Starting phenix.real_space_refine on Mon Aug 25 11:07:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kbg_62224/08_2025/9kbg_62224.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kbg_62224/08_2025/9kbg_62224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kbg_62224/08_2025/9kbg_62224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kbg_62224/08_2025/9kbg_62224.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kbg_62224/08_2025/9kbg_62224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kbg_62224/08_2025/9kbg_62224.map" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.133 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 12 5.21 5 S 143 5.16 5 C 17727 2.51 5 N 4631 2.21 5 O 5141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27690 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2282 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 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: "B" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2272 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2278 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2273 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2263 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 2270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2270 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2274 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2274 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2274 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2269 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 276} Chain breaks: 1 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 Chain: "K" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2274 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2274 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 6.64, per 1000 atoms: 0.24 Number of scatterers: 27690 At special positions: 0 Unit cell: (153.44, 150.563, 139.055, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 143 16.00 P 36 15.00 Mg 12 11.99 O 5141 8.00 N 4631 7.00 C 17727 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: 2.19 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6550 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 24 sheets defined 52.2% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 210 through 226 Processing helix chain 'A' and resid 230 through 238 Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.501A pdb=" N TYR A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 269 removed outlier: 3.560A pdb=" N GLN A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 removed outlier: 4.060A pdb=" N PHE A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 289 Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.616A pdb=" N LYS A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.700A pdb=" N ASP A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.742A pdb=" N ILE A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 removed outlier: 3.508A pdb=" N ALA A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 431 through 437 removed outlier: 3.779A pdb=" N LYS A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 437 " --> pdb=" O LYS A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 3.784A pdb=" N GLN A 470 " --> pdb=" O TRP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 495 through 499 removed outlier: 3.528A pdb=" N LEU A 498 " --> pdb=" O HIS A 495 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 495 through 499' Processing helix chain 'B' and resid 210 through 226 Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.518A pdb=" N TYR B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 269 removed outlier: 3.530A pdb=" N GLN B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 removed outlier: 4.094A pdb=" N PHE B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 289 Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.769A pdb=" N ASP B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 Processing helix chain 'B' and resid 380 through 389 removed outlier: 3.529A pdb=" N ALA B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.574A pdb=" N GLN B 470 " --> pdb=" O TRP B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 480 removed outlier: 3.981A pdb=" N ASN B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP B 478 " --> pdb=" O HIS B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 226 Processing helix chain 'C' and resid 230 through 238 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.521A pdb=" N TYR C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 269 removed outlier: 3.558A pdb=" N GLN C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 286 through 289 Processing helix chain 'C' and resid 290 through 299 Processing helix chain 'C' and resid 302 through 314 Processing helix chain 'C' and resid 333 through 343 removed outlier: 3.856A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 389 Processing helix chain 'C' and resid 393 through 401 Processing helix chain 'C' and resid 431 through 437 Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.599A pdb=" N ALA C 469 " --> pdb=" O THR C 465 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN C 470 " --> pdb=" O TRP C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'D' and