Starting phenix.real_space_refine on Sat Feb 7 00:32:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3j_72199/02_2026/9q3j_72199.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3j_72199/02_2026/9q3j_72199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q3j_72199/02_2026/9q3j_72199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3j_72199/02_2026/9q3j_72199.map" model { file = "/net/cci-nas-00/data/ceres_data/9q3j_72199/02_2026/9q3j_72199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3j_72199/02_2026/9q3j_72199.cif" } resolution = 3.15 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= 0.004 sd= 0.152 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: 4 Type Number sf(0) Gaussians S 235 5.16 5 C 18400 2.51 5 N 4831 2.21 5 O 5366 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28832 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3597 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3603 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3606 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 452, 3600 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 452, 3600 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 3689 Chain: "D" Number of atoms: 3597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3597 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 3618 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3598 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 451, 3598 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 bond proxies already assigned to first conformer: 3670 Chain: "F" Number of atoms: 3608 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3598 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 451, 3598 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 bond proxies already assigned to first conformer: 3682 Chain: "G" Number of atoms: 3604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3604 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "H" Number of atoms: 3599 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 450, 3592 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 450, 3592 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 22, 'TRANS': 427} Chain breaks: 2 bond proxies already assigned to first conformer: 3679 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AHIS E 139 " occ=0.68 ... (18 atoms not shown) pdb=" NE2BHIS E 139 " occ=0.32 residue: pdb=" N AHIS E 370 " occ=0.47 ... (18 atoms not shown) pdb=" NE2BHIS E 370 " occ=0.53 residue: pdb=" N AHIS F 370 " occ=0.55 ... (18 atoms not shown) pdb=" NE2BHIS F 370 " occ=0.45 Time building chain proxies: 9.38, per 1000 atoms: 0.33 Number of scatterers: 28832 At special positions: 0 Unit cell: (135.16, 135.16, 123.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 235 16.00 O 5366 8.00 N 4831 7.00 C 18400 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: 2.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6656 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 44 sheets defined 42.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 41 through 52 Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 85 through 101 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 138 removed outlier: 6.756A pdb=" N GLU A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N GLU A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A 133 " --> pdb=" O PHE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.777A pdb=" N SER A 199 " --> pdb=" O GLY A 195 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.880A pdb=" N SER A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 248 Processing helix chain 'A' and resid 272 through 287 Proline residue: A 277 - end of helix removed outlier: 3.844A pdb=" N LEU A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.607A pdb=" N ASN A 378 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG A 379 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.733A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 413 through 419 removed outlier: 3.731A pdb=" N MET A 417 " --> pdb=" O HIS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 4.436A pdb=" N ALA A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 455 Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 58 through 63 Processing helix chain 'B' and resid 85 through 102 Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 121 through 138 removed outlier: 6.579A pdb=" N GLU B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N GLU B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU B 133 " --> pdb=" O PHE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 170 through 174 Processing helix chain 'B' and resid 194 through 203 removed outlier: 3.950A pdb=" N SER B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.887A pdb=" N SER B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 248 Processing helix chain 'B' and resid 272 through 287 Proline residue: B 277 - end of helix removed outlier: 3.857A pdb=" N LEU B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 331 Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 373 through 379 removed outlier: 3.662A pdb=" N ASN B 378 " --> pdb=" O PRO B 375 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG B 379 " --> pdb=" O ASP B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.624A pdb=" N THR B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 397 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 419 removed outlier: 3.557A pdb=" N MET B 417 " --> pdb=" O HIS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 436 removed outlier: 4.337A pdb=" N ALA B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 455 Processing helix chain 'C' and resid 41 through 52 Processing helix chain 'C' and resid 58 through 63 removed outlier: 3.635A pdb=" N LEU C 62 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 101 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 121 through 138 removed outlier: 6.631A pdb=" N GLU C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N GLU C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C 133 " --> pdb=" O PHE C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 170 through 175 Processing helix chain 'C' and resid 197 through 203 removed outlier: 3.600A pdb=" N ILE C 203 " --> pdb=" O SER C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.779A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 248 Processing helix chain 'C' and resid 272 through 287 Proline residue: C 277 - end of helix removed outlier: 3.739A pdb=" N LEU C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 332 Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.720A pdb=" N ASN C 378 " --> pdb=" O PRO C 375 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG C 379 " --> pdb=" O ASP C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.665A pdb=" N THR C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 397 Processing helix chain 'C' and resid 401 through 407 removed outlier: 4.058A pdb=" N GLY C 405 " --> pdb=" O PRO C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 429 through 436 removed outlier: 4.300A pdb=" N ALA C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 455 Processing helix chain 'D' and resid 41 through 52 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.514A pdb=" N LEU D 62 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 101 Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 121 through 130 Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 170 through 175 removed outlier: 3.566A pdb=" N CYS D 175 " --> pdb=" O TYR D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.683A pdb=" N SER D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 203 " --> pdb=" O SER D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 248 Processing helix chain 'D' and resid 272 through 287 Proline residue: D 277 - end of helix removed outlier: 3.627A pdb=" N LEU D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 331 Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 373 through 379 removed outlier: 3.595A pdb=" N ASN D 378 " --> pdb=" O PRO D 375 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG D 379 " --> pdb=" O ASP D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 386 removed outlier: 3.753A pdb=" N THR D 386 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 397 Processing helix chain 'D' and resid 403 through 407 Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 429 through 436 removed outlier: 4.311A pdb=" N ALA D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 455 Processing helix chain 'E' and resid 