN cc_start: 0.9084 (tp40) cc_final: 0.8381 (tm-30) REVERT: D 28 MET cc_start: 0.8522 (pmt) cc_final: 0.8249 (pmt) REVERT: D 44 ILE cc_start: 0.8855 (pt) cc_final: 0.8346 (mm) REVERT: E 275 GLU cc_start: 0.8444 (pt0) cc_final: 0.7593 (pp20) REVERT: E 307 MET cc_start: 0.8820 (mpp) cc_final: 0.8186 (mpp) REVERT: F 128 MET cc_start: 0.9185 (tpp) cc_final: 0.8694 (tmm) REVERT: F 173 MET cc_start: 0.9110 (mmm) cc_final: 0.8770 (mmm) REVERT: G 34 HIS cc_start: 0.8516 (t-90) cc_final: 0.8012 (t70) REVERT: G 57 ASN cc_start: 0.8488 (m-40) cc_final: 0.8186 (m-40) REVERT: G 118 LYS cc_start: 0.7624 (mmtp) cc_final: 0.7233 (mmtm) REVERT: H 13 MET cc_start: 0.8425 (tpt) cc_final: 0.7986 (tmm) REVERT: H 44 ILE cc_start: 0.9080 (mm) cc_final: 0.8850 (pt) outliers start: 75 outliers final: 45 residues processed: 249 average time/residue: 0.1081 time to fit residues: 44.2289 Evaluate side-chains 215 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 255 CYS Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 423 MET Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 119 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 11 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 59 optimal weight: 0.0020 chunk 15 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 219 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 190 optimal weight: 0.0070 chunk 126 optimal weight: 2.9990 overall best weight: 1.8012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS ** G 123 HIS ** 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 = 0.3382 r_free = 0.3382 target = 0.059241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048254 restraints weight = 93477.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.049702 restraints weight = 50164.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050670 restraints weight = 33141.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.051284 restraints weight = 25207.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.051707 restraints weight = 21092.877| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18226 Z= 0.146 Angle : 0.700 11.751 24656 Z= 0.347 Chirality : 0.046 0.182 2760 Planarity : 0.005 0.064 3124 Dihedral : 7.745 170.437 2470 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 4.24 % Allowed : 15.18 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % 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: -1.63 (0.18), residues: 2226 helix: 0.04 (0.17), residues: 970 sheet: -1.31 (0.35), residues: 234 loop : -2.16 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 271 TYR 0.011 0.001 TYR B 342 PHE 0.012 0.001 PHE A 209 TRP 0.012 0.001 TRP H 15 HIS 0.007 0.001 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00319 (18224) covalent geometry : angle 0.70002 (24656) hydrogen bonds : bond 0.04233 ( 670) hydrogen bonds : angle 4.79436 ( 1920) Misc. bond : bond 0.00001 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 190 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 VAL cc_start: 0.9048 (t) cc_final: 0.8696 (p) REVERT: A 183 ASP cc_start: 0.7168 (m-30) cc_final: 0.6506 (m-30) REVERT: A 275 GLU cc_start: 0.8574 (pt0) cc_final: 0.8319 (pt0) REVERT: A 307 MET cc_start: 0.8686 (mpp) cc_final: 0.8184 (mpp) REVERT: B 126 LEU cc_start: 0.9230 (mp) cc_final: 0.8931 (tt) REVERT: B 128 MET cc_start: 0.9004 (mmm) cc_final: 0.8568 (tpt) REVERT: B 374 MET cc_start: 0.7979 (tmm) cc_final: 0.7547 (tmm) REVERT: B 472 MET cc_start: 0.8693 (tpp) cc_final: 0.8432 (tpp) REVERT: C 34 HIS cc_start: 0.8594 (t-90) cc_final: 0.7977 (t70) REVERT: C 118 LYS cc_start: 0.8048 (mptt) cc_final: 0.7621 (mmtm) REVERT: D 13 MET cc_start: 0.8409 (tpt) cc_final: 0.8008 (tmm) REVERT: D 19 GLN