Starting phenix.real_space_refine on Sun Sep 13 12:24:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/3jd2_6635/09_2026/3jd2_6635.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd2_6635/09_2026/3jd2_6635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jd2_6635/09_2026/3jd2_6635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd2_6635/09_2026/3jd2_6635.map" model { file = "/net/cci-nas-00/data/ceres_data/3jd2_6635/09_2026/3jd2_6635.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd2_6635/09_2026/3jd2_6635.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/3jd2_6635/09_2026/3jd2_6635.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/3jd2_6635/09_2026/3jd2_6635.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 114 5.16 5 C 14976 2.51 5 N 4158 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23814 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "B" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "C" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "D" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "E" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "F" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1B NAI A 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI A 602 " occ=0.35 residue: pdb=" C1B NAI B 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI B 602 " occ=0.35 residue: pdb=" C1B NAI C 601 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI C 601 " occ=0.35 residue: pdb=" C1B NAI D 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI D 602 " occ=0.35 residue: pdb=" C1B NAI E 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI E 602 " occ=0.35 residue: pdb=" C1B NAI F 601 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI F 601 " occ=0.35 Time building chain proxies: 4.50, per 1000 atoms: 0.19 Number of scatterers: 23814 At special positions: 0 Unit cell: (114.92, 118.3, 165.62, 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 114 16.00 P 24 15.00 O 4542 8.00 N 4158 7.00 C 14976 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=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 15 sheets defined 54.8% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 118 removed outlier: 3.634A pdb=" N TYR A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 187 removed outlier: 3.700A pdb=" N TRP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.567A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.557A pdb=" N LYS A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.603A pdb=" N LEU A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 removed outlier: 3.539A pdb=" N VAL A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 418 Processing helix chain 'A' and resid 419 through 420 No H-bonds generated for 'chain 'A' and resid 419 through 420' Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 476 through 495 removed outlier: 3.973A pdb=" N ALA A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 14 " --> pdb=" O PHE B 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS B 41 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.635A pdb=" N TYR B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 187 removed outlier: 3.699A pdb=" N TRP B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.568A pdb=" N ILE B 223 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 225 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 236 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS B 258 " --> pdb=" O ASN B 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.556A pdb=" N LYS B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.602A pdb=" N LEU B 373 " --> pdb=" O PRO B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 391 removed outlier: 3.539A pdb=" N VAL B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 418 Processing helix chain 'B' and resid 419 through 420 No H-bonds generated for 'chain 'B' and resid 419 through 420' Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 476 through 495 removed outlier: 3.972A pdb=" N ALA B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 14 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 118 removed outlier: 3.634A pdb=" N TYR C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU C 142 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 187 removed outlier: 3.700A pdb=" N TRP C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.566A pdb=" N ILE C 223 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 225 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS C 258 " --> pdb=" O ASN C 254 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 removed outlier: 3.557A pdb=" N LYS C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.603A pdb=" N LEU C 373 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 391 removed outlier: 3.538A pdb=" N VAL C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 418 Processing helix chain 'C' and resid 419 through 420 No H-bonds generated for 'chain 'C' and resid 419 through 420' Processing helix chain 'C' and resid 421 through 425 Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA C 454 " --> pdb=" O HIS C 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 471 Processing helix chain 'C' and resid 476 through 495 removed outlier: 3.973A pdb=" N ALA C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 14 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 24 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS D 41 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 118 removed outlier: 3.634A pdb=" N TYR D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 187 removed outlier: 3.700A pdb=" N TRP D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.567A pdb=" N ILE D 223 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN D 225 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 removed outlier: 3.557A pdb=" N LYS D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.603A pdb=" N LEU D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 391 removed outlier: 3.539A pdb=" N VAL D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 418 Processing helix chain 'D' and resid 419 through 420 No H-bonds generated for 'chain 'D' and resid 419 through 420' Processing helix chain 'D' and resid 421 through 425 Processing helix chain 'D' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 471 Processing helix chain 