resid 210 through 226 Processing helix chain 'D' and resid 230 through 238 Processing helix chain 'D' and resid 238 through 246 removed outlier: 3.533A pdb=" N TYR D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 269 removed outlier: 3.613A pdb=" N GLN D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 removed outlier: 4.087A pdb=" N PHE D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 299 Processing helix chain 'D' and resid 304 through 315 removed outlier: 3.689A pdb=" N ASP D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 removed outlier: 3.721A pdb=" N LYS D 343 " --> pdb=" O MET D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 389 Processing helix chain 'D' and resid 393 through 401 removed outlier: 3.544A pdb=" N MET D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 437 removed outlier: 3.534A pdb=" N GLU D 437 " --> pdb=" O LYS D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 removed outlier: 3.909A pdb=" N GLN D 470 " --> pdb=" O TRP D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 480 removed outlier: 3.605A pdb=" N ASN D 477 " --> pdb=" O ASP D 473 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TRP D 478 " --> pdb=" O HIS D 474 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 480 " --> pdb=" O GLU D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 499 Processing helix chain 'E' and resid 210 through 226 Processing helix chain 'E' and resid 230 through 238 Processing helix chain 'E' and resid 238 through 246 removed outlier: 3.566A pdb=" N TYR E 242 " --> pdb=" O ASP E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 268 removed outlier: 3.564A pdb=" N GLN E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 276 Processing helix chain 'E' and resid 286 through 289 Processing helix chain 'E' and resid 290 through 299 Processing helix chain 'E' and resid 302 through 315 removed outlier: 3.815A pdb=" N ASP E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 345 removed outlier: 3.681A pdb=" N VAL E 345 " --> pdb=" O ILE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 389 Processing helix chain 'E' and resid 393 through 399 Processing helix chain 'E' and resid 431 through 438 removed outlier: 3.923A pdb=" N ARG E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 470 Processing helix chain 'E' and resid 474 through 479 removed outlier: 3.569A pdb=" N TRP E 478 " --> pdb=" O HIS E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 499 Processing helix chain 'F' and resid 210 through 226 Processing helix chain 'F' and resid 230 through 238 Processing helix chain 'F' and resid 238 through 246 removed outlier: 3.625A pdb=" N TYR F 242 " --> pdb=" O ASP F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 269 removed outlier: 3.576A pdb=" N GLN F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 290 through 299 Processing helix chain 'F' and resid 302 through 315 removed outlier: 3.730A pdb=" N ASP F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 345 removed outlier: 3.519A pdb=" N ALA F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL F 345 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 390 removed outlier: 3.660A pdb=" N ALA F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 401 Processing helix chain 'F' and resid 431 through 438 Processing helix chain 'F' and resid 456 through 469 removed outlier: 3.647A pdb=" N VAL F 460 " --> pdb=" O THR F 456 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA F 469 " --> pdb=" O THR F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 479 removed outlier: 4.321A pdb=" N TRP F 478 " --> pdb=" O HIS F 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 226 Processing helix chain 'G' and resid 230 through 238 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.574A pdb=" N TYR G 242 " --> pdb=" O ASP G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 268 removed outlier: 3.580A pdb=" N GLN G 256 " --> pdb=" O SER G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 276 Processing helix chain 'G' and resid 286 through 289 Processing helix chain 'G' and resid 290 through 299 Processing helix chain 'G' and resid 302 through 315 removed outlier: 3.661A pdb=" N ASP G 315 " --> pdb=" O LEU G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 342 Processing helix chain 'G' and resid 380 through 389 Processing helix chain 'G' and resid 393 through 400 Processing helix chain 'G' and resid 431 through 437 Processing helix chain 'G' and resid 456 through 470 removed outlier: 3.666A pdb=" N GLN G 470 " --> pdb=" O TRP G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 480 removed outlier: 3.851A pdb=" N GLU G 476 " --> pdb=" O TRP G 472 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN G 477 " --> pdb=" O ASP G 473 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TRP G 478 " --> pdb=" O HIS G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'H' and resid 210 through 226 Processing helix chain 'H' and resid 230 through 238 Processing helix chain 'H' and resid 238 through 246 removed outlier: 3.510A pdb=" N TYR H 242 " --> pdb=" O ASP H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 268 removed outlier: 3.549A pdb=" N GLN H 256 " --> pdb=" O SER H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'H' and