cc_start: 0.9024 (tp40) cc_final: 0.8347 (tm-30) REVERT: D 37 PHE cc_start: 0.9231 (t80) cc_final: 0.9003 (t80) REVERT: D 40 MET cc_start: 0.8797 (tpp) cc_final: 0.8140 (mmp) REVERT: E 183 ASP cc_start: 0.7547 (m-30) cc_final: 0.6789 (m-30) REVERT: E 275 GLU cc_start: 0.8572 (pt0) cc_final: 0.7805 (pp20) REVERT: E 307 MET cc_start: 0.8734 (mpp) cc_final: 0.8175 (mpp) REVERT: F 126 LEU cc_start: 0.9242 (mp) cc_final: 0.8989 (tt) REVERT: F 128 MET cc_start: 0.9127 (tpp) cc_final: 0.8730 (tmm) REVERT: F 173 MET cc_start: 0.9070 (mmm) cc_final: 0.8681 (mmm) REVERT: G 34 HIS cc_start: 0.8532 (t-90) cc_final: 0.7948 (t70) REVERT: G 57 ASN cc_start: 0.8442 (m-40) cc_final: 0.8131 (m-40) REVERT: H 13 MET cc_start: 0.8313 (tpt) cc_final: 0.7891 (tmm) REVERT: H 19 GLN cc_start: 0.9095 (tp40) cc_final: 0.8198 (tm-30) REVERT: H 37 PHE cc_start: 0.9176 (t80) cc_final: 0.8966 (t80) outliers start: 81 outliers final: 45 residues processed: 252 average time/residue: 0.1063 time to fit residues: 43.8340 Evaluate side-chains 220 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 423 MET Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 119 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 209 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 115 optimal weight: 30.0000 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 59 optimal weight: 0.0670 chunk 120 optimal weight: 4.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN B 154 HIS ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 GLN F 154 HIS ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** 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 = 0.3397 r_free = 0.3397 target = 0.059695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048840 restraints weight = 93352.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.050213 restraints weight = 52429.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.051168 restraints weight = 35289.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051785 restraints weight = 26939.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.052229 restraints weight = 22605.541| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18226 Z= 0.121 Angle : 0.718 13.782 24656 Z= 0.344 Chirality : 0.046 0.394 2760 Planarity : 0.004 0.062 3124 Dihedral : 7.601 174.767 2470 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 3.14 % Allowed : 16.39 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.38 (0.18), residues: 2226 helix: 0.35 (0.17), residues: 958 sheet: -1.33 (0.35), residues: 234 loop : -2.07 (0.19), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 151 TYR 0.011 0.001 TYR B 342 PHE 0.011 0.001 PHE A 209 TRP 0.010 0.001 TRP H 32 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00259 (18224) covalent geometry : angle 0.71823 (24656) hydrogen bonds : bond 0.03878 ( 670) hydrogen bonds : angle 4.68804 ( 1920) Misc. bond : bond 0.00001 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 196 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8654 (mt) REVERT: A 183 ASP cc_start: 0.6978 (m-30) cc_final: 0.6358 (m-30) REVERT: A 275 GLU cc_start: 0.8547 (pt0) cc_final: 0.8041 (pp20) REVERT: B 126 LEU cc_start: 0.9258 (mp) cc_final: 0.9001 (tt) REVERT: B 128 MET cc_start: 0.9017 (mmm) cc_final: 0.8575 (tpt) REVERT: B 374 MET cc_start: 0.7802 (tmm) cc_final: 0.7558 (tmm) REVERT: B 472 MET cc_start: 0.8558 (tpp) cc_final: 0.8238 (tpp) REVERT: C 34 HIS cc_start: 0.8655 (t-90) cc_final: 0.8015 (t70) REVERT: C 118 LYS cc_start: 0.7989 (mptt) cc_final: 0.7592 (mmtm) REVERT: D 13 MET cc_start: 0.8389 (tpt) cc_final: 0.7908 (tmm) REVERT: D 19 GLN cc_start: 0.9021 (tp40) cc_final: 0.8190 (tm-30) REVERT: D 37 PHE cc_start: 0.9225 (t80) cc_final: 0.8987 (t80) REVERT: D 49 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7101 (pp) REVERT: E 183 ASP cc_start: 0.7395 (m-30) cc_final: 0.6703 (m-30) REVERT: E 307 MET cc_start: 0.8660 (mpp) cc_final: 0.8119 (mpp) REVERT: F 126 LEU cc_start: 0.9198 (mp) cc_final: 0.8984 (tt) REVERT: F 128 MET cc_start: 0.9093 (tpp) cc_final: 0.8665 (tmm) REVERT: F 173 MET cc_start: 0.9147 (mmm) cc_final: 0.8829 (mmm) REVERT: F 472 MET cc_start: 0.8629 (tpp) cc_final: 0.8409 (tpp) REVERT: G 34 HIS cc_start: 0.8489 (t-90) cc_final: 0.7859 (t70) REVERT: G 57 ASN cc_start: 0.8446 (m-40) cc_final: 0.8194 (m-40) REVERT: H 13 MET cc_start: 0.8291 (tpt) cc_final: 0.7879 (tmm) REVERT: H 37 PHE cc_start: 0.9186 (t80) cc_final: 0.8979 (t80) outliers start: 60 outliers final: 30 residues processed: 243 average time/residue: 0.1085 time to fit residues: 42.7510 Evaluate side-chains 207 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain H residue 28 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 212 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 138 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.058180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.047523 restraints weight = 95770.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.048842 restraints weight = 54049.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.049744 restraints weight = 36788.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.050283 restraints weight = 28557.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050688 restraints weight = 24299.593| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18226 Z= 0.200 Angle : 0.757 14.039 24656 Z= 0.369 Chirality : 0.048 0.228 2760 Planarity : 0.005 0.062 3124 Dihedral : 7.631 175.051 2470 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 3.14 % Allowed : 17.70 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.19 (0.18), residues: 2226 helix: 0.50 (0.17), residues: 970 sheet: -1.42 (0.34), residues: 234 loop : -1.93 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 151 TYR 0.016 0.001 TYR B 342 PHE 0.013 0.001 PHE G 111 TRP 0.014 0.002 TRP B 134 HIS 0.005 0.001 HIS E 211 Details of bonding type rmsd covalent geometry : bond 0.00440 (18224) covalent geometry : angle 0.75695 (24656) hydrogen bonds : bond 0.03953 ( 670) hydrogen bonds : angle 4.73518 ( 1920) Misc. bond : bond 0.00002 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 175 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8560 (pt0) cc_final: 0.8319 (pt0) REVERT: B 173 MET cc_start: 0.8615 (mmm) cc_final: 0.8376 (mmm) REVERT: B 374 MET cc_start: 0.7836 (tmm) cc_final: 0.7501 (tmm) REVERT: B 472 MET cc_start: 0.8445 (tpp) cc_final: 0.8108 (tpp) REVERT: C 34 HIS cc_start: 0.8631 (t-90) cc_final: 0.8001 (t70) REVERT: C 57 ASN cc_start: 0.8332 (m-40) cc_final: 0.8062 (m-40) REVERT: C 118 LYS cc_start: 0.8023 (mptt) cc_final: 0.7625 (mmtm) REVERT: D 13 MET cc_start: 0.8454 (tpt) cc_final: 0.7902 (tmm) REVERT: D 19 GLN cc_start: 0.9032 (tp40) cc_final: 0.8312 (tm-30) REVERT: D 40 MET cc_start: 0.8656 (tmm) cc_final: 0.8364 (tmm) REVERT: D 49 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7269 (pp) REVERT: E 275 GLU cc_start: 0.8318 (pt0) cc_final: 0.7714 (pp20) REVERT: E 307 MET cc_start: 0.8621 (mpp) cc_final: 0.8074 (mpp) REVERT: F 173 MET cc_start: 0.9128 (mmm) cc_final: 0.8769 (mmm) REVERT: G 34 HIS cc_start: 0.8603 (t-90) cc_final: 0.7972 (t70) REVERT: G 57 ASN cc_start: 0.8555 (m-40) cc_final: 0.8260 (m-40) REVERT: G 89 MET cc_start: 0.8679 (mmm) cc_final: 0.8271 (mmm) REVERT: H 13 MET cc_start: 0.8462 (tpt) cc_final: 0.7973 (tmm) REVERT: H 40 MET cc_start: 0.8574 (tmm) cc_final: 0.8227 (mtt) outliers