'D' and resid 476 through 495 removed outlier: 3.973A pdb=" N ALA D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 491 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 492 " --> pdb=" O LYS D 488 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 14 " --> pdb=" O PHE E 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 24 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 118 removed outlier: 3.635A pdb=" N TYR E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA E 116 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU E 142 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 187 removed outlier: 3.699A pdb=" N TRP E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 228 removed outlier: 3.568A pdb=" N ILE E 223 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN E 225 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 236 " --> pdb=" O TYR E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS E 258 " --> pdb=" O ASN E 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR E 262 " --> pdb=" O HIS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.556A pdb=" N LYS E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.602A pdb=" N LEU E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 391 removed outlier: 3.539A pdb=" N VAL E 380 " --> pdb=" O GLY E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 418 Processing helix chain 'E' and resid 419 through 420 No H-bonds generated for 'chain 'E' and resid 419 through 420' Processing helix chain 'E' and resid 421 through 425 Processing helix chain 'E' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA E 454 " --> pdb=" O HIS E 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'E' and resid 476 through 495 removed outlier: 3.972A pdb=" N ALA E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG E 491 " --> pdb=" O GLU E 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR E 493 " --> pdb=" O VAL E 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU E 495 " --> pdb=" O ARG E 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET F 12 " --> pdb=" O ASN F 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU F 14 " --> pdb=" O PHE F 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 118 removed outlier: 3.634A pdb=" N TYR F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU F 142 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 152 " --> pdb=" O PHE F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 187 removed outlier: 3.700A pdb=" N TRP F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 197 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.566A pdb=" N ILE F 223 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN F 225 " --> pdb=" O HIS F 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 236 " --> pdb=" O TYR F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS F 258 " --> pdb=" O ASN F 254 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR F 262 " --> pdb=" O HIS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.557A pdb=" N LYS F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN F 297 " --> pdb=" O ASP F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS F 358 " --> pdb=" O PRO F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 374 removed outlier: 3.603A pdb=" N LEU F 373 " --> pdb=" O PRO F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 391 removed outlier: 3.538A pdb=" N VAL F 380 " --> pdb=" O GLY F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 418 Processing helix chain 'F' and resid 419 through 420 No H-bonds generated for 'chain 'F' and resid 419 through 420' Processing helix chain 'F' and resid 421 through 425 Processing helix chain 'F' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 458 " --> pdb=" O ALA F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 471 Processing helix chain 'F' and resid 476 through 495 removed outlier: 3.973A pdb=" N ALA F 480 " --> pdb=" O ASP F 476 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 491 " --> pdb=" O GLU F 487 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR F 493 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU F 495 " --> pdb=" O ARG F 491 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.592A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 79 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG E 79 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=C, first strand: chain 'A' and resid 308 through 309 removed outlier: 3.625A pdb=" N GLY A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE A 247 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR A 272 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 321 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.591A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG B 79 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 79 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY D 92 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=F, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.625A pdb=" N GLY B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE B 247 " --> pdb=" O CYS B 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR B 272 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 321 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 344 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.592A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY C 92 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 79 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG F 79 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'C' and resid 63 through 66 Processing sheet with id=I, first strand: chain 'C' and resid 308 through 309 removed outlier: 3.626A pdb=" N GLY C 278 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N PHE C 247 " --> pdb=" O CYS C 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR C 272 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 321 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 344 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'D' and resid 63 through 66 Processing sheet with id=K, first strand: chain 'D' and resid 308 through 309 removed outlier: 3.625A pdb=" N GLY D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE D 247 " --> pdb=" O CYS D 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR D 272 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 