resid 286 through 289 removed outlier: 3.528A pdb=" N ASP H 289 " --> pdb=" O CYS H 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 286 through 289' Processing helix chain 'H' and resid 290 through 299 removed outlier: 3.512A pdb=" N GLN H 299 " --> pdb=" O LEU H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 315 removed outlier: 3.887A pdb=" N ASP H 315 " --> pdb=" O LEU H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 345 removed outlier: 3.761A pdb=" N SER H 344 " --> pdb=" O ALA H 340 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL H 345 " --> pdb=" O ILE H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 390 removed outlier: 3.601A pdb=" N GLY H 390 " --> pdb=" O ALA H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 401 Processing helix chain 'H' and resid 431 through 437 Processing helix chain 'H' and resid 456 through 469 removed outlier: 3.830A pdb=" N VAL H 460 " --> pdb=" O THR H 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 480 removed outlier: 3.683A pdb=" N TRP H 478 " --> pdb=" O HIS H 474 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 226 Processing helix chain 'I' and resid 230 through 238 Processing helix chain 'I' and resid 238 through 246 removed outlier: 3.660A pdb=" N TYR I 242 " --> pdb=" O ASP I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 269 removed outlier: 3.595A pdb=" N GLN I 256 " --> pdb=" O SER I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 277 removed outlier: 4.058A pdb=" N PHE I 275 " --> pdb=" O PRO I 271 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU I 276 " --> pdb=" O THR I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 299 Processing helix chain 'I' and resid 302 through 315 removed outlier: 3.739A pdb=" N GLY I 307 " --> pdb=" O PRO I 303 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS I 312 " --> pdb=" O GLN I 308 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP I 315 " --> pdb=" O LEU I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 343 Processing helix chain 'I' and resid 377 through 379 No H-bonds generated for 'chain 'I' and resid 377 through 379' Processing helix chain 'I' and resid 380 through 389 Processing helix chain 'I' and resid 393 through 401 Processing helix chain 'I' and resid 431 through 437 removed outlier: 3.531A pdb=" N GLU I 437 " --> pdb=" O LYS I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 470 Processing helix chain 'I' and resid 472 through 481 removed outlier: 3.911A pdb=" N GLU I 476 " --> pdb=" O TRP I 472 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ASN I 477 " --> pdb=" O ASP I 473 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TRP I 478 " --> pdb=" O HIS I 474 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN I 481 " --> pdb=" O ASN I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 490 through 494 removed outlier: 3.829A pdb=" N LEU I 494 " --> pdb=" O ALA I 491 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 226 Processing helix chain 'J' and resid 230 through 238 Processing helix chain 'J' and resid 238 through 246 removed outlier: 3.537A pdb=" N TYR J 242 " --> pdb=" O ASP J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 248 through 269 removed outlier: 3.587A pdb=" N GLN J 256 " --> pdb=" O SER J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 277 removed outlier: 4.111A pdb=" N PHE J 275 " --> pdb=" O PRO J 271 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU J 276 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 289 Processing helix chain 'J' and resid 290 through 299 Processing helix chain 'J' and resid 302 through 315 removed outlier: 3.661A pdb=" N ASP J 315 " --> pdb=" O LEU J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 345 Processing helix chain 'J' and resid 380 through 389 Processing helix chain 'J' and resid 393 through 401 Processing helix chain 'J' and resid 431 through 437 removed outlier: 3.600A pdb=" N GLU J 437 " --> pdb=" O LYS J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 470 removed outlier: 3.525A pdb=" N ALA J 469 " --> pdb=" O THR J 465 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN J 470 " --> pdb=" O TRP J 466 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 481 removed outlier: 3.716A pdb=" N TRP J 478 " --> pdb=" O HIS J 474 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN J 481 " --> pdb=" O ASN J 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 226 Processing helix chain 'K' and resid 230 through 238 Processing helix chain 'K' and resid 238 through 246 removed outlier: 3.657A pdb=" N TYR K 242 " --> pdb=" O ASP K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 269 removed outlier: 3.586A pdb=" N GLN K 256 " --> pdb=" O SER K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 277 removed outlier: 3.670A pdb=" N LEU K 276 " --> pdb=" O THR K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 289 Processing helix chain 'K' and resid 290 through 299 removed outlier: 3.527A pdb=" N GLN K 299 " --> pdb=" O LEU K 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 314 Processing helix chain 'K' and resid 334 through 342 removed outlier: 3.680A pdb=" N ILE K 341 " --> pdb=" O LEU K 337 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA K 342 " --> pdb=" O ALA