start: 60 outliers final: 44 residues processed: 219 average time/residue: 0.1131 time to fit residues: 40.3447 Evaluate side-chains 218 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 119 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 189 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 206 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 115 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 HIS ** G 123 HIS ** 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 = 0.3383 r_free = 0.3383 target = 0.059039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048236 restraints weight = 96379.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.049603 restraints weight = 54230.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050513 restraints weight = 36968.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051088 restraints weight = 28774.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.051488 restraints weight = 24471.722| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18226 Z= 0.130 Angle : 0.726 12.288 24656 Z= 0.347 Chirality : 0.047 0.370 2760 Planarity : 0.004 0.060 3124 Dihedral : 7.593 178.172 2470 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 3.14 % Allowed : 17.75 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.01 (0.18), residues: 2226 helix: 0.67 (0.17), residues: 972 sheet: -1.47 (0.35), residues: 216 loop : -1.81 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 151 TYR 0.011 0.001 TYR B 342 PHE 0.030 0.001 PHE G 124 TRP 0.014 0.001 TRP H 32 HIS 0.004 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00286 (18224) covalent geometry : angle 0.72616 (24656) hydrogen bonds : bond 0.03695 ( 670) hydrogen bonds : angle 4.59844 ( 1920) Misc. bond : bond 0.00002 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 182 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7008 (m-30) cc_final: 0.6432 (m-30) REVERT: A 275 GLU cc_start: 0.8494 (pt0) cc_final: 0.8247 (pt0) REVERT: B 126 LEU cc_start: 0.9251 (mp) cc_final: 0.8951 (tt) REVERT: B 173 MET cc_start: 0.8599 (mmm) cc_final: 0.8346 (mmm) REVERT: B 374 MET cc_start: 0.7730 (tmm) cc_final: 0.7334 (tmm) REVERT: B 472 MET cc_start: 0.8491 (tpp) cc_final: 0.8164 (tpp) REVERT: C 34 HIS cc_start: 0.8659 (t-90) cc_final: 0.7974 (t70) REVERT: C 118 LYS cc_start: 0.7930 (mptt) cc_final: 0.7509 (mmtm) REVERT: D 13 MET cc_start: 0.8488 (tpt) cc_final: 0.7903 (tmm) REVERT: D 19 GLN cc_start: 0.8983 (tp40) cc_final: 0.8190 (tm-30) REVERT: D 40 MET cc_start: 0.8841 (tmm) cc_final: 0.8516 (tmm) REVERT: D 44 ILE cc_start: 0.8827 (mm) cc_final: 0.8591 (pt) REVERT: E 275 GLU cc_start: 0.8341 (pt0) cc_final: 0.7752 (pp20) REVERT: E 307 MET cc_start: 0.8536 (mpp) cc_final: 0.8006 (mpp) REVERT: F 128 MET cc_start: 0.9038 (tpp) cc_final: 0.8704 (tmm) REVERT: F 173 MET cc_start: 0.9175 (mmm) cc_final: 0.8815 (mmm) REVERT: G 34 HIS cc_start: 0.8556 (t-90) cc_final: 0.7999 (t70) REVERT: G 57 ASN cc_start: 0.8506 (m-40) cc_final: 0.8212 (m-40) REVERT: H 13 MET cc_start: 0.8413 (tpt) cc_final: 0.7913 (tmm) outliers start: 60 outliers final: 46 residues processed: 228 average time/residue: 0.1047 time to fit residues: 38.8880 Evaluate side-chains 215 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 24 HIS Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain H residue 26 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 154 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 206 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.058868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048252 restraints weight = 96176.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.049591 restraints weight = 53523.