321 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 344 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'E' and resid 63 through 66 Processing sheet with id=M, first strand: chain 'E' and resid 308 through 309 removed outlier: 3.625A pdb=" N GLY E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE E 247 " --> pdb=" O CYS E 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR E 272 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 321 " --> pdb=" O THR E 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 344 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=O, first strand: chain 'F' and resid 308 through 309 removed outlier: 3.626A pdb=" N GLY F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N PHE F 247 " --> pdb=" O CYS F 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR F 272 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 321 " --> pdb=" O THR F 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE F 344 " --> pdb=" O ILE F 368 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3006 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7714 1.33 - 1.45: 3666 1.45 - 1.57: 12740 1.57 - 1.69: 48 1.69 - 1.81: 192 Bond restraints: 24360 Sorted by residual: bond pdb=" C3N NAI C 601 " pdb=" C7N NAI C 601 " ideal model delta sigma weight residual 1.473 1.592 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C3N NAI F 601 " pdb=" C7N NAI F 601 " ideal model delta sigma weight residual 1.473 1.592 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C3N NAI A 602 " pdb=" C7N NAI A 602 " ideal model delta sigma weight residual 1.473 1.591 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C3N NAI D 602 " pdb=" C7N NAI D 602 " ideal model delta sigma weight residual 1.473 1.591 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C3N NAI B 602 " pdb=" C7N NAI B 602 " ideal model delta sigma weight residual 1.473 1.591 -0.118 2.00e-02 2.50e+03 3.46e+01 ... (remaining 24355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 32428 3.14 - 6.27: 430 6.27 - 9.41: 94 9.41 - 12.55: 18 12.55 - 15.68: 24 Bond angle restraints: 32994 Sorted by residual: angle pdb=" O2A NAI E 601 " pdb=" PA NAI E 601 " pdb=" O5B NAI E 601 " ideal model delta sigma weight residual 105.34 121.02 -15.68 3.00e+00 1.11e-01 2.73e+01 angle pdb=" O2A NAI B 601 " pdb=" PA NAI B 601 " pdb=" O5B NAI B 601 " ideal model delta sigma weight residual 105.34 121.02 -15.68 3.00e+00 1.11e-01 2.73e+01 angle pdb=" O2A NAI D 601 " pdb=" PA NAI D 601 " pdb=" O5B NAI D 601 " ideal model delta sigma weight residual 105.34 121.00 -15.66 3.00e+00 1.11e-01 2.72e+01 angle pdb=" O2A NAI A 601 " pdb=" PA NAI A 601 " pdb=" O5B NAI A 601 " ideal model delta sigma weight residual 105.34 121.00 -15.66 3.00e+00 1.11e-01 2.72e+01 angle pdb=" O2A NAI F 602 " pdb=" PA NAI F 602 " pdb=" O5B NAI F 602 " ideal model delta sigma weight residual 105.34 120.98 -15.64 3.00e+00 1.11e-01 2.72e+01 ... (remaining 32989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 14014 16.86 - 33.71: 266 33.71 - 50.57: 72 50.57 - 67.43: 12 67.43 - 84.28: 18 Dihedral angle restraints: 14382 sinusoidal: 5904 harmonic: 8478 Sorted by residual: dihedral pdb=" CA ALA F 375 " pdb=" C ALA F 375 " pdb=" N GLY F 376 " pdb=" CA GLY F 376 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ALA C 375 " pdb=" C ALA C 375 " pdb=" N GLY C 376 " pdb=" CA GLY C 376 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ALA A 375 " pdb=" C ALA A 375 " pdb=" N GLY A 376 " pdb=" CA GLY A 376 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 14379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3142 0.080 - 0.161: 386 0.161 - 0.241: 20 0.241 - 0.321: 28 0.321 - 0.401: 12 Chirality restraints: 3588 Sorted by residual: chirality pdb=" C3B NAI B 601 " pdb=" C2B NAI B 601 " pdb=" C4B NAI B 601 " pdb=" O3B NAI B 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C3B NAI E 601 " pdb=" C2B NAI E 601 " pdb=" C4B NAI E 601 " pdb=" O3B NAI E 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C3B NAI A 601 " pdb=" C2B NAI A 601 " pdb=" C4B NAI A 601 " pdb=" O3B NAI A 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.40 2.00e-01 2.50e+01 3.99e+00 ... (remaining 3585 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 336 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO D 337 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 337 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 337 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 336 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 337 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 336 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO E 337 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " -0.036 5.00e-02 4.00e+02 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4320 2.75 - 3.29: 22798 3.29 - 3.83: 36841 3.83 - 4.36: 47046 4.36 - 4.90: 78853 Nonbonded interactions: 189858 Sorted by model distance: nonbonded pdb=" O THR B 239 " pdb=" NZ LYS B 245 " model vdw 2.219 3.120 nonbonded pdb=" O THR E 239 " pdb=" NZ LYS E 245 " model vdw 2.219 3.120 nonbonded pdb=" O THR F 239 " pdb=" NZ LYS F 245 " model vdw 2.219 3.120 nonbonded pdb=" O THR C 239 " pdb=" NZ LYS C 245 " model vdw 2.219 3.120 nonbonded pdb=" O THR A 239 " pdb=" NZ LYS A 245 " model vdw 2.220 3.120 ... (remaining 189853 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.35 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 20.210 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.119 24360 Z= 0.521 Angle : 1.045 15.681 32994 Z= 0.484 Chirality : 0.061 0.401 3588 Planarity : 0.005 0.065 4224 Dihedral : 8.836 84.282 8982 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.81 % Allowed : 5.60 % Favored : 93.59 % Rotamer: Outliers : 0.72 % Allowed : 0.48 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -5.54 (0.11), residues: 2964 helix: -3.94 (0.08), residues: 1374 sheet: -3.14 (0.21), residues: 450 loop : -3.25 (0.15), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 396 TYR 0.025 0.003 TYR A 382 PHE 0.025 0.003 PHE B 399 TRP 0.023 0.003 TRP F 72 HIS 0.007 0.002 HIS B 391 Details of bonding type rmsd/Z covalent geometry : bond 0.01104 / 0.52 (24360) covalent geometry : angle 1.04498 / 0.48 (32994) hydrogen bonds : bond 0.28989 / 19.21 ( 1068) hydrogen bonds : angle 9.47585 / 6.65 ( 3006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 487 time to evaluate : 0.934 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: A 500 PHE cc_start: 0.7108 (m-10) cc_final: 0.6127 (m-10) REVERT: B 500 PHE cc_start: 0.7200 (m-10) cc_final: 0.5813 (m-10) REVERT: C 500 PHE cc_start: 0.7076 (m-10) cc_final: 0.5977 (t80) REVERT: D 500 PHE cc_start: 0.7103 (m-10) cc_final: 0.6126 (m-10) REVERT: E 500 PHE cc_start: 0.7191 (m-10) cc_final: 0.5805 (m-10) REVERT: F 500 PHE cc_start: 0.7073 (m-10) cc_final: 0.5975 (t80) outliers start: 18 outliers final: 12 residues processed: 505 average time/residue: 0.2016 time to fit residues: 147.3997 Evaluate side-chains 249 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 overall best weight: 3.