K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 343 through 345 No H-bonds generated for 'chain 'K' and resid 343 through 345' Processing helix chain 'K' and resid 380 through 389 removed outlier: 3.726A pdb=" N ALA K 386 " --> pdb=" O GLU K 382 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 399 Processing helix chain 'K' and resid 435 through 437 No H-bonds generated for 'chain 'K' and resid 435 through 437' Processing helix chain 'K' and resid 456 through 470 Processing helix chain 'K' and resid 472 through 480 removed outlier: 3.585A pdb=" N GLU K 476 " --> pdb=" O TRP K 472 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE K 480 " --> pdb=" O GLU K 476 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 226 Processing helix chain 'L' and resid 230 through 238 Processing helix chain 'L' and resid 238 through 246 removed outlier: 3.588A pdb=" N TYR L 242 " --> pdb=" O ASP L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 269 removed outlier: 3.546A pdb=" N GLN L 256 " --> pdb=" O SER L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 277 removed outlier: 3.865A pdb=" N LEU L 277 " --> pdb=" O THR L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 299 Processing helix chain 'L' and resid 302 through 315 removed outlier: 3.741A pdb=" N ASP L 315 " --> pdb=" O LEU L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 345 removed outlier: 3.658A pdb=" N VAL L 345 " --> pdb=" O ILE L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 380 through 389 removed outlier: 3.646A pdb=" N ALA L 386 " --> pdb=" O GLU L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 401 Processing helix chain 'L' and resid 431 through 438 removed outlier: 3.736A pdb=" N ARG L 438 " --> pdb=" O ALA L 434 " (cutoff:3.500A) Processing helix chain 'L' and resid 456 through 470 removed outlier: 3.534A pdb=" N VAL L 460 " --> pdb=" O THR L 456 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN L 470 " --> pdb=" O TRP L 466 " (cutoff:3.500A) Processing helix chain 'L' and resid 472 through 480 removed outlier: 3.868A pdb=" N GLU L 476 " --> pdb=" O TRP L 472 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN L 477 " --> pdb=" O ASP L 473 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE L 480 " --> pdb=" O GLU L 476 " (cutoff:3.500A) Processing helix chain 'L' and resid 495 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 348 through 350 Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 423 Processing sheet with id=AA3, first strand: chain 'B' and resid 348 through 350 removed outlier: 6.668A pdb=" N GLY B 349 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ASP B 372 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 324 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N SER B 414 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE B 326 " --> pdb=" O SER B 414 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 421 through 423 Processing sheet with id=AA5, first strand: chain 'C' and resid 349 through 350 removed outlier: 6.599A pdb=" N GLY C 349 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP C 372 " --> pdb=" O GLY C 349 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 421 through 423 Processing sheet with id=AA7, first strand: chain 'D' and resid 348 through 350 removed outlier: 6.508A pdb=" N GLY D 349 " --> pdb=" O VAL D 370 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL D 369 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N THR D 413 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP D 371 " --> pdb=" O THR D 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 421 through 423 Processing sheet with id=AA9, first strand: chain 'E' and resid 349 through 350 removed outlier: 6.467A pdb=" N GLY E 349 " --> pdb=" O VAL E 370 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP E 372 " --> pdb=" O GLY E 349 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 421 through 423 Processing sheet with id=AB2, first strand: chain 'F' and resid 349 through 350 removed outlier: 6.790A pdb=" N GLY F 349 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ASP F 372 " --> pdb=" O GLY F 349 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 421 through 423 Processing sheet with id=AB4, first strand: chain 'G' and resid 349 through 350 removed outlier: 6.590A pdb=" N GLY G 349 " --> pdb=" O VAL G 370 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ASP G 372 " --> pdb=" O GLY G 349 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU G 324 " --> pdb=" O ILE G 412 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N SER G 414 " --> pdb=" O LEU G 324 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE G 326 " --> pdb=" O SER G 414 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 421 through 423 Processing sheet with id=AB6, first strand: chain 'H' and resid 349 through 350 removed outlier: 6.694A pdb=" N GLY H 349 " --> pdb=" O VAL H 370 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP H 372 " --> pdb=" O GLY H 349 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 421 through 423 Processing sheet with id=AB8, first strand: chain 'I' and resid 348 through 350 Processing sheet with id=AB9, first strand: chain 'I' and resid 421 through 423 Processing sheet with id=AC1, first strand: chain 'J' and resid 348 through 350 removed outlier: 6.506A pdb=" N GLY J 349 " --> pdb=" O VAL J 370 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP J 372 " --> pdb=" O GLY J 349 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 421 through 423 Processing sheet with id=AC3, first strand: chain 'K' and resid 348 through 350 Processing sheet with id=AC4, first strand: chain 'K' and resid 421 through 422 Processing sheet with id=AC5, first strand: chain 'L' and resid 348 through 350 Processing sheet with id=AC6, first strand: chain 'L' and resid 421 through 423 removed outlier: 3.567A pdb=" N VAL L 421 " --> pdb=" O THR L 428 " (cutoff:3.500A) 1217 hydrogen bonds defined for protein. 