41 through 52 Processing helix chain 'E' and resid 58 through 63 Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'E' and resid 131 through 138 removed outlier: 3.598A pdb=" N ASN E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 194 through 203 removed outlier: 3.671A pdb=" N HIS E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE E 203 " --> pdb=" O SER E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 210 Processing helix chain 'E' and resid 235 through 248 Processing helix chain 'E' and resid 272 through 287 Proline residue: E 277 - end of helix removed outlier: 3.850A pdb=" N LEU E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 331 Processing helix chain 'E' and resid 358 through 368 Processing helix chain 'E' and resid 373 through 379 removed outlier: 3.664A pdb=" N ASN E 378 " --> pdb=" O PRO E 375 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG E 379 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 386 removed outlier: 3.550A pdb=" N THR E 386 " --> pdb=" O GLU E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 397 Processing helix chain 'E' and resid 401 through 407 removed outlier: 3.965A pdb=" N GLY E 405 " --> pdb=" O PRO E 402 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER E 407 " --> pdb=" O HIS E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 417 removed outlier: 3.999A pdb=" N GLU E 416 " --> pdb=" O GLY E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 436 removed outlier: 4.201A pdb=" N ALA E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 455 Processing helix chain 'F' and resid 41 through 51 Processing helix chain 'F' and resid 58 through 63 Processing helix chain 'F' and resid 85 through 102 Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 121 through 130 Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.669A pdb=" N ASN F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 170 through 175 removed outlier: 3.515A pdb=" N CYS F 175 " --> pdb=" O TYR F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 204 removed outlier: 3.789A pdb=" N THR F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 Processing helix chain 'F' and resid 235 through 248 Processing helix chain 'F' and resid 272 through 288 Proline residue: F 277 - end of helix removed outlier: 3.986A pdb=" N LEU F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS F 285 " --> pdb=" O LYS F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 331 Processing helix chain 'F' and resid 358 through 368 Processing helix chain 'F' and resid 374 through 379 removed outlier: 4.737A pdb=" N ARG F 379 " --> pdb=" O ASP F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 386 removed outlier: 3.518A pdb=" N THR F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 397 Processing helix chain 'F' and resid 403 through 407 Processing helix chain 'F' and resid 411 through 412 No H-bonds generated for 'chain 'F' and resid 411 through 412' Processing helix chain 'F' and resid 413 through 419 removed outlier: 3.612A pdb=" N ASN F 418 " --> pdb=" O ILE F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 436 removed outlier: 4.288A pdb=" N ALA F 433 " --> pdb=" O GLU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 455 Processing helix chain 'G' and resid 41 through 52 Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 85 through 102 Processing helix chain 'G' and resid 121 through 138 removed outlier: 7.287A pdb=" N GLU G 131 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N GLU G 132 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU G 133 " --> pdb=" O PHE G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 141 No H-bonds generated for 'chain 'G' and resid 139 through 141' Processing helix chain 'G' and resid 170 through 175 Processing helix chain 'G' and resid 194 through 204 removed outlier: 3.743A pdb=" N HIS G 198 " --> pdb=" O GLY G 194 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE G 203 " --> pdb=" O SER G 199 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR G 204 " --> pdb=" O ALA G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 211 removed outlier: 3.503A pdb=" N ILE G 209 " --> pdb=" O ASN G 205 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 248 Processing helix chain 'G' and resid 272 through 288 Proline residue: G 277 - end of helix removed outlier: 3.987A pdb=" N LEU G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS G 285 " --> pdb=" O LYS G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 331 Processing helix chain 'G' and resid 358 through 368 Processing helix chain 'G' and resid 374 through 379 removed outlier: 4.400A pdb=" N ARG G 379 " --> pdb=" O ASP G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 386 removed outlier: 3.524A pdb=" N THR G 386 " --> pdb=" O GLU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 397 Processing helix chain 'G' and resid 403 through 407 Processing helix chain 'G' and resid 414 through 418 removed outlier: 3.965A pdb=" N ASN G 418 " --> pdb=" O ILE G 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 414 through 418' Processing helix chain 'G' and resid 429 through 436 removed outlier: 4.209A pdb=" N ALA G 433 " --> pdb=" O GLU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 455 Processing helix chain 'H' and resid 41 through 52 Processing helix chain 'H' and resid 58 through 63 Processing helix chain 'H' and resid 85 through 102 Processing helix chain 'H' and resid 121 through 138 removed outlier: 7.255A pdb=" N GLU H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N GLU H 132 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU H 133 " --> pdb=" O PHE H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 141 No H-bonds generated for 'chain 'H' and resid 139 through 141' Processing helix chain 'H' and resid 170 through 174 Processing helix chain 'H' and resid 195 through 203 removed outlier: 3.682A pdb=" N ILE H 203 " --> pdb=" O SER H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 210 Processing helix chain 'H' and resid 235 through 248 Processing helix chain 'H' and resid 272 through 287 Proline residue: H 277 - end of helix removed outlier: 3.893A pdb=" N LEU H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG H 286 " --> pdb=" O LEU H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 331 Processing helix chain 'H' and resid 358 through 368 Processing helix chain 'H' and resid 374 through 379 removed outlier: 4.468A pdb=" N ARG H 379 " --> pdb=" O ASP H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 386 removed outlier: 3.553A pdb=" N THR H 386 " --> pdb=" O GLU H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 397 Processing helix chain 'H' and resid 413 through 419 Processing helix chain 'H' and resid 429 through 436 removed outlier: 4.233A pdb=" N ALA H 433 " --> pdb=" O GLU H 429 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 455 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 removed outlier: 3.693A pdb=" N TYR A 9 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.107A pdb=" N ASP A 23 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU A 463 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL A 298 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP A 297 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE A 342 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA A 344 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N PHE A 301 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA A 421 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N CYS A 339 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N TYR A 423 " --> pdb=" O CYS A 339 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE A 341 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 425 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N CYS A 343 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 145 removed outlier: 8.635A pdb=" N ILE A 144 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE A 110 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL A 69 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE A 111 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 71 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER A 113 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 73 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N HIS A 183 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N CYS A 254 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 180 " --> pdb=" O CYS A 254 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA A 256 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY A 182 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU A 258 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL A 184 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A 266 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 159 removed outlier: 6.949A pdb=" N VAL A 166 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA6, first strand: chain 'A' and resid 306 through 307 removed outlier: 3.569A pdb=" N PHE A 307 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 9 Processing sheet with id=AA8, first strand: chain 'B' and resid 23 through 24 removed outlier: 6.140A pdb=" N ASP B 23 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B 463 " --> pdb=" O TYR B 296 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 298 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP B 297 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE B 342 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA B 344 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N PHE B 301 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ALA B 421 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N CYS B 339 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N TYR B 423 " --> pdb=" O CYS B 339 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 341 " --> pdb=" O TYR B 423 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL B 425 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N CYS B 343 " --> pdb=" O VAL B 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 143 through 145 removed outlier: 8.572A pdb=" N ILE B 144 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE B 110 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 69 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE B 111 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE B 71 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N SER B 113 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 73 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR B 70 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE B 181 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 72 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N HIS B 183 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 13.646A pdb=" N GLN B 185 " --> pdb=" O PRO B 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 143 through 145 removed outlier: 8.572A pdb=" N ILE B 144 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE B 110 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 69 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE B 111 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE B 71 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N SER B 113 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 73 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N THR B 70 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE B 181 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 72 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N HIS B 183 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 13.646A pdb=" N GLN B 185 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N CYS B 254 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU B 180 " --> pdb=" O CYS B 254 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ALA B 256 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLY B 182 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU B 258 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL B 184 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA B 266 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 154 through 159 removed outlier: 6.886A pdb=" N VAL B 166 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 288 through 290 Processing sheet with id=AB4, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AB5, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.217A pdb=" N ASP C 23 " --> pdb=" O ALA C 464 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU C 463 " --> pdb=" O TYR C 296 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL C 298 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU C 465 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL C 300 " --> pdb=" O LEU C 465 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASP C 297 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N ALA C 421 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS C 339 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N TYR C 423 " --> pdb=" O CYS C 339 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 341 " --> pdb=" O TYR C 423 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL C 425 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N CYS C 343 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 145 removed outlier: 8.641A pdb=" N ILE C 144 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE C 110 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL C 69 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE C 111 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ILE C 71 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N SER C 113 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 73 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N HIS C 183 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 182 " --> pdb=" O CYS C 254 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 266 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB8, first strand: chain 'C' and resid 288 through 290 Processing sheet with id=AB9, first strand: chain 'C' and resid 306 through 307 removed outlier: 3.708A pdb=" N PHE C 307 " --> pdb=" O GLY C 310 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AC2, first strand: chain 'D' and resid 23 through 24 removed outlier: 6.215A pdb=" N ASP D 23 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU D 463 " --> pdb=" O TYR D 296 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL D 298 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP D 297 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE D 342 " --> pdb=" O ASP D 297 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA D 344 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N PHE D 301 " --> pdb=" O ALA D 344 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ALA D 421 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N CYS D 339 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR D 423 " --> pdb=" O CYS D 339 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 341 " --> pdb=" O TYR D 423 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL D 425 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N CYS D 343 " --> pdb=" O VAL D 425 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 143 through 145 removed outlier: 8.632A pdb=" N ILE D 144 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE D 110 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL D 69 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE D 111 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE D 71 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER D 113 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 73 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR D 70 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE D 181 " --> pdb=" O THR D 70 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL D 72 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N HIS D 183 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N CYS D 254 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU D 180 " --> pdb=" O CYS D 254 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA D 256 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY D 182 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU D 258 " --> pdb=" O GLY D 182 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL D 184 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA D 266 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 154 through 159 removed outlier: 6.882A pdb=" N VAL D 166 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 288 through 290 Processing sheet with id=AC6, first strand: chain 'D' and resid 306 through 307 removed outlier: 3.625A pdb=" N PHE D 307 " --> pdb=" O GLY D 310 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 5 through 9 removed outlier: 3.580A pdb=" N TYR E 9 " --> pdb=" O GLY E 12 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 23 through 24 removed outlier: 6.034A pdb=" N ASP E 23 " --> pdb=" O ALA E 464 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASP E 297 " --> pdb=" O ASN E 338 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N THR E 419 " --> pdb=" O MET E 335 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N ASP E 337 " --> pdb=" O THR E 419 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ALA E 421 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N CYS E 339 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N TYR E 423 " --> pdb=" O CYS E 339 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE E 341 " --> pdb=" O TYR E 423 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL E 425 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS E 343 " --> pdb=" O VAL E 425 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 143 through 145 removed outlier: 8.827A pdb=" N HIS E 183 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY E 182 " --> pdb=" O CYS E 254 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 258 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS E 253 " --> pdb=" O SER E 269 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER E 269 " --> pdb=" O CYS E 253 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP E 255 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE E 267 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL E 257 " --> pdb=" O ILE E 265 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 154 through 159 removed outlier: 6.066A pdb=" N VAL E 166 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 288 through 292 removed outlier: 6.779A pdb=" N HIS E 475 " --> pdb=" O TYR E 288 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N HIS E 290 " --> pdb=" O HIS E 475 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYS E 477 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 5 through 9 Processing sheet with id=AD4, first strand: chain 'F' and resid 23 through 24 removed outlier: 6.150A pdb=" N ASP F 23 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY F 302 " --> pdb=" O LEU F 465 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASP F 297 " --> pdb=" O ASN F 338 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA F 421 " --> pdb=" O CYS F 339 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 143 through 145 removed outlier: 8.565A pdb=" N ILE F 144 " --> pdb=" O ILE F 108 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N PHE F 110 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N HIS F 183 " --> pdb=" O PRO F 74 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N CYS F 254 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU F 180 " --> pdb=" O CYS F 254 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA F 256 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY F 182 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU F 258 " --> pdb=" O GLY F 182 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL F 184 " --> pdb=" O LEU F 258 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA F 266 " --> pdb=" O VAL F 257 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 154 through 159 removed outlier: 6.156A pdb=" N VAL F 166 " --> pdb=" O LEU F 157 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 289 through 292 removed outlier: 6.364A pdb=" N VAL F 289 " --> pdb=" O CYS F 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AD9, first strand: chain 'G' and resid 23 through 24 removed outlier: 6.144A pdb=" N ASP G 23 " --> pdb=" O ALA G 464 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU G 463 " --> pdb=" O TYR G 296 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL G 298 " --> pdb=" O LEU G 463 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU G 465 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 300 " --> pdb=" O LEU G 465 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASP G 297 " --> pdb=" O ASN G 338 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N THR G 419 " --> pdb=" O MET G 335 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N ASP G 337 " --> pdb=" O THR G 419 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA G 421 " --> pdb=" O ASP G 337 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N CYS G 339 " --> pdb=" O ALA G 421 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N TYR G 423 " --> pdb=" O CYS G 339 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE G 341 " --> pdb=" O TYR G 423 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL G 425 " --> pdb=" O ILE G 341 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N CYS G 343 " --> pdb=" O VAL G 425 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 143 through 145 removed outlier: 9.046A pdb=" N HIS G 183 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY G 182 " --> pdb=" O CYS G 254 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU G 258 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS G 253 " --> pdb=" O SER G 269 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER G 269 " --> pdb=" O CYS G 253 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP G 255 " --> pdb=" O ILE G 267 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE G 267 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL G 257 " --> pdb=" O ILE G 265 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 154 through 159 removed outlier: 5.843A pdb=" N VAL G 166 " --> pdb=" O LEU G 157 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 289 through 292 removed outlier: 6.136A pdb=" N VAL G 289 " --> pdb=" O CYS G 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'H' and resid 5 through 9 removed outlier: 3.627A pdb=" N TYR H 9 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 23 through 24 removed outlier: 6.129A pdb=" N ASP H 23 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP H 297 " --> pdb=" O ASN H 338 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA H 421 " --> pdb=" O CYS H 339 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE H 422 " --> pdb=" O LYS H 439 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 143 through 145 removed outlier: 8.840A pdb=" N HIS H 183 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY H 182 " --> pdb=" O CYS H 254 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 256 " --> pdb=" O GLY H 182 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU H 258 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N CYS H 253 " --> pdb=" O SER H 269 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER H 269 " --> pdb=" O CYS H 253 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP H 255 " --> pdb=" O ILE H 267 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE H 267 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL H 257 " --> pdb=" O ILE H 265 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 154 through 159 removed outlier: 6.028A pdb=" N VAL H 166 " --> pdb=" O LEU H 157 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 288 through 292 removed outlier: 6.397A pdb=" N VAL H 289 " --> pdb=" O CYS H 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 1055 hydrogen bonds defined for protein. 2976 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: 5.36 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9347 1.34 - 1.46: 6333 1.46 - 1.58: 13524 1.58 - 1.69: 2 1.69 - 1.81: 403 Bond restraints: 29609 Sorted by residual: bond pdb=" N PRO H 57 " pdb=" CD PRO H 57 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.13e+01 bond pdb=" N PRO F 57 " pdb=" CD PRO F 57 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.70e+01 bond pdb=" CG PRO F 57 " pdb=" CD PRO F 57 " ideal model delta sigma weight residual 1.503 1.383 0.120 3.40e-02 8.65e+02 1.24e+01 bond pdb=" N PRO F 57 " pdb=" CA PRO F 57 " ideal model delta sigma weight residual 1.464 1.432 0.031 9.30e-03 1.16e+04 1.11e+01 bond pdb=" CB PRO H 57 " pdb=" CG PRO H 57 " ideal model delta sigma weight residual 1.492 1.649 -0.157 5.00e-02 4.00e+02 9.86e+00 ... (remaining 29604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 39859 3.42 - 6.83: 136 6.83 - 10.25: 7 10.25 - 13.66: 2 13.66 - 17.08: 2 Bond angle restraints: 40006 Sorted by residual: angle pdb=" CA PRO H 57 " pdb=" N PRO H 57 " pdb=" CD PRO H 57 " ideal model delta sigma weight residual 112.00 94.92 17.08 1.40e+00 5.10e-01 1.49e+02 angle pdb=" CA PRO F 57 " pdb=" N PRO F 57 " pdb=" CD PRO F 57 " ideal model delta sigma weight residual 112.00 96.47 15.53 1.40e+00 5.10e-01 1.23e+02 angle pdb=" N PRO F 57 " pdb=" CD PRO F 57 " pdb=" CG PRO F 57 " ideal model delta sigma weight residual 103.20 92.97 10.23 1.50e+00 4.44e-01 4.65e+01 angle pdb=" N PRO H 57 " pdb=" CD PRO H 57 " pdb=" CG PRO H 57 " ideal model delta sigma weight residual 103.20 93.17 10.03 1.50e+00 4.44e-01 4.47e+01 angle pdb=" N PRO H 57 " pdb=" CA PRO H 57 " pdb=" CB