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.050493 restraints weight = 36276.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051096 restraints weight = 28084.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.051493 restraints weight = 23622.346| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18226 Z= 0.136 Angle : 0.738 13.040 24656 Z= 0.352 Chirality : 0.047 0.330 2760 Planarity : 0.004 0.059 3124 Dihedral : 7.536 179.455 2470 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.83 % Allowed : 18.59 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.93 (0.19), residues: 2226 helix: 0.75 (0.17), residues: 958 sheet: -1.53 (0.35), residues: 218 loop : -1.74 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 151 TYR 0.027 0.001 TYR F 461 PHE 0.029 0.001 PHE G 124 TRP 0.011 0.001 TRP H 32 HIS 0.017 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00304 (18224) covalent geometry : angle 0.73787 (24656) hydrogen bonds : bond 0.03651 ( 670) hydrogen bonds : angle 4.59467 ( 1920) Misc. bond : bond 0.00003 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 175 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.6992 (m-30) cc_final: 0.6444 (m-30) REVERT: A 275 GLU cc_start: 0.8458 (pt0) cc_final: 0.8242 (pt0) REVERT: A 304 SER cc_start: 0.9219 (t) cc_final: 0.8900 (p) REVERT: B 126 LEU cc_start: 0.9241 (mp) cc_final: 0.9010 (tt) REVERT: B 173 MET cc_start: 0.8613 (mmm) cc_final: 0.8357 (mmm) REVERT: B 374 MET cc_start: 0.7782 (tmm) cc_final: 0.7376 (tmm) REVERT: B 472 MET cc_start: 0.8473 (tpp) cc_final: 0.8144 (tpp) REVERT: C 34 HIS cc_start: 0.8642 (t-90) cc_final: 0.7966 (t70) REVERT: C 118 LYS cc_start: 0.7907 (mptt) cc_final: 0.7506 (mmtm) REVERT: D 13 MET cc_start: 0.8505 (tpt) cc_final: 0.7924 (tmm) REVERT: D 19 GLN cc_start: 0.8978 (tp40) cc_final: 0.8184 (tm-30) REVERT: D 40 MET cc_start: 0.8786 (tmm) cc_final: 0.8402 (tmm) REVERT: D 44 ILE cc_start: 0.8797 (mm) cc_final: 0.8558 (pt) REVERT: E 275 GLU cc_start: 0.8396 (pt0) cc_final: 0.7783 (pp20) REVERT: E 307 MET cc_start: 0.8551 (mpp) cc_final: 0.8033 (mpp) REVERT: F 128 MET cc_start: 0.9039 (tpp) cc_final: 0.8694 (tmm) REVERT: F 173 MET cc_start: 0.9176 (mmm) cc_final: 0.8807 (mmm) REVERT: G 34 HIS cc_start: 0.8548 (t-90) cc_final: 0.7988 (t70) REVERT: G 57 ASN cc_start: 0.8497 (m-40) cc_final: 0.8193 (m-40) REVERT: H 13 MET cc_start: 0.8411 (tpt) cc_final: 0.7914 (tmm) REVERT: H 28 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8335 (pmm) REVERT: H 44 ILE cc_start: 0.8984 (mm) cc_final: 0.8695 (pt) outliers start: 54 outliers final: 46 residues processed: 216 average time/residue: 0.1070 time to fit residues: 38.0641 Evaluate side-chains 218 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 171 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain F residue 111 PHE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 190 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 147 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 186 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 191 optimal weight: 0.3980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.059451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048745 restraints weight = 95412.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.050077 restraints weight = 53197.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050996 restraints weight = 36341.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.051603 restraints weight = 28093.