3486 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4416 1.29 - 1.42: 7263 1.42 - 1.55: 16388 1.55 - 1.69: 65 1.69 - 1.82: 214 Bond restraints: 28346 Sorted by residual: bond pdb=" N3B ANP D 601 " pdb=" PG ANP D 601 " ideal model delta sigma weight residual 1.795 1.595 0.200 2.00e-02 2.50e+03 9.96e+01 bond pdb=" N3B ANP I 601 " pdb=" PG ANP I 601 " ideal model delta sigma weight residual 1.795 1.597 0.198 2.00e-02 2.50e+03 9.79e+01 bond pdb=" N3B ANP F 601 " pdb=" PG ANP F 601 " ideal model delta sigma weight residual 1.795 1.598 0.197 2.00e-02 2.50e+03 9.70e+01 bond pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 1.795 1.598 0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" N3B ANP K 601 " pdb=" PG ANP K 601 " ideal model delta sigma weight residual 1.795 1.598 0.197 2.00e-02 2.50e+03 9.66e+01 ... (remaining 28341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 37985 2.97 - 5.93: 583 5.93 - 8.90: 87 8.90 - 11.86: 23 11.86 - 14.83: 12 Bond angle restraints: 38690 Sorted by residual: angle pdb=" C PRO B 329 " pdb=" CA PRO B 329 " pdb=" CB PRO B 329 " ideal model delta sigma weight residual 110.92 100.22 10.70 1.22e+00 6.72e-01 7.69e+01 angle pdb=" N THR F 335 " pdb=" CA THR F 335 " pdb=" C THR F 335 " ideal model delta sigma weight residual 113.18 102.63 10.55 1.21e+00 6.83e-01 7.60e+01 angle pdb=" N ALA E 340 " pdb=" CA ALA E 340 " pdb=" C ALA E 340 " ideal model delta sigma weight residual 113.12 102.72 10.40 1.25e+00 6.40e-01 6.93e+01 angle pdb=" C PRO F 329 " pdb=" CA PRO F 329 " pdb=" CB PRO F 329 " ideal model delta sigma weight residual 110.92 101.16 9.76 1.22e+00 6.72e-01 6.41e+01 angle pdb=" N ALA D 340 " pdb=" CA ALA D 340 " pdb=" C ALA D 340 " ideal model delta sigma weight residual 113.12 103.21 9.91 1.25e+00 6.40e-01 6.29e+01 ... (remaining 38685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.21: 16350 33.21 - 66.42: 392 66.42 - 99.63: 58 99.63 - 132.84: 0 132.84 - 166.05: 12 Dihedral angle restraints: 16812 sinusoidal: 6711 harmonic: 10101 Sorted by residual: dihedral pdb=" C PRO B 329 " pdb=" N PRO B 329 " pdb=" CA PRO B 329 " pdb=" CB PRO B 329 " ideal model delta harmonic sigma weight residual -120.70 -106.39 -14.31 0 2.50e+00 1.60e-01 3.28e+01 dihedral pdb=" CD ARG J 447 " pdb=" NE ARG J 447 " pdb=" CZ ARG J 447 " pdb=" NH1 ARG J 447 " ideal model delta sinusoidal sigma weight residual 0.00 -47.03 47.03 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CA VAL J 405 " pdb=" C VAL J 405 " pdb=" N PRO J 406 " pdb=" CA PRO J 406 " ideal model delta harmonic sigma weight residual 180.00 -153.39 -26.61 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 16809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 4247 0.108 - 0.216: 135 0.216 - 0.324: 19 0.324 - 0.432: 7 0.432 - 0.540: 7 Chirality restraints: 4415 Sorted by residual: chirality pdb=" CA SER B 331 " pdb=" N SER B 331 " pdb=" C SER B 331 " pdb=" CB SER B 331 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.30e+00 chirality pdb=" CA PRO I 330 " pdb=" N PRO I 330 " pdb=" C PRO I 330 " pdb=" CB PRO I 330 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CA SER I 331 " pdb=" N SER I 331 " pdb=" C SER I 331 " pdb=" CB SER I 331 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.90e+00 ... (remaining 4412 not shown) Planarity restraints: 4764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 447 " 0.803 9.50e-02 1.11e+02 3.60e-01 7.86e+01 pdb=" NE ARG J 447 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG J 447 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG J 447 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG J 447 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 447 " -0.604 9.50e-02 1.11e+02 2.71e-01 4.47e+01 pdb=" NE ARG D 447 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG D 447 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 447 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 447 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS E 495 " 0.086 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO E 496 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO E 496 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO E 496 " 0.067 5.00e-02 4.00e+02 ... (remaining 4761 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 267 2.60 - 3.18: 22453 3.18 - 3.75: 41344 3.75 - 4.33: 58724 4.33 - 4.90: 98074 Nonbonded interactions: 220862 Sorted by model distance: nonbonded pdb=" O2B ANP A 601 " pdb="MG MG A 602 " model vdw 2.029 2.170 nonbonded pdb="MG MG E 602 " pdb=" O HOH E 702 " model vdw 2.035 2.170 nonbonded pdb="MG MG C 602 " pdb=" O