PRO H 57 " ideal model delta sigma weight residual 103.25 98.74 4.51 1.05e+00 9.07e-01 1.84e+01 ... (remaining 40001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14909 17.93 - 35.87: 1930 35.87 - 53.80: 568 53.80 - 71.73: 102 71.73 - 89.67: 29 Dihedral angle restraints: 17538 sinusoidal: 7093 harmonic: 10445 Sorted by residual: dihedral pdb=" CA LYS A 454 " pdb=" C LYS A 454 " pdb=" N TYR A 455 " pdb=" CA TYR A 455 " ideal model delta harmonic sigma weight residual -180.00 -156.93 -23.07 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LYS C 454 " pdb=" C LYS C 454 " pdb=" N TYR C 455 " pdb=" CA TYR C 455 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LYS D 454 " pdb=" C LYS D 454 " pdb=" N TYR D 455 " pdb=" CA TYR D 455 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 17535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3190 0.045 - 0.091: 643 0.091 - 0.136: 320 0.136 - 0.182: 3 0.182 - 0.227: 3 Chirality restraints: 4159 Sorted by residual: chirality pdb=" CB ILE B 54 " pdb=" CA ILE B 54 " pdb=" CG1 ILE B 54 " pdb=" CG2 ILE B 54 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA PRO H 57 " pdb=" N PRO H 57 " pdb=" C PRO H 57 " pdb=" CB PRO H 57 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 4156 not shown) Planarity restraints: 5189 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET H 56 " 0.069 5.00e-02 4.00e+02 9.27e-02 1.38e+01 pdb=" N PRO H 57 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO H 57 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO H 57 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 56 " 0.065 5.00e-02 4.00e+02 8.84e-02 1.25e+01 pdb=" N PRO F 57 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 57 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 57 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO H 57 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C PRO H 57 " 0.036 2.00e-02 2.50e+03 pdb=" O PRO H 57 " -0.014 2.00e-02 2.50e+03 pdb=" N THR H 58 " -0.012 2.00e-02 2.50e+03 ... (remaining 5186 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4236 2.76 - 3.29: 25739 3.29 - 3.83: 48031 3.83 - 4.36: 59090 4.36 - 4.90: 104592 Nonbonded interactions: 241688 Sorted by model distance: nonbonded pdb=" OH TYR D 192 " pdb=" OD1 ASP D 284 " model vdw 2.222 3.040 nonbonded pdb=" O TYR H 309 " pdb=" NH1 ARG H 355 " model vdw 2.226 3.120 nonbonded pdb=" OD2 ASP B 164 " pdb=" OG SER B 211 " model vdw 2.231 3.040 nonbonded pdb=" O ALA D 200 " pdb=" OG1 THR D 204 " model vdw 2.246 3.040 nonbonded pdb=" OH TYR H 192 " pdb=" OD1 ASP H 284 " model vdw 2.254 3.040 ... (remaining 241683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 138 or resid 140 through 210 or resid 234 throug \ h 284 or resid 286 through 369 or resid 371 through 480)) selection = (chain 'B' and (resid 4 through 138 or resid 140 through 210 or resid 234 throug \ h 283 or (resid 284 and (name N or name CA or name C or name O or name CB )) or \ resid 286 through 369 or resid 371 through 413 or (resid 414 through 415 and (na \ me N or name CA or name C or name O or name CB )) or resid 416 through 480)) selection = (chain 'C' and (resid 4 through 138 or resid 140 through 210 or resid 234 throug \ h 284 or resid 286 through 369 or resid 371 through 413 or (resid 414 through 41 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 416 through \ 480)) selection = (chain 'D' and (resid 4 through 138 or resid 140 through 210 or resid 234 throug \ h 283 or (resid 284 and (name N or name CA or name C or name O or name CB )) or \ resid 286 through 369 or resid 371 through 413 or (resid 414 through 415 and (na \ me N or name CA or name C or name O or name CB )) or resid 416 through 480)) selection = (chain 'E' and (resid 4 through 138 or resid 140 through 283 or (resid 284 and ( \ name N or name CA or name C or name O or name CB )) or resid 286 through 369 or \ resid 371 through 407 or resid 412 through 413 or (resid 414 through 415 and (na \ me N or name CA or name C or name O or name CB )) or resid 416 through 480)) selection = (chain 'F' and (resid 4 through 138 or resid 140 through 283 or (resid 284 and ( \ name N or name CA or name C or name O or name CB )) or resid 286 through 369 or \ resid 371 through 407 or resid 412 through 413 or (resid 414 through 415 and (na \ me N or name CA or name C or name O or name CB )) or resid 416 through 480)) selection = (chain 'G' and (resid 4 through 138 or resid 140 through 210 or resid 234 throug \ h 283 or (resid 284 and (name N or name CA or name C or name O or name CB )) or \ resid 286 through 369 or resid 371 through 407 or resid 412 through 413 or (resi \ d 414 through 415 and (name N or name CA or name C or name O or name CB )) or re \ sid 416 through 480)) selection = (chain 'H' and (resid 4 through 138 or resid 140 through 283 or (resid 284 and ( \ name N or name CA or name C or name O or name CB )) or resid 286 through 369 or \ resid 371 through 413 or (resid 414 through 415 and (name N or name CA or name C \ or name O or name CB )) or resid 416 through 480)) } 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=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.040 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 29.210 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 0.003 0.157 29609 Z= 0.122 Angle : 0.552 17.079 40006 Z= 0.297 Chirality : 0.043 0.227 4159 Planarity : 0.004 0.093 5189 Dihedral : 17.490 89.666 10882 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.10 % Allowed : 23.19 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3574 helix: 0.30 (0.15), residues: 1270 sheet: 1.08 (0.24), residues: 497 loop : -0.47 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 162 TYR 0.011 0.001 TYR B 9 PHE 0.018 0.001 PHE B 173 TRP 0.014 0.001 TRP G 138 HIS 0.007 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00297 (29609) covalent geometry : angle 0.55159 (40006) hydrogen bonds : bond 0.14317 ( 1055) hydrogen bonds : angle 6.48848 ( 2976) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 353 time to evaluate : 1.093 Fit side-chains REVERT: G 450 ASP cc_start: 0.8771 (t0) cc_final: 0.8327 (t0) outliers start: 3 outliers final: 2 residues processed: 355 average time/residue: 0.1722 time to fit residues: 99.7208 Evaluate side-chains 347 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 345 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain H residue 52 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.1980 chunk 298 optimal weight: 4.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 HIS C 372 ASN G 183 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.111017 restraints weight = 69122.590| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.55 r_work: 0.3058 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 29609 Z= 0.283 Angle : 0.610 8.369 40006 Z= 0.311 Chirality : 0.048 0.217 4159 Planarity : 0.004 0.050 5189 Dihedral : 4.735 39.469 3912 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.90 % Allowed : 21.98 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.14), residues: 3574 helix: 0.19 (0.14), residues: 1351 sheet: 0.96 (0.25), residues: 477 loop : -0.66 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 441 TYR 0.015 0.002 TYR B 9 PHE 0.025 0.002 PHE H 134 TRP 0.010 0.002 TRP A 356 HIS 0.007 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00698 (29609) covalent geometry : angle 0.60995 (40006) hydrogen bonds : bond 0.04178 ( 1055) hydrogen bonds : angle 5.26940 ( 2976) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 353 time to evaluate : 0.851 Fit side-chains REVERT: A 26 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7582 (mm) REVERT: B 261 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: B 417 MET cc_start: 0.7558 (ptp) cc_final: 0.7317 (ptp) REVERT: C 235 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7006 (tttt) REVERT: C 417 MET cc_start: 0.7987 (mtp) cc_final: 0.7450 (mtt) REVERT: E 285 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8635 (ttpt) REVERT: G 239 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8122 (mp) REVERT: H 152 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7968 (pm20) outliers start: 58 outliers final: 38 residues processed: 390 average time/residue: 0.1726 time to fit residues: 109.8832 Evaluate side-chains 380 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 336 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 275 MET Chi-restraints excluded: chain G residue 276 MET Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 253 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 240 