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.051988 restraints weight = 23683.317| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18226 Z= 0.131 Angle : 0.742 12.340 24656 Z= 0.352 Chirality : 0.048 0.446 2760 Planarity : 0.004 0.060 3124 Dihedral : 7.324 174.942 2470 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 2.83 % Allowed : 18.80 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.86 (0.19), residues: 2226 helix: 0.80 (0.17), residues: 962 sheet: -1.55 (0.35), residues: 206 loop : -1.68 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 151 TYR 0.018 0.001 TYR F 461 PHE 0.030 0.001 PHE G 124 TRP 0.009 0.001 TRP H 32 HIS 0.003 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00290 (18224) covalent geometry : angle 0.74218 (24656) hydrogen bonds : bond 0.03546 ( 670) hydrogen bonds : angle 4.58848 ( 1920) Misc. bond : bond 0.00005 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.6969 (m-30) cc_final: 0.6397 (m-30) REVERT: A 275 GLU cc_start: 0.8509 (pt0) cc_final: 0.8279 (pt0) REVERT: A 304 SER cc_start: 0.9199 (t) cc_final: 0.8852 (p) REVERT: A 420 MET cc_start: 0.8786 (tpp) cc_final: 0.8410 (tmm) REVERT: B 173 MET cc_start: 0.8631 (mmm) cc_final: 0.8359 (mmm) REVERT: B 374 MET cc_start: 0.7762 (tmm) cc_final: 0.7290 (tmm) REVERT: B 472 MET cc_start: 0.8492 (tpp) cc_final: 0.8173 (tpp) REVERT: C 34 HIS cc_start: 0.8609 (t-90) cc_final: 0.7929 (t70) REVERT: C 118 LYS cc_start: 0.7812 (mptt) cc_final: 0.7407 (mmtm) REVERT: D 13 MET cc_start: 0.8574 (tpt) cc_final: 0.7954 (tmm) REVERT: D 19 GLN cc_start: 0.8956 (tp40) cc_final: 0.8199 (tm-30) REVERT: D 40 MET cc_start: 0.8745 (tmm) cc_final: 0.8326 (tmm) REVERT: D 44 ILE cc_start: 0.8805 (mm) cc_final: 0.8550 (pt) REVERT: E 183 ASP cc_start: 0.7305 (m-30) cc_final: 0.6745 (m-30) REVERT: E 275 GLU cc_start: 0.8429 (pt0) cc_final: 0.7841 (pp20) REVERT: E 304 SER cc_start: 0.8968 (t) cc_final: 0.8326 (p) REVERT: F 173 MET cc_start: 0.9208 (mmm) cc_final: 0.8813 (mmm) REVERT: G 34 HIS cc_start: 0.8528 (t-90) cc_final: 0.7947 (t70) REVERT: G 57 ASN cc_start: 0.8509 (m-40) cc_final: 0.8221 (m-40) REVERT: H 13 MET cc_start: 0.8502 (tpt) cc_final: 0.7949 (tmm) REVERT: H 28 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8344 (pmm) REVERT: H 44 ILE cc_start: 0.8957 (mm) cc_final: 0.8660 (pt) outliers start: 54 outliers final: 43 residues processed: 218 average time/residue: 0.1110 time to fit residues: 39.4277 Evaluate side-chains 213 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 111 PHE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 189 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 196 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 116 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 ASN ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 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 = 0.3406 r_free = 0.3406 target = 0.059985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.049219 restraints weight = 95157.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050592 restraints weight = 53571.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.051513 restraints weight = 36491.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.052105 restraints weight = 28300.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.052496 restraints weight = 23932.617| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18226 Z= 0.118 Angle : 0.750 13.750 24656 Z= 0.352 Chirality : 0.048 0.420 2760 Planarity : 0.004 0.059 3124 Dihedral : 6.795 164.490 2470 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 2.46 % Allowed : 19.21 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.83 (0.19), residues: 2226 helix: 0.84 (0.17), residues: 980 sheet: -1.56 (0.35), residues: 206 loop : -1.72 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 151 TYR 0.016 0.001 TYR F 461 PHE 0.030 0.001 PHE G 124 TRP 0.010 0.001 TRP H 32 HIS 0.003 