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 56 ASN A 57 HIS A 84 GLN A 437 GLN B 40 GLN B 56 ASN B 57 HIS B 84 GLN B 205 GLN B 209 HIS B 437 GLN C 56 ASN C 57 HIS C 84 GLN C 205 GLN C 209 HIS D 40 GLN D 56 ASN D 57 HIS D 84 GLN D 437 GLN E 40 GLN E 56 ASN E 57 HIS E 84 GLN E 205 GLN E 209 HIS E 437 GLN F 56 ASN F 57 HIS F 84 GLN F 209 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.114235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.082966 restraints weight = 46268.250| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.60 r_work: 0.2974 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24360 Z= 0.154 Angle : 0.582 5.468 32994 Z= 0.309 Chirality : 0.045 0.166 3588 Planarity : 0.006 0.070 4224 Dihedral : 8.555 80.999 3414 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.96 % Allowed : 5.73 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.11 (0.14), residues: 2964 helix: -1.56 (0.12), residues: 1350 sheet: -2.28 (0.23), residues: 432 loop : -2.41 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 478 TYR 0.018 0.001 TYR F 382 PHE 0.024 0.002 PHE A 16 TRP 0.041 0.003 TRP D 281 HIS 0.005 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (24360) covalent geometry : angle 0.58198 / 0.31 (32994) hydrogen bonds : bond 0.04974 / 3.31 ( 1068) hydrogen bonds : angle 4.84826 / 3.36 ( 3006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 308 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 VAL cc_start: 0.8957 (t) cc_final: 0.8547 (m) REVERT: A 269 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7989 (ptmt) REVERT: A 281 TRP cc_start: 0.7466 (t60) cc_final: 0.7251 (t60) REVERT: A 330 GLN cc_start: 0.8085 (tp40) cc_final: 0.7859 (tp40) REVERT: B 249 VAL cc_start: 0.8941 (t) cc_final: 0.8506 (m) REVERT: C 11 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8247 (mttp) REVERT: C 249 VAL cc_start: 0.8926 (t) cc_final: 0.8540 (m) REVERT: C 281 TRP cc_start: 0.7597 (t60) cc_final: 0.7115 (t60) REVERT: D 181 ASP cc_start: 0.8709 (t70) cc_final: 0.8038 (t70) REVERT: D 249 VAL cc_start: 0.8967 (t) cc_final: 0.8558 (m) REVERT: D 269 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7992 (ptmt) REVERT: D 308 LYS cc_start: 0.7656 (pptt) cc_final: 0.7434 (pttp) REVERT: D 330 GLN cc_start: 0.8088 (tp40) cc_final: 0.7860 (tp40) REVERT: D 466 ARG cc_start: 0.8354 (ttm110) cc_final: 0.7977 (tpp-160) REVERT: E 249 VAL cc_start: 0.8949 (t) cc_final: 0.8517 (m) REVERT: F 11 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8248 (mttp) REVERT: F 249 VAL cc_start: 0.8929 (t) cc_final: 0.8546 (m) REVERT: F 281 TRP cc_start: 0.7583 (t60) cc_final: 0.7109 (t60) outliers start: 24 outliers final: 19 residues processed: 317 average time/residue: 0.1592 time to fit residues: 79.9230 Evaluate side-chains 251 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 469 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 273 optimal weight: 9.9990 chunk 33 optimal weight: 0.1980 chunk 214 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 228 optimal weight: 0.0470 chunk 56 optimal weight: 10.0000 chunk 174 optimal weight: 40.0000 chunk 248 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 84 GLN A 225 ASN A 330 GLN A 437 GLN B 84 GLN B 225 ASN B 437 GLN C 225 ASN D 40 GLN D 84 GLN D 225 ASN D 330 GLN D 437 GLN E 84 GLN E 225 ASN E 437 GLN F 225 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.115184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084492 restraints weight = 46048.237| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.62 r_work: 0.3016 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 24360 Z= 0.091 Angle : 0.481 4.980 32994 Z= 0.251 Chirality : 0.042 0.158 3588 Planarity : 0.004 0.039 4224 Dihedral : 7.804 74.621 3402 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.28 % Allowed : 7.49 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.68 (0.15), residues: 2964 helix: -0.13 (0.14), residues: 1338 sheet: -1.71 (0.25), residues: 432 loop : -1.93 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 478 TYR 0.009 0.001 TYR B 382 PHE 0.020 0.002 PHE B 500 TRP 0.037 0.002 TRP D 281 HIS 0.004 0.001 HIS B 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (24360) covalent geometry : angle 0.48088 / 0.25 (32994) hydrogen bonds : bond 0.03453 / 2.27 ( 1068) hydrogen bonds : angle 4.12876 / 2.86 ( 3006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 326 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 VAL cc_start: 0.9013 (t) cc_final: 0.8693 (m) REVERT: A 330 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7572 (mm110) REVERT: A 424 HIS cc_start: 0.5464 (m170) cc_final: 0.5177 (m170) REVERT: B 78 TYR cc_start: 0.8825 (m-80) cc_final: 0.8608 (m-80) REVERT: B 181 ASP cc_start: 0.8682 (t70) cc_final: 0.7874 (t0) REVERT: B 249 VAL cc_start: 0.9003 (t) cc_final: 0.8656 (m) REVERT: B 281 TRP cc_start: 0.7578 (t60) cc_final: 0.7172 (t60) REVERT: C 78 TYR cc_start: 0.8732 (m-80) cc_final: 0.8320 (m-80) REVERT: C 138 ASP cc_start: 0.8630 (m-30) cc_final: 0.8412 (m-30) REVERT: C 249 VAL cc_start: 0.8985 (t) cc_final: 0.8685 (m) REVERT: C 281 TRP cc_start: 0.7558 (t60) cc_final: 0.7026 (t60) REVERT: C 330 GLN cc_start: 0.8052 (tp40) cc_final: 0.7729 (tp40) REVERT: C 407 TYR cc_start: 0.8467 (m-80) cc_final: 0.8242 (m-10) REVERT: D 249 VAL cc_start: 0.9037 (t) cc_final: 0.8723 (m) REVERT: D 330 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7571 (mm110) REVERT: D 424 HIS cc_start: 0.5468 (m170) cc_final: 0.5182 (m170) REVERT: D 466 ARG cc_start: 0.8356 (ttm110) cc_final: 0.7953 (tpp-160) REVERT: E 78 TYR cc_start: 0.8834 (m-80) cc_final: 0.8618 (m-80) REVERT: E 181 ASP cc_start: 0.8676 (t70) cc_final: 0.8248 (t0) REVERT: E 249 VAL cc_start: 0.9006 (t) cc_final: 0.8658 (m) REVERT: E 281 TRP cc_start: 0.7581 (t60) cc_final: 0.7181 (t60) REVERT: F 78 TYR cc_start: 0.8732 (m-80) cc_final: 0.8326 (m-80) REVERT: F 138 ASP cc_start: 0.8645 (m-30) cc_final: 0.8436 (m-30) REVERT: F 249 VAL cc_start: 0.8985 (t) cc_final: 0.8681 (m) REVERT: F 281 TRP cc_start: 0.7564 (t60) cc_final: 0.7036 (t60) REVERT: F 407 TYR cc_start: 0.8465 (m-80) cc_final: 0.8242 (m-10) outliers start: 32 outliers final: 20 residues processed: 338 average time/residue: 0.1569 time to fit residues: 84.6765 Evaluate side-chains 259 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 276 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 185 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN B 84 GLN B 437 GLN C 56 ASN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN D 40 GLN D 84 GLN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 GLN E 84 GLN E 437 GLN F 56 ASN F 205 GLN F 437 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.109988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.076644 restraints weight = 46539.535| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.70 r_work: 0.2860 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 24360 Z= 0.243 Angle : 0.613 5.582 32994 Z= 0.321 Chirality : 0.047 0.156 3588 Planarity : 0.005 0.044 4224 Dihedral : 8.081 73.399 3402 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.88 % Allowed : 9.09 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.55 (0.15), residues: 2964 helix: -0.17 (0.14), residues: 1398 sheet: -1.68 (0.25), residues: 450 loop : -1.71 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 42 TYR 0.020 0.002 TYR F 382 PHE 0.024 0.003 PHE D 122 TRP 0.009 0.002 TRP B 385 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.24 (24360) covalent geometry : angle 0.61330 / 0.32 (32994) hydrogen bonds : bond 0.05343 / 3.57 ( 1068) hydrogen bonds : angle 4.46573 / 3.10 ( 3006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 270 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.9012 (m-80) cc_final: 0.8803 (m-80) REVERT: A 233 MET cc_start: 0.8143 (mmm) cc_final: 0.7430 (mmp) REVERT: A 238 MET cc_start: 0.6884 (ptt) cc_final: 0.6270 (pmm) REVERT: A 249 VAL cc_start: 0.8908 (t) cc_final: 0.8492 (m) REVERT: A 346 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7000 (pt0) REVERT: B 281 TRP cc_start: 0.7642 (t60) cc_final: 0.7142 (t60) REVERT: B 357 ASP cc_start: 0.7949 (m-30) cc_final: 0.7683 (m-30) REVERT: C 46 ARG cc_start: 0.8173 (mtt90) cc_final: 0.7913 (mtt90) REVERT: C 249 VAL cc_start: 0.8817 (t) cc_final: 0.8404 (m) REVERT: D 12 MET cc_start: 0.7715 (mtp) cc_final: 0.7494 (mtm) REVERT: D 78 TYR cc_start: 0.9018 (m-80) cc_final: 0.8808 (m-80) REVERT: D 249 VAL cc_start: 0.8925 (t) cc_final: 0.8513 (m) REVERT: D 308 LYS cc_start: 0.7618 (pptt) cc_final: 0.7362 (pttm) REVERT: D 346 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7008 (pt0) REVERT: D 466 ARG cc_start: 0.8442 (ttm110) cc_final: 0.8017 (tpp-160) REVERT: E 281 TRP cc_start: 0.7634 (t60) cc_final: 0.7126 (t60) REVERT: E 357 ASP cc_start: 0.7940 (m-30) cc_final: 0.7674 (m-30) REVERT: F 46 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7914 (mtt90) REVERT: F 249 VAL cc_start: 0.8817 (t) cc_final: 0.8390 (m) outliers start: 47 outliers final: 34 residues processed: 290 average time/residue: 0.1530 time to fit residues: 71.4652 Evaluate side-chains 271 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 431 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 130 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 277 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 237 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 56 ASN A 209 HIS ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN B 56 ASN B 437 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN D 56 ASN D 209 HIS ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN E 56 ASN E 437 GLN F 437 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.111692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079443 restraints weight = 46041.704| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.61 r_work: 0.2911 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (16 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24360 Z= 0.139 Angle : 0.504 6.631 32994 Z= 0.264 Chirality : 0.044 0.149 3588 Planarity : 0.004 0.040 4224 Dihedral : 7.411 69.178 3402 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.68 % Allowed : 9.78 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.00 (0.16), residues: 2964 helix: 0.32 (0.14), residues: 1398 sheet: -1.28 (0.26), residues: 450 loop : -1.55 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 478 TYR 0.012 0.001 TYR D 382 PHE 0.016 0.002 PHE D 122 TRP 0.014 0.001 TRP C 72 HIS 0.003 0.001 HIS E 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (24360) covalent geometry : angle 0.50352 / 0.26 (32994) hydrogen bonds : bond 0.04012 / 2.67 ( 1068) hydrogen bonds : angle 4.08590 / 2.83 ( 3006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 258 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7777 (mtp) cc_final: 0.7291 (mtm) REVERT: A 249 VAL cc_start: 0.8927 (t) cc_final: 0.8555 (m) REVERT: A 330 GLN cc_start: 0.7968 (mm110) cc_final: 0.7717 (mm-40) REVERT: A 346 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6936 (pt0) REVERT: B 11 LYS cc_start: 0.8374 (mtpp) cc_final: 0.8095 (mttp) REVERT: B 181 ASP cc_start: 0.8799 (t70) cc_final: 0.8510 (t0) REVERT: B 249 VAL cc_start: 0.8928 (t) cc_final: 0.8515 (m) REVERT: B 281 TRP cc_start: 0.7638 (t60) cc_final: 0.7128 (t60) REVERT: B 291 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8713 (tt) REVERT: C 46 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7902 (mtt90) REVERT: C 249 VAL cc_start: 0.8855 (t) cc_final: 0.8493 (m) REVERT: C 281 TRP cc_start: 0.7615 (t60) cc_final: 0.7066 (t60) REVERT: C 330 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7749 (mm110) REVERT: D 12 MET cc_start: 0.7664 (mtp) cc_final: 0.7305 (mtm) REVERT: D 238 MET cc_start: 0.6729 (ptt) cc_final: 0.6388 (pmm) REVERT: D 249 VAL cc_start: 0.8937 (t) cc_final: 0.8551 (m) REVERT: D 308 LYS cc_start: 0.7668 (pptt) cc_final: 0.7401 (pttm) REVERT: D 330 GLN cc_start: 0.7970 (mm110) cc_final: 