HOH C 703 " model vdw 2.064 2.170 nonbonded pdb=" O2B ANP C 601 " pdb="MG MG C 602 " model vdw 2.068 2.170 nonbonded pdb="MG MG C 602 " pdb=" O HOH C 701 " model vdw 2.068 2.170 ... (remaining 220857 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 202 through 277 or resid 286 through 287 or (resid 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 through 450 o \ r (resid 451 through 452 and (name N or name CA or name C or name O or name CB ) \ ) or resid 453 through 475 or (resid 476 through 477 and (name N or name CA or n \ ame C or name O or name CB )) or resid 478 through 494 or (resid 495 and (name N \ or name CA or name C or name O or name CB )) or resid 496 through 602)) selection = (chain 'B' and (resid 202 through 277 or resid 286 through 287 or (resid 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 through 450 o \ r (resid 451 through 452 and (name N or name CA or name C or name O or name CB ) \ ) or resid 453 through 475 or (resid 476 through 477 and (name N or name CA or n \ ame C or name O or name CB )) or resid 478 through 602)) selection = (chain 'C' and (resid 202 through 277 or resid 286 through 287 or (resid 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 through 450 o \ r (resid 451 through 452 and (name N or name CA or name C or name O or name CB ) \ ) or resid 453 through 476 or (resid 477 and (name N or name CA or name C or nam \ e O or name CB )) or resid 478 through 494 or (resid 495 and (name N or name CA \ or name C or name O or name CB )) or resid 496 through 602)) selection = (chain 'D' and (resid 202 through 277 or resid 286 through 287 or (resid 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 through 450 o \ r (resid 451 through 452 and (name N or name CA or name C or name O or name CB ) \ ) or resid 453 through 476 or (resid 477 and (name N or name CA or name C or nam \ e O or name CB )) or resid 478 through 494 or (resid 495 and (name N or name CA \ or name C or name O or name CB )) or resid 496 through 602)) selection = (chain 'E' and (resid 202 through 277 or resid 286 through 450 or (resid 451 thr \ ough 452 and (name N or name CA or name C or name O or name CB )) or resid 453 t \ hrough 494 or (resid 495 and (name N or name CA or name C or name O or name CB ) \ ) or resid 496 through 602)) selection = (chain 'F' and (resid 202 through 277 or resid 286 through 287 or (resid 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 through 451 o \ r (resid 452 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 53 through 476 or (resid 477 and (name N or name CA or name C or name O or name \ CB )) or resid 478 through 494 or (resid 495 and (name N or name CA or name C or \ name O or name CB )) or resid 496 through 602)) selection = (chain 'G' and (resid 202 through 277 or resid 286 through 287 or (resid 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 through 451 o \ r (resid 452 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 53 through 475 or (resid 476 through 477 and (name N or name CA or name C or nam \ e O or name CB )) or resid 478 through 494 or (resid 495 and (name N or name CA \ or name C or name O or name CB )) or resid 496 through 602)) selection = (chain 'H' and (resid 202 through 277 or resid 286 through 287 or (resid 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 through 451 o \ r (resid 452 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 53 through 475 or (resid 476 through 477 and (name N or name CA or name C or nam \ e O or name CB )) or resid 478 through 494 or (resid 495 and (name N or name CA \ or name C or name O or name CB )) or resid 496 through 602)) selection = (chain 'I' and (resid 202 through 277 or resid 286 through 287 or (resid 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 through 451 o \ r (resid 452 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 53 through 475 or (resid 476 through 477 and (name N or name CA or name C or nam \ e O or name CB )) or resid 478 through 494 or (resid 495 and (name N or name CA \ or name C or name O or name CB )) or resid 496 through 602)) selection = (chain 'J' and (resid 202 through 287 or (resid 288 and (name N or name CA or na \ me C or name O or name CB )) or resid 289 through 451 or (resid 452 and (name N \ or name CA or name C or name O or name CB )) or resid 453 through 475 or (resid \ 476 through 477 and (name N or name CA or name C or name O or name CB )) or resi \ d 478 through 494 or (resid 495 and (name N or name CA or name C or name O or na \ me CB )) or resid 496 through 602)) selection = (chain 'K' and (resid 202 through 277 or resid 286 through 287 or (resid 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 through 451 o \ r (resid 452 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 53 through 475 or (resid 476 through 477 and (name N or name CA or name C or nam \ e O or name CB )) or resid 478 through 494 or (resid 495 and (name N or name CA \ or name C or name O or name CB )) or resid 496 through 602)) selection = (chain 'L' and (resid 202 through 277 or resid 286 through 287 or (resid 288 and \ (name N or name CA or name C or name O or name CB )) or resid 289 through 451 o \ r (resid 452 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 53 through 475 or (resid 476 through 477 and (name N