optimal weight: 0.8980 chunk 299 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 321 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112168 restraints weight = 67475.175| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.63 r_work: 0.3076 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29609 Z= 0.167 Angle : 0.530 7.716 40006 Z= 0.271 Chirality : 0.045 0.198 4159 Planarity : 0.004 0.049 5189 Dihedral : 4.573 38.716 3912 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.70 % Allowed : 22.44 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3574 helix: 0.37 (0.14), residues: 1352 sheet: 0.86 (0.24), residues: 501 loop : -0.60 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 355 TYR 0.014 0.001 TYR B 9 PHE 0.019 0.001 PHE E 134 TRP 0.008 0.001 TRP A 356 HIS 0.006 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00416 (29609) covalent geometry : angle 0.52954 (40006) hydrogen bonds : bond 0.03258 ( 1055) hydrogen bonds : angle 4.94041 ( 2976) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 367 time to evaluate : 1.121 Fit side-chains REVERT: A 26 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7519 (mm) REVERT: A 105 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8027 (tttp) REVERT: A 152 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: B 162 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7007 (mtp180) REVERT: B 273 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8643 (ttmm) REVERT: C 235 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7265 (ttpt) REVERT: C 417 MET cc_start: 0.7999 (mtp) cc_final: 0.7474 (mtt) REVERT: F 371 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7886 (mtt) REVERT: G 126 LYS cc_start: 0.8628 (mmtm) cc_final: 0.8412 (tppp) REVERT: G 239 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8060 (mp) REVERT: H 152 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7945 (pm20) outliers start: 52 outliers final: 30 residues processed: 398 average time/residue: 0.1669 time to fit residues: 108.5268 Evaluate side-chains 389 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 350 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 276 MET Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 311 ASP Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 168 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 372 ASN D 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109122 restraints weight = 66410.993| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.56 r_work: 0.3042 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 29609 Z= 0.349 Angle : 0.647 9.910 40006 Z= 0.329 Chirality : 0.050 0.203 4159 Planarity : 0.005 0.051 5189 Dihedral : 4.857 32.336 3910 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.52 % Allowed : 22.21 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.14), residues: 3574 helix: 0.21 (0.14), residues: 1351 sheet: 0.75 (0.25), residues: 475 loop : -0.80 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 441 TYR 0.019 0.002 TYR C 93 PHE 0.023 0.002 PHE H 134 TRP 0.010 0.002 TRP D 291 HIS 0.006 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00861 (29609) covalent geometry : angle 0.64654 (40006) hydrogen bonds : bond 0.04210 ( 1055) hydrogen bonds : angle 5.11833 ( 2976) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 340 time to evaluate : 1.086 Fit side-chains REVERT: A 26 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7688 (mm) REVERT: A 48 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: A 105 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8098 (tttt) REVERT: A 152 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: A 318 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8320 (mm) REVERT: B 162 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7091 (mtp180) REVERT: B 261 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: B 273 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8631 (ttmm) REVERT: B 318 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8749 (mm) REVERT: C 235 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7016 (tttt) REVERT: D 338 ASN cc_start: 0.6926 (p0) cc_final: 0.6653 (p0) REVERT: E 180 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8881 (mp) REVERT: F 134 PHE cc_start: 0.8831 (t80) cc_final: 0.8601 (t80) REVERT: G 126 LYS cc_start: 0.8699 (mmtm) cc_final: 0.8258 (tppp) REVERT: G 152 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: G 239 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8178 (mp) REVERT: H 48 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6398 (tt0) REVERT: H 152 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8163 (pm20) outliers start: 77 outliers final: 44 residues processed: 391 average time/residue: 0.1704 time to fit residues: 108.6635 Evaluate side-chains 391 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 332 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 269 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 417 MET Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 339 CYS Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 275 MET Chi-restraints excluded: chain G residue 276 MET Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 311 ASP Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 127 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 183 optimal weight: 0.0000 chunk 143 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 316 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.144462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.114022 restraints weight = 64132.509| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.57 r_work: 0.3112 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29609 Z= 0.111 Angle : 0.495 7.263 40006 Z= 0.254 Chirality : 0.043 0.216 4159 Planarity : 0.004 0.049 5189 Dihedral : 4.415 23.739 3910 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.09 % Allowed : 22.34 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.05 (0.14), residues: 3574 helix: 0.59 (0.14), residues: 1334 sheet: 0.73 (0.24), residues: 501 loop : -0.54 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 392 TYR 0.013 0.001 TYR B 9 PHE 0.017 0.001 PHE H 134 TRP 0.009 0.001 TRP H 356 HIS 0.005 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00276 (29609) covalent geometry : angle 0.49543 (40006) hydrogen bonds : bond 0.02722 ( 1055) hydrogen bonds : angle 4.73027 ( 2976) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 372 time to evaluate : 0.768 Fit side-chains REVERT: A 26 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7379 (mm) REVERT: A 105 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7993 (tttp) REVERT: A 152 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 318 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8238 (mm) REVERT: B 26 ILE cc_start: 0.7626 (mm) cc_final: 0.7419 (mm) REVERT: B 43 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7668 (tp30) REVERT: B 162 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6957 (mtp180) REVERT: B 273 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8597 (ttmm) REVERT: C 235 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7359 (ttpt) REVERT: D 180 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8002 (mp) REVERT: D 261 GLN cc_start: 0.7770 (mt0) cc_final: 0.7493 (mt0) REVERT: D 338 ASN cc_start: 0.6627 (p0) cc_final: 0.6417 (p0) REVERT: F 338 ASN cc_start: 0.7833 (p0) cc_final: 0.7616 (p0) REVERT: F 371 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7787 (mtt) REVERT: G 126 LYS cc_start: 0.8597 (mmtm) cc_final: 0.8240 (tppp) REVERT: G 152 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: G 235 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6368 (tttm) REVERT: G 239 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7933 (mp) REVERT: G 434 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8190 (mtm-85) REVERT: G 450 ASP cc_start: 0.8750 (t0) cc_final: 0.8244 (t0) REVERT: H 152 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7919 (pm20) outliers start: 64 outliers final: 30 residues processed: 415 average time/residue: 0.1759 time to fit residues: 118.1864 Evaluate side-chains 398 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 353 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 275 MET Chi-restraints excluded: chain G residue 276 MET Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 336 optimal weight: 0.7980 chunk 289 optimal weight: 9.9990 chunk 328 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 290 optimal weight: 0.3980 chunk 184 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 