0.7715 (mm-40) REVERT: D 346 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6971 (pt0) REVERT: D 466 ARG cc_start: 0.8438 (ttm110) cc_final: 0.8045 (tpp-160) REVERT: E 11 LYS cc_start: 0.8368 (mtpp) cc_final: 0.8085 (mttp) REVERT: E 249 VAL cc_start: 0.8919 (t) cc_final: 0.8502 (m) REVERT: E 291 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8711 (tt) REVERT: F 46 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7893 (mtt90) REVERT: F 249 VAL cc_start: 0.8857 (t) cc_final: 0.8501 (m) REVERT: F 281 TRP cc_start: 0.7619 (t60) cc_final: 0.7072 (t60) outliers start: 42 outliers final: 25 residues processed: 279 average time/residue: 0.1481 time to fit residues: 66.5003 Evaluate side-chains 270 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 28 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 280 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN B 437 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN E 437 GLN F 437 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.110546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.078119 restraints weight = 46259.016| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.63 r_work: 0.2881 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24360 Z= 0.184 Angle : 0.534 4.866 32994 Z= 0.281 Chirality : 0.045 0.152 3588 Planarity : 0.004 0.041 4224 Dihedral : 7.384 72.031 3402 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.80 % Allowed : 10.54 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.79 (0.16), residues: 2964 helix: 0.55 (0.14), residues: 1398 sheet: -1.17 (0.26), residues: 450 loop : -1.55 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.014 0.001 TYR D 382 PHE 0.021 0.002 PHE F 500 TRP 0.012 0.001 TRP C 72 HIS 0.003 0.001 HIS C 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (24360) covalent geometry : angle 0.53437 / 0.28 (32994) hydrogen bonds : bond 0.04517 / 3.01 ( 1068) hydrogen bonds : angle 4.16386 / 2.90 ( 3006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 250 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7770 (mtp) cc_final: 0.7398 (mtm) REVERT: A 249 VAL cc_start: 0.8888 (t) cc_final: 0.8472 (m) REVERT: A 330 GLN cc_start: 0.7962 (mm110) cc_final: 0.7707 (mm-40) REVERT: A 346 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6914 (pt0) REVERT: B 181 ASP cc_start: 0.8878 (t70) cc_final: 0.8463 (t0) REVERT: B 281 TRP cc_start: 0.7633 (t60) cc_final: 0.7116 (t60) REVERT: B 291 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8728 (tt) REVERT: B 357 ASP cc_start: 0.7939 (m-30) cc_final: 0.7658 (m-30) REVERT: C 46 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7969 (mtt90) REVERT: C 238 MET cc_start: 0.6148 (pmm) cc_final: 0.5606 (pmm) REVERT: C 249 VAL cc_start: 0.8824 (t) cc_final: 0.8421 (m) REVERT: D 249 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8453 (m) REVERT: D 330 GLN cc_start: 0.7963 (mm110) cc_final: 0.7707 (mm-40) REVERT: D 346 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6932 (pt0) REVERT: D 466 ARG cc_start: 0.8463 (ttm110) cc_final: 0.8056 (tpp-160) REVERT: E 11 LYS cc_start: 0.8373 (mtpp) cc_final: 0.8079 (mttp) REVERT: E 281 TRP cc_start: 0.7635 (t60) cc_final: 0.7157 (t60) REVERT: E 291 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8729 (tt) REVERT: E 357 ASP cc_start: 0.7936 (m-30) cc_final: 0.7647 (m-30) REVERT: F 238 MET cc_start: 0.6120 (pmm) cc_final: 0.5587 (pmm) REVERT: F 249 VAL cc_start: 0.8817 (t) cc_final: 0.8415 (m) outliers start: 45 outliers final: 28 residues processed: 269 average time/residue: 0.1552 time to fit residues: 67.1169 Evaluate side-chains 266 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 93 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 202 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 255 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN B 437 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN E 437 GLN F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.111661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.079547 restraints weight = 46089.139| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.61 r_work: 0.2913 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24360 Z= 0.137 Angle : 0.495 7.187 32994 Z= 0.260 Chirality : 0.043 0.147 3588 Planarity : 0.004 0.040 4224 Dihedral : 7.097 71.159 3402 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.52 % Allowed : 11.02 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.51 (0.16), residues: 2964 helix: 0.86 (0.14), residues: 1404 sheet: -0.98 (0.27), residues: 450 loop : -1.57 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 46 TYR 0.011 0.001 TYR D 382 PHE 0.016 0.002 PHE D 122 TRP 0.015 0.001 TRP C 72 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (24360) covalent geometry : angle 0.49508 / 0.26 (32994) hydrogen bonds : bond 0.03936 / 2.63 ( 1068) hydrogen bonds : angle 3.98948 / 2.77 ( 3006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.946 Fit side-chains REVERT: A 12 MET cc_start: 0.7727 (mtp) cc_final: 0.7353 (mtm) REVERT: A 248 VAL cc_start: 0.8283 (OUTLIER) cc_final: 0.8075 (t) REVERT: A 249 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8490 (m) REVERT: A 330 GLN cc_start: 0.7938 (mm110) cc_final: 0.7697 (mm-40) REVERT: A 346 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6945 (pt0) REVERT: A 366 MET cc_start: 0.8399 (ttm) cc_final: 0.8099 (ttm) REVERT: B 181 ASP cc_start: 0.8859 (t70) cc_final: 0.8310 (t0) REVERT: B 291 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8686 (tt) REVERT: C 238 MET cc_start: 0.6206 (pmm) cc_final: 0.5671 (pmm) REVERT: C 249 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8450 (m) REVERT: C 281 TRP cc_start: 0.7617 (t60) cc_final: 0.7049 (t60) REVERT: C 330 GLN cc_start: 0.8099 (mm110) cc_final: 0.7808 (mm-40) REVERT: C 389 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9241 (mp) REVERT: D 11 LYS cc_start: 0.8203 (mttp) cc_final: 0.7927 (pttt) REVERT: D 248 VAL cc_start: 0.8321 (m) cc_final: 0.8115 (t) REVERT: D 249 VAL cc_start: 0.8887 (t) cc_final: 0.8496 (m) REVERT: D 308 LYS cc_start: 0.7675 (pptt) cc_final: 0.7341 (pttm) REVERT: D 330 GLN cc_start: 0.7962 (mm110) cc_final: 0.7718 (mm-40) REVERT: D 346 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6961 (pt0) REVERT: D 366 MET cc_start: 0.8404 (ttm) cc_final: 0.8097 (ttm) REVERT: D 466 ARG cc_start: 0.8433 (ttm110) cc_final: 0.8022 (tpp-160) REVERT: E 11 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8055 (mttp) REVERT: E 291 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8684 (tt) REVERT: F 238 MET cc_start: 0.6179 (pmm) cc_final: 0.5643 (pmm) REVERT: F 249 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8436 (m) REVERT: F 389 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9238 (mp) outliers start: 38 outliers final: 26 residues processed: 259 average time/residue: 0.1463 time to fit residues: 62.1756 Evaluate side-chains 273 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 163 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 168 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 289 optimal weight: 0.9990 chunk 75 optimal weight: 30.0000 chunk 195 optimal weight: 0.4980 chunk 46 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 225 ASN A 364 ASN B 437 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN D 225 ASN D 364 ASN E 437 GLN F 437 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.113072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.081842 restraints weight = 46346.329| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.65 r_work: 0.2952 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24360 Z= 0.098 Angle : 0.471 8.972 32994 Z= 0.244 Chirality : 0.042 0.148 3588 Planarity : 0.004 0.042 4224 Dihedral : 6.646 70.091 3402 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.24 % Allowed : 11.58 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.12 (0.16), residues: 2964 helix: 1.26 (0.14), residues: 1404 sheet: -0.67 (0.27), residues: 438 loop : -1.54 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 42 TYR 0.008 0.001 TYR D 382 PHE 0.014 0.001 PHE F 500 TRP 0.016 0.001 TRP C 72 HIS 0.003 0.001 HIS F 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (24360) covalent geometry : angle 0.47130 / 0.24 (32994) hydrogen bonds : bond 0.03348 / 2.23 ( 1068) hydrogen bonds : angle 3.80454 / 2.64 ( 3006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 0.947 Fit side-chains REVERT: A 12 MET cc_start: 0.7728 (mtp) cc_final: 0.7341 (mtm) REVERT: A 248 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8015 (t) REVERT: A 249 VAL cc_start: 0.8918 (t) cc_final: 0.8573 (m) REVERT: A 330 GLN cc_start: 0.7866 (mm110) cc_final: 0.7649 (mm-40) REVERT: A 466 ARG cc_start: 0.8233 (ttm170) cc_final: 0.7938 (tpp-160) REVERT: B 181 ASP cc_start: 0.8814 (t70) cc_final: 0.8277 (t0) REVERT: B 248 VAL cc_start: 0.8171 (m) cc_final: 0.7944 (t) REVERT: B 249 VAL cc_start: 0.8864 (t) cc_final: 0.8550 (m) REVERT: B 291 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8714 (tt) REVERT: C 78 TYR cc_start: 0.8929 (m-80) cc_final: 0.8449 (m-80) REVERT: C 238 MET cc_start: 0.6204 (pmm) cc_final: 0.5616 (pmm) REVERT: C 249 VAL cc_start: 0.8817 (t) cc_final: 0.8470 (m) REVERT: C 330 GLN cc_start: 0.8023 (mm110) cc_final: 0.7774 (mm-40) REVERT: D 248 VAL cc_start: 0.8288 (m) cc_final: 0.8060 (t) REVERT: D 249 VAL cc_start: 0.8923 (t) cc_final: 0.8557 (m) REVERT: D 308 LYS cc_start: 0.7717 (pptt) cc_final: 0.7369 (pttm) REVERT: D 330 GLN cc_start: 0.7871 (mm110) cc_final: 0.7652 (mm-40) REVERT: D 466 ARG cc_start: 0.8410 (ttm110) cc_final: 0.8023 (tpp-160) REVERT: E 11 LYS cc_start: 0.8344 (mtpp) cc_final: 0.7921 (mttp) REVERT: E 248 VAL cc_start: 0.8179 (m) cc_final: 0.7951 (t) REVERT: E 249 VAL cc_start: 0.8858 (t) cc_final: 0.8540 (m) REVERT: E 291 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8713 (tt) REVERT: E 308 LYS cc_start: 0.8341 (ptpp) cc_final: 0.7932 (pttm) REVERT: F 78 TYR cc_start: 0.8886 (m-80) cc_final: 0.8480 (m-80) REVERT: F 238 MET cc_start: 0.6210 (pmm) cc_final: 0.5619 (pmm) REVERT: F 249 VAL cc_start: 0.8815 (t) cc_final: 0.8465 (m) outliers start: 31 outliers final: 17 residues processed: 271 average time/residue: 0.1565 time to fit residues: 69.0504 Evaluate side-chains 259 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 10 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 224 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 364 ASN B 437 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN D 40 GLN D 364 ASN E 437 GLN F 437 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.113587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.082334 restraints weight = 46721.753| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.67 r_work: 0.2961 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24360 Z= 0.092 Angle : 0.470 10.129 32994 Z= 0.243 Chirality : 0.042 0.148 3588 Planarity : 0.004 0.041 4224 Dihedral : 6.398 70.345 3402 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.04 % Allowed : 12.06 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.17 (0.16), residues: 2964 helix: 1.54 (0.14), residues: 1404 sheet: -0.63 (0.27), residues: 432 loop : -1.43 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 42 TYR 0.007 0.001 TYR D 382 PHE 0.012 0.001 PHE F 500 TRP 0.014 0.001 TRP C 72 HIS 0.003 0.001 HIS C 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (24360) covalent geometry : angle 0.46973 / 0.24 (32994) hydrogen bonds : bond 0.03190 / 2.13 ( 1068) hydrogen bonds : angle 3.73958 / 2.59 ( 3006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 0.952 Fit side-chains REVERT: A 11 LYS cc_start: 0.8350 (mtmm) cc_final: 0.8067 (mttp) REVERT: A 12 MET cc_start: 0.7732 (mtp) cc_final: 0.7351 (mtm) REVERT: A 249 VAL cc_start: 0.8921 (t) cc_final: 0.8560 (m) REVERT: A 308 LYS cc_start: 0.7753 (pptt) cc_final: 0.7488 (pttm) REVERT: A 330 GLN cc_start: 0.7858 (mm110) cc_final: 0.7641 (mm-40) REVERT: A 466 ARG cc_start: 0.8206 (ttm170) cc_final: 0.7920 (tpp-160) REVERT: B 78 TYR cc_start: 0.8907 (m-80) cc_final: 0.8630 (m-80) REVERT: B 181 ASP cc_start: 0.8778 (t70) cc_final: 0.8244 (t0) REVERT: B 248 VAL cc_start: 0.8132 (m) cc_final: 0.7885 (t) REVERT: B 249 VAL cc_start: 0.8845 (t) cc_final: 0.8537 (m) REVERT: B 291 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8732 (tt) REVERT: B 308 LYS cc_start: 0.8501 (ptpp) cc_final: 0.8036 (pttm) REVERT: B 466 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7822 (tpp-160) REVERT: C 78 TYR cc_start: 0.8844 (m-80) cc_final: 0.8468 (m-80) REVERT: C 238 MET cc_start: 0.6208 (pmm) cc_final: 0.5648 (pmm) REVERT: C 249 VAL cc_start: 0.8803 (t) cc_final: 0.8455 (m) REVERT: C 330 GLN cc_start: 0.8051 (mm110) cc_final: 0.7827 (mm-40) REVERT: D 248 VAL cc_start: 0.8243 (m) cc_final: 0.8018 (t) REVERT: D 249 VAL cc_start: 0.8917 (t) cc_final: 0.8552 (m) REVERT: D 330 GLN cc_start: 0.7876 (mm110) cc_final: 0.7656 (mm-40) REVERT: D 466 ARG cc_start: 0.8408 (ttm110) cc_final: 0.8038 (tpp-160) REVERT: E 11 LYS cc_start: 0.8347 (mtpp) cc_final: 0.7918 (mttp) REVERT: E 248 VAL cc_start: 0.8147 (m) cc_final: 0.7903 (t) REVERT: E 249 VAL cc_start: 0.8840 (t) cc_final: 0.8530 (m) REVERT: E 291 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8733 (tt) REVERT: F 78 TYR cc_start: 0.8851 (m-80) cc_final: 0.8496 (m-80) REVERT: F 238 MET cc_start: 0.6165 (pmm) cc_final: 0.5615 (pmm) REVERT: F 249 VAL cc_start: 0.8810 (t) cc_final: 0.8461 (m) REVERT: F 407 TYR cc_start: 0.8450 (m-80) cc_final: 0.8112 (m-10) outliers start: 26 outliers final: 17 residues processed: 271 average time/residue: 0.1571 time to fit residues: 69.2549 Evaluate side-chains 263 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 249 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 227 optimal weight: 0.0170 chunk 5 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 overall best weight: 1.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN B 437 GLN C 437 GLN D 40 GLN D 364 ASN E 437 GLN F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.113451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082024 restraints weight = 46764.604| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.68 r_work: 0.2954 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24360 Z= 0.095 Angle : 0.473 9.716 32994 Z= 0.244 Chirality : 0.042 0.146 3588 Planarity : 0.004 0.041 4224 Dihedral : 6.165 70.819 3398 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.76 % Allowed : 12.34 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.35 (0.16), residues: 2964 helix: 1.71 (0.14), residues: 1410 sheet: -0.55 (0.27), residues: 432 loop : -1.39 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.008 0.001 TYR D 382 PHE 0.013 0.001 PHE F 500 TRP 0.012 0.001 TRP C 72 HIS 0.003 0.001 HIS F 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.09 (24360) covalent geometry : angle 0.47285 / 0.24 (32994) hydrogen bonds : bond 0.03203 / 2.14 ( 1068) hydrogen bonds : angle 3.69910 / 2.56 ( 3006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 257 time to evaluate : 1.023 Fit side-chains REVERT: A 11 LYS cc_start: 0.8364 (mtmm) cc_final: 0.8135 (mttp) REVERT: A 12 MET cc_start: 0.7710 (mtp) cc_final: 0.7330 (mtm) REVERT: A 249 VAL cc_start: 0.8800 (t) cc_final: 0.8380 (m) REVERT: A 308 LYS cc_start: 0.7664 (pptt) cc_final: 0.7354 (pttm) REVERT: A 466 ARG cc_start: 0.8236 (ttm170) cc_final: 0.7934 (tpp-160) REVERT: B 78 TYR cc_start: 0.8898 (m-80) cc_final: 0.8641 (m-80) REVERT: B 181 ASP cc_start: 0.8776 (t70) cc_final: 0.8241 (t0) REVERT: B 248 VAL cc_start: 0.8086 (m) cc_final: 0.7840 (t) REVERT: B 249 VAL cc_start: 0.8855 (t) cc_final: 0.8507 (m) REVERT: B 281 TRP cc_start: 0.7705 (t60) cc_final: 0.7356 (t60) REVERT: B 308 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8059 (pttm) REVERT: B 330 GLN cc_start: 0.8038 (mm110) cc_final: 0.7750 (mm-40) REVERT: B 466 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7864 (tpp-160) REVERT: C 78 TYR cc_start: 0.8817 (m-80) cc_final: 0.8493 (m-80) REVERT: C 238 MET cc_start: 0.6224 (pmm) cc_final: 0.5644 (pmm) REVERT: C 248 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7913 (t) REVERT: C 249 VAL cc_start: 0.8816 (t) cc_final: 0.8478 (m) REVERT: C 308 LYS cc_start: 0.8358 (ptpp) cc_final: 0.8122 (pttm) REVERT: C 330 GLN cc_start: 0.8039 (mm110) cc_final: 0.7826 (mm-40) REVERT: D 12 MET cc_start: 0.7641 (mtp) cc_final: 0.7406 (mtm) REVERT: D 248 VAL cc_start: 0.8169 (m) cc_final: 0.7938 (t) REVERT: D 249 VAL cc_start: 0.8791 (t) cc_final: 0.8369 (m) REVERT: D 466 ARG cc_start: 0.8420 (ttm110) cc_final: 0.8054 (tpp-160) REVERT: E 11 LYS cc_start: 0.8342 (mtpp) cc_final: 0.7905 (mttp) REVERT: E 78 TYR cc_start: 0.8912 (m-80) cc_final: 0.8651 (m-80) REVERT: E 248 VAL cc_start: 0.8093 (m) cc_final: 0.7835 (t) REVERT: E 249 VAL cc_start: 0.8854 (t) cc_final: 0.8499 (m) REVERT: E 330 GLN cc_start: 0.8055 (mm110) cc_final: 0.7766 (mm-40) REVERT: E 466 ARG cc_start: 0.8249 (ttm170) cc_final: 0.7888 (tpp-160) REVERT: F 78 TYR cc_start: 0.8857 (m-80) cc_final: 0.8540 (m-80) REVERT: F 238 MET cc_start: 0.6204 (pmm) cc_final: 0.5645 (pmm) REVERT: F 249 VAL cc_start: 0.8809 (t) cc_final: 0.8465 (m) REVERT: F 308 LYS cc_start: 0.8380 (ptpp) cc_final: 0.8143 (pttm) REVERT: F 407 TYR cc_start: 0.8467 (m-80) cc_final: 0.8108 (m-10) outliers start: 19 outliers final: 15 residues processed: 264 average time/residue: 0.1637 time to fit residues: 69.1710 Evaluate side-chains 260 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 457 MET Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 457 MET Chi-restraints excluded: chain F residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 181 optimal weight: 5.9990 chunk 261 optimal weight: 0.0170 chunk 275 optimal weight: 0.0470 chunk 35 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 364 ASN C 437 GLN D 40 GLN D 364 ASN F 205 GLN F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.112960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081574 restraints weight = 46227.249| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.64 r_work: 0.2950 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24360 Z= 0.104 Angle : 0.478 8.971 32994 Z= 0.247 Chirality : 0.042 0.148 3588 Planarity : 0.004 0.042 4224 Dihedral : 6.068 71.463 3394 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.04 % Allowed : 12.30 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.43 (0.16), residues: 2964 helix: 1.80 (0.14), residues: 1410 sheet: -0.52 (0.28), residues: 432 loop : -1.39 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 46 TYR 0.009 0.001 TYR D 382 PHE 0.014 0.001 PHE D 122 TRP 0.011 0.001 TRP C 72 HIS 0.003 0.001 HIS C 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (24360) covalent geometry : angle 0.47753 / 0.25 (32994) hydrogen bonds : bond 0.03336 / 2.23 ( 1068) hydrogen bonds : angle 3.70903 / 2.57 ( 3006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4833.45 seconds wall clock time: 84 minutes 7.83 seconds (5047.83 seconds total)