or name CA or name C or nam \ e O or name CB )) or resid 478 through 494 or (resid 495 and (name N or name CA \ or name C or name O or name CB )) or resid 496 through 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.200 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.007 0.200 28346 Z= 0.441 Angle : 0.861 14.831 38690 Z= 0.491 Chirality : 0.052 0.540 4415 Planarity : 0.009 0.360 4764 Dihedral : 15.842 166.055 10262 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.76 % Allowed : 3.28 % Favored : 95.96 % Rotamer: Outliers : 1.26 % Allowed : 1.00 % Favored : 97.74 % Cbeta Deviations : 0.27 % 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 aren not related in a simple way. whole: 0.50 (0.15), residues: 3443 helix: 0.77 (0.13), residues: 1644 sheet: 2.41 (0.28), residues: 362 loop : -0.68 (0.16), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 394 TYR 0.016 0.001 TYR J 348 PHE 0.016 0.001 PHE C 358 TRP 0.027 0.001 TRP E 466 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00745 (28346) covalent geometry : angle 0.86143 (38690) hydrogen bonds : bond 0.18404 ( 1217) hydrogen bonds : angle 6.45220 ( 3486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 397 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 334 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7845 (mtmp) REVERT: D 219 MET cc_start: 0.9026 (ttp) cc_final: 0.8571 (ttp) REVERT: D 447 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6849 (ttt180) REVERT: G 339 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8629 (mmt) REVERT: G 452 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.5220 (ptt) REVERT: I 439 MET cc_start: 0.8251 (mtp) cc_final: 0.8019 (mtm) REVERT: I 452 MET cc_start: 0.7229 (ttt) cc_final: 0.6917 (ttp) REVERT: J 452 MET cc_start: 0.5996 (OUTLIER) cc_final: 0.5356 (ttp) outliers start: 38 outliers final: 18 residues processed: 424 average time/residue: 0.7128 time to fit residues: 347.1586 Evaluate side-chains 343 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 320 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 334 LYS Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 334 LYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 339 MET Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 447 ARG Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 334 LYS Chi-restraints excluded: chain F residue 334 LYS Chi-restraints excluded: chain G residue 334 LYS Chi-restraints excluded: chain G residue 339 MET Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain J residue 449 SER Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain L residue 417 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.0570 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.4980 overall best weight: 1.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 HIS A 474 HIS B 361 ASN C 278 HIS E 470 GLN H 217 GLN H 462 GLN I 226 ASN I 308 GLN I 397 GLN I 461 GLN I 474 HIS K 268 ASN ** K 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 477 ASN L 217 GLN L 226 ASN L 474 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117085 restraints weight = 35432.540| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.16 r_work: 0.3245 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28346 Z= 0.119 Angle : 0.526 7.183 38690 Z= 0.277 Chirality : 0.041 0.167 4415 Planarity : 0.005 0.077 4764 Dihedral : 11.208 141.861 4038 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.58 % Favored : 97.07 % Rotamer: Outliers : 1.66 % Allowed : 8.27 % Favored : 90.07 % 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 aren not related in a simple way. whole: 0.63 (0.15), residues: 3443 helix: 0.71 (0.13), residues: 1777 sheet: 2.78 (0.31), residues: 300 loop : -0.42 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 394 TYR 0.010 0.001 TYR K 475 PHE 0.013 0.001 PHE C 358 TRP 0.023 0.001 TRP E 466 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00281 (28346) covalent geometry : angle 0.52584 (38690) hydrogen bonds : bond 0.04436 ( 1217) hydrogen bonds : angle 4.36402 ( 3486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 349 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASP cc_start: 0.8584 (m-30) cc_final: 0.8261 (p0) REVERT: A 481 ASN cc_start: 0.7603 (m110) cc_final: 0.7202 (m110) REVERT: D 219 MET cc_start: 0.9147 (ttp) cc_final: 0.8810 (ttp) REVERT: D 433 LYS cc_start: 0.8318 (tptt) cc_final: 0.7787 (tptp) REVERT: D 447 ARG cc_start: 0.7251 (ttt180) cc_final: 0.6925 (tpp80) REVERT: E 227 ARG cc_start: 0.8685 (mtt-85) cc_final: 0.7850 (mtp85) REVERT: F 225 GLU cc_start: 0.7892 (tt0) cc_final: 0.7646 (tt0) REVERT: G 452 MET cc_start: 0.5949 (ttm) cc_final: 0.4513 (ppp) REVERT: I 452 MET cc_start: 0.7152 (ttt) cc_final: 0.6613 (ttp) REVERT: J 452 MET cc_start: 0.5704 (OUTLIER) cc_final: 0.4607 (ttp) REVERT: L 399 MET cc_start: 0.5814 (mmt) cc_final: 0.5569 (ttp) REVERT: L 417 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8447 (t70) outliers start: 50 outliers final: 19 residues processed: 378 average time/residue: 0.7232 time to fit residues: 315.4507 Evaluate side-chains 338 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 317 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 HIS Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 459 