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00259 (18224) covalent geometry : angle 0.75018 (24656) hydrogen bonds : bond 0.03461 ( 670) hydrogen bonds : angle 4.52067 ( 1920) Misc. bond : bond 0.00009 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.6838 (m-30) cc_final: 0.6365 (m-30) REVERT: A 304 SER cc_start: 0.9216 (t) cc_final: 0.8789 (p) REVERT: A 420 MET cc_start: 0.8715 (tpp) cc_final: 0.8365 (tmm) REVERT: B 173 MET cc_start: 0.8591 (mmm) cc_final: 0.8332 (mmm) REVERT: B 209 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7558 (mm-30) REVERT: B 374 MET cc_start: 0.7790 (tmm) cc_final: 0.7336 (tmm) REVERT: B 472 MET cc_start: 0.8437 (tpp) cc_final: 0.8158 (tpp) REVERT: C 34 HIS cc_start: 0.8613 (t-90) cc_final: 0.7921 (t70) REVERT: C 118 LYS cc_start: 0.7671 (mptt) cc_final: 0.7287 (mmtm) REVERT: D 13 MET cc_start: 0.8536 (tpt) cc_final: 0.7936 (tmm) REVERT: D 19 GLN cc_start: 0.8938 (tp40) cc_final: 0.8188 (tm-30) REVERT: D 40 MET cc_start: 0.8696 (tmm) cc_final: 0.8340 (tmm) REVERT: D 44 ILE cc_start: 0.8725 (mm) cc_final: 0.8454 (pt) REVERT: E 183 ASP cc_start: 0.7345 (m-30) cc_final: 0.6734 (m-30) REVERT: E 275 GLU cc_start: 0.8343 (pt0) cc_final: 0.7753 (pp20) REVERT: E 304 SER cc_start: 0.8901 (t) cc_final: 0.8514 (p) REVERT: F 173 MET cc_start: 0.9188 (mmm) cc_final: 0.8693 (mmm) REVERT: F 209 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7660 (mm-30) REVERT: G 34 HIS cc_start: 0.8540 (t-90) cc_final: 0.7919 (t70) REVERT: G 57 ASN cc_start: 0.8552 (m-40) cc_final: 0.8256 (m-40) REVERT: H 13 MET cc_start: 0.8540 (tpt) cc_final: 0.7975 (tmm) REVERT: H 28 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8384 (pmm) REVERT: H 44 ILE cc_start: 0.8899 (mm) cc_final: 0.8536 (pt) outliers start: 47 outliers final: 39 residues processed: 226 average time/residue: 0.1161 time to fit residues: 42.1258 Evaluate side-chains 215 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 55 PHE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 161 LYS Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 28 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 163 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 184 optimal weight: 0.0060 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 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 = 0.3387 r_free = 0.3387 target = 0.059242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.048473 restraints weight = 95207.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.049839 restraints weight = 52622.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.050780 restraints weight = 35560.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.051406 restraints weight = 27202.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051778 restraints weight = 22748.684| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18226 Z= 0.159 Angle : 0.769 13.199 24656 Z= 0.367 Chirality : 0.049 0.378 2760 Planarity : 0.004 0.057 3124 Dihedral : 6.247 144.575 2470 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 2.30 % Allowed : 19.74 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.19), residues: 2226 helix: 0.87 (0.17), residues: 960 sheet: -1.57 (0.35), residues: 206 loop : -1.63 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 151 TYR 0.015 0.001 TYR F 461 PHE 0.031 0.001 PHE G 124 TRP 0.013 0.001 TRP B 134 HIS 0.004 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00357 (18224) covalent geometry : angle 0.76902 (24656) hydrogen bonds : bond 0.03571 ( 670) hydrogen bonds : angle 4.61655 ( 1920) Misc. bond : bond 0.00053 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2770.24 seconds wall clock time: 48 minutes 54.39 seconds (2934.39 seconds total)