321 optimal weight: 3.9990 chunk 224 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 372 ASN D 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.142821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.112245 restraints weight = 78035.383| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.83 r_work: 0.3070 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29609 Z= 0.172 Angle : 0.527 8.231 40006 Z= 0.268 Chirality : 0.045 0.227 4159 Planarity : 0.004 0.050 5189 Dihedral : 4.412 21.406 3909 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.19 % Allowed : 22.80 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.14), residues: 3574 helix: 0.53 (0.14), residues: 1352 sheet: 0.86 (0.25), residues: 480 loop : -0.61 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 162 TYR 0.013 0.001 TYR B 9 PHE 0.021 0.001 PHE G 134 TRP 0.010 0.001 TRP H 138 HIS 0.005 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00429 (29609) covalent geometry : angle 0.52660 (40006) hydrogen bonds : bond 0.03078 ( 1055) hydrogen bonds : angle 4.71973 ( 2976) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 356 time to evaluate : 1.010 Fit side-chains REVERT: A 26 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7428 (mm) REVERT: A 105 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7990 (tttp) REVERT: A 152 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: A 318 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8135 (mm) REVERT: B 43 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: B 162 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6966 (mtp180) REVERT: B 261 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7524 (mt0) REVERT: B 273 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8611 (ttmm) REVERT: D 180 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8044 (mp) REVERT: D 261 GLN cc_start: 0.7873 (mt0) cc_final: 0.7548 (mt0) REVERT: D 372 ASN cc_start: 0.8957 (m110) cc_final: 0.8734 (m-40) REVERT: F 338 ASN cc_start: 0.7878 (p0) cc_final: 0.7645 (p0) REVERT: F 371 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.7860 (mtt) REVERT: G 152 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: G 235 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6406 (tttm) REVERT: G 239 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7993 (mp) REVERT: G 434 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.8286 (mtm-85) REVERT: H 152 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7944 (pm20) REVERT: H 180 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8907 (mp) outliers start: 67 outliers final: 40 residues processed: 399 average time/residue: 0.1748 time to fit residues: 113.2328 Evaluate side-chains 403 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 347 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 261 GLN Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 275 MET Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 236 optimal weight: 0.0770 chunk 286 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 319 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 336 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112274 restraints weight = 64931.797| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.59 r_work: 0.3083 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29609 Z= 0.171 Angle : 0.530 8.557 40006 Z= 0.270 Chirality : 0.045 0.216 4159 Planarity : 0.004 0.050 5189 Dihedral : 4.433 21.267 3909 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.29 % Allowed : 22.73 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3574 helix: 0.55 (0.14), residues: 1352 sheet: 0.85 (0.25), residues: 480 loop : -0.60 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 162 TYR 0.013 0.001 TYR B 9 PHE 0.021 0.001 PHE G 134 TRP 0.010 0.001 TRP H 138 HIS 0.005 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00426 (29609) covalent geometry : angle 0.53050 (40006) hydrogen bonds : bond 0.03050 ( 1055) hydrogen bonds : angle 4.70119 ( 2976) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 353 time to evaluate : 1.125 Fit side-chains REVERT: A 26 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7486 (mm) REVERT: A 105 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8030 (tttp) REVERT: A 152 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: A 318 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8212 (mm) REVERT: B 43 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7685 (tp30) REVERT: B 82 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: B 162 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6970 (mtp180) REVERT: B 273 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8645 (ttmm) REVERT: C 235 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7280 (ttpt) REVERT: D 180 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8124 (mp) REVERT: D 261 GLN cc_start: 0.7875 (mt0) cc_final: 0.7552 (mt0) REVERT: D 372 ASN cc_start: 0.8950 (m110) cc_final: 0.8735 (m-40) REVERT: F 338 ASN cc_start: 0.7859 (p0) cc_final: 0.7628 (p0) REVERT: F 371 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7890 (mtt) REVERT: G 152 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: G 235 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6717 (ttpt) REVERT: G 239 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8032 (mp) REVERT: G 434 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8307 (mtm-85) REVERT: H 152 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7932 (pm20) REVERT: H 180 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8925 (mp) outliers start: 70 outliers final: 44 residues processed: 400 average time/residue: 0.1692 time to fit residues: 110.1289 Evaluate side-chains 411 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 350 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 275 MET Chi-restraints excluded: chain G residue 276 MET Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 152 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 311 ASP Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 329 optimal weight: 9.9990 chunk 201 optimal weight: 0.8980 chunk 347 optimal weight: 0.0970 chunk 334 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 358 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 352 HIS F 114 ASN G 187 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.145170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.114774 restraints weight = 62699.947| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.54 r_work: 0.3122 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29609 Z= 0.114 Angle : 0.490 8.356 40006 Z= 0.250 Chirality : 0.043 0.226 4159 Planarity : 0.004 0.049 5189 Dihedral : 4.238 21.631 3909 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.96 % Allowed : 22.96 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3574 helix: 0.70 (0.15), residues: 1347 sheet: 0.78 (0.24), residues: 501 loop : -0.47 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 162 TYR 0.013 0.001 TYR B 9 PHE 0.032 0.001 PHE G 134 TRP 0.012 0.001 TRP G 138 HIS 0.005 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00284 (29609) covalent geometry : angle 0.48975 (40006) hydrogen bonds : bond 0.02621 ( 1055) hydrogen bonds : angle 4.57991 ( 2976) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 365 time to evaluate : 1.069 Fit side-chains REVERT: A 105 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7984 (tttp) REVERT: A 152 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: A 318 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8270 (mm) REVERT: B 43 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: B 82 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: B 162 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7000 (mtp180) REVERT: B 261 GLN cc_start: 0.7731 (mt0) cc_final: 0.7386 (tt0) REVERT: B 273 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8618 (ttmm) REVERT: C 235 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7311 (tttt) REVERT: D 180 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8004 (mp) REVERT: D 261 GLN cc_start: 0.7758 (mt0) cc_final: 0.7446 (mt0) REVERT: D 372 ASN cc_start: 0.8890 (m110) cc_final: 0.8675 (m-40) REVERT: F 371 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7791 (mtt) REVERT: G 152 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8022 (pm20) REVERT: G 235 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6419 (tttm) REVERT: G 239 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7998 (mp) REVERT: G 434 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8252 (mtm-85) outliers start: 60 outliers final: 38 residues processed: 407 average time/residue: 0.1665 time to fit residues: 110.3900 Evaluate side-chains 409 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 357 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 126 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 104 optimal weight: 0.0570 chunk 294 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 244 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 overall best weight: 1.6904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114584 restraints weight = 55998.270| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.38 r_work: 0.3120 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29609 Z= 0.140 Angle : 0.509 9.176 40006 Z= 0.260 Chirality : 0.044 0.218 4159 Planarity : 0.004 0.049 5189 Dihedral : 4.266 21.267 3909 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.03 % Allowed : 22.64 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3574 helix: 0.69 (0.14), residues: 1350 sheet: 0.88 (0.25), residues: 487 loop : -0.49 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 162 TYR 0.013 0.001 TYR B 9 PHE 0.026 0.001 PHE G 134 TRP 0.016 0.001 TRP G 138 HIS 0.005 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00351 (29609) covalent geometry : angle 0.50944 (40006) hydrogen bonds : bond 0.02800 ( 1055) hydrogen bonds : angle 4.58198 ( 2976) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 359 time to evaluate : 1.020 Fit side-chains REVERT: A 105 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7990 (tttp) REVERT: A 152 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 318 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8246 (mm) REVERT: B 43 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7696 (tp30) REVERT: B 82 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: B 162 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7002 (mtp180) REVERT: B 261 GLN cc_start: 0.7748 (mt0) cc_final: 0.7397 (tt0) REVERT: C 235 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7311 (tttt) REVERT: D 180 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8035 (mp) REVERT: D 261 GLN cc_start: 0.7829 (mt0) cc_final: 0.7503 (mt0) REVERT: D 372 ASN cc_start: 0.8887 (m110) cc_final: 0.8672 (m-40) REVERT: F 338 ASN cc_start: 0.7855 (p0) cc_final: 0.7646 (p0) REVERT: F 371 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7832 (mtt) REVERT: G 152 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.8019 (pm20) REVERT: G 235 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6718 (ttpt) REVERT: G 239 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.8019 (mp) REVERT: G 434 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8289 (mtm-85) REVERT: H 285 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8427 (ttpt) outliers start: 62 outliers final: 42 residues processed: 399 average time/residue: 0.1706 time to fit residues: 111.1931 Evaluate side-chains 413 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 357 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 275 MET Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 285 LYS Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 225 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 291 optimal weight: 4.9990 chunk 277 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 331 optimal weight: 6.9990 chunk 332 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 312 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 114 ASN G 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111604 restraints weight = 63845.300| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.47 r_work: 0.3068 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 29609 Z= 0.255 Angle : 0.590 10.730 40006 Z= 0.301 Chirality : 0.047 0.222 4159 Planarity : 0.004 0.050 5189 Dihedral : 4.594 21.219 3909 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.00 % Allowed : 22.67 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3574 helix: 0.45 (0.14), residues: 1354 sheet: 0.78 (0.25), residues: 475 loop : -0.64 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 162 TYR 0.017 0.002 TYR C 196 PHE 0.035 0.002 PHE G 134 TRP 0.016 0.002 TRP G 138 HIS 0.005 0.001 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00632 (29609) covalent geometry : angle 0.59032 (40006) hydrogen bonds : bond 0.03579 ( 1055) hydrogen bonds : angle 4.80514 ( 2976) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7148 Ramachandran restraints generated. 3574 Oldfield, 0 Emsley, 3574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 344 time to evaluate : 1.111 Fit side-chains REVERT: A 152 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: A 318 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8299 (mm) REVERT: B 43 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7749 (tp30) REVERT: B 82 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8259 (pm20) REVERT: B 162 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.7064 (mtp180) REVERT: C 235 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7042 (tttt) REVERT: D 180 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8231 (mp) REVERT: D 261 GLN cc_start: 0.7978 (mt0) cc_final: 0.7671 (mt0) REVERT: D 372 ASN cc_start: 0.9020 (m110) cc_final: 0.8784 (m-40) REVERT: E 134 PHE cc_start: 0.8717 (t80) cc_final: 0.8511 (t80) REVERT: F 338 ASN cc_start: 0.8001 (p0) cc_final: 0.7500 (p0) REVERT: F 371 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8128 (mtt) REVERT: G 152 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8211 (pm20) REVERT: G 235 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6929 (ttmt) REVERT: G 239 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8141 (mp) REVERT: G 434 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8417 (mtm-85) REVERT: H 48 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6403 (tt0) REVERT: H 285 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8569 (ttpt) REVERT: H 338 ASN cc_start: 0.7858 (p0) cc_final: 0.7445 (p0) outliers start: 61 outliers final: 43 residues processed: 382 average time/residue: 0.1744 time to fit residues: 109.0186 Evaluate side-chains 398 residues out of total 3054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 341 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 162 ARG Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 269 SER Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 56 MET Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain F residue 52 HIS Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 420 SER Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 104 GLU Chi-restraints excluded: chain G residue 114 ASN Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 235 LYS Chi-restraints excluded: chain G residue 239 ILE Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 275 MET Chi-restraints excluded: chain G residue 276 MET Chi-restraints excluded: chain G residue 373 THR Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 443 THR Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 285 LYS Chi-restraints excluded: chain H residue 443 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 247 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 289 optimal weight: 2.9990 chunk 195 optimal weight: 8.9990 chunk 265 optimal weight: 0.0980 chunk 318 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 319 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 114 ASN G 187 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.146207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.115693 restraints weight = 66397.473| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.63 r_work: 0.3130 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 29609 Z= 0.098 Angle : 0.491 8.399 40006 Z= 0.253 Chirality : 0.043 0.144 4159 Planarity : 0.004 0.049 5189 Dihedral : 4.245 21.966 3909 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.60 % Allowed : 23.09 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.14), residues: 3574 helix: 0.74 (0.15), residues: 1346 sheet: 0.86 (0.25), residues: 488 loop : -0.41 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 162 TYR 0.012 0.001 TYR B 9 PHE 0.016 0.001 PHE E 134 TRP 0.016 0.001 TRP G 138 HIS 0.005 0.000 HIS G 36 Details of bonding type rmsd covalent geometry : bond 0.00233 (29609) covalent geometry : angle 0.49131 (40006) hydrogen bonds : bond 0.02472 ( 1055) hydrogen bonds : angle 4.54069 ( 2976) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6197.79 seconds wall clock time: 107 minutes 19.80 seconds (6439.80 seconds total)