ASP Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 459 ASP Chi-restraints excluded: chain L residue 460 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 118 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 339 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 257 optimal weight: 0.8980 chunk 280 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 102 optimal weight: 0.0070 overall best weight: 0.9978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS B 206 ASN B 361 ASN C 278 HIS D 361 ASN F 240 ASN F 336 ASN F 443 ASN I 461 GLN I 474 HIS K 240 ASN K 268 ASN K 477 ASN L 474 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.154993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117341 restraints weight = 35525.349| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.14 r_work: 0.3250 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28346 Z= 0.108 Angle : 0.485 7.488 38690 Z= 0.259 Chirality : 0.040 0.160 4415 Planarity : 0.005 0.069 4764 Dihedral : 9.930 135.547 3992 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.41 % Favored : 97.24 % Rotamer: Outliers : 2.09 % Allowed : 9.86 % Favored : 88.04 % 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 aren not related in a simple way. whole: 0.88 (0.14), residues: 3443 helix: 0.94 (0.13), residues: 1744 sheet: 2.81 (0.31), residues: 300 loop : -0.29 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 394 TYR 0.011 0.001 TYR K 475 PHE 0.009 0.001 PHE C 358 TRP 0.017 0.001 TRP E 466 HIS 0.015 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00256 (28346) covalent geometry : angle 0.48469 (38690) hydrogen bonds : bond 0.04105 ( 1217) hydrogen bonds : angle 4.02165 ( 3486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 333 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 GLU cc_start: 0.7718 (mp0) cc_final: 0.7418 (mp0) REVERT: A 481 ASN cc_start: 0.7592 (m110) cc_final: 0.7153 (m110) REVERT: B 225 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7862 (tp30) REVERT: D 300 ASN cc_start: 0.6208 (t0) cc_final: 0.5888 (m-40) REVERT: D 433 LYS cc_start: 0.8304 (tptt) cc_final: 0.7782 (tptp) REVERT: D 447 ARG cc_start: 0.7218 (ttt180) cc_final: 0.6845 (tpp80) REVERT: E 399 MET cc_start: 0.5444 (ptt) cc_final: 0.5186 (mmm) REVERT: F 225 GLU cc_start: 0.7877 (tt0) cc_final: 0.7627 (tt0) REVERT: F 447 ARG cc_start: 0.7674 (ptm160) cc_final: 0.7459 (ptm-80) REVERT: G 452 MET cc_start: 0.5746 (ttm) cc_final: 0.4371 (ptt) REVERT: I 452 MET cc_start: 0.6940 (ttt) cc_final: 0.6322 (ttp) REVERT: J 452 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.4449 (ttp) REVERT: L 399 MET cc_start: 0.5873 (mmt) cc_final: 0.5543 (ttp) REVERT: L 417 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8422 (t70) outliers start: 63 outliers final: 33 residues processed: 378 average time/residue: 0.6336 time to fit residues: 277.9459 Evaluate side-chains 356 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 321 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 459 ASP Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 419 THR Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 427 THR Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 395 VAL Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 459 ASP Chi-restraints excluded: chain L residue 460 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 156 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 310 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 331 optimal weight: 0.9990 chunk 260 optimal weight: 0.9980 chunk 303 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 149 optimal weight: 0.1980 chunk 188 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN C 278 HIS D 256 GLN D 361 ASN F 240 ASN I 256 GLN I 474 HIS K 268 ASN K 477 ASN L 240 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.119098 restraints weight = 34967.162| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.18 r_work: 0.3268 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 28346 Z= 0.090 Angle : 0.454 8.851 38690 Z= 0.242 Chirality : 0.039 0.156 4415 Planarity : 0.005 0.074 4764 Dihedral : 9.586 133.394 3989 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.53 % Favored : 97.18 % Rotamer: Outliers : 1.66 % Allowed : 10.96 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.15), residues: 3443 helix: 1.05 (0.13), residues: 1778 sheet: 2.79 (0.31), residues: 300 loop : -0.15 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 394 TYR 0.011 0.001 TYR H 327 PHE 0.009 0.001 PHE C 358 TRP 0.018 0.001 TRP E 466 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00207 (28346) covalent geometry : angle 0.45423 (38690) hydrogen bonds : bond 0.03361 ( 1217) hydrogen bonds : angle 3.75009 ( 3486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 335 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 476 GLU cc_start: 0.7813 (mp0) cc_final: 0.7538 (mp0) REVERT: A 481 ASN cc_start: 0.7631 (m110) cc_final: 0.7146 (m110) REVERT: C 456 THR cc_start: 0.7303 (OUTLIER) cc_final: 0.6961 (p) REVERT: D 433 LYS cc_start: 0.8374 (tptt) cc_final: 0.7868 (tptp) REVERT: E 399 MET cc_start: 0.5439 (ptt) cc_final: 0.5214 (mmm) REVERT: F 225 GLU cc_start: 0.7938 (tt0) cc_final: 0.7717 (tt0) REVERT: F 447 ARG cc_start: 0.7662 (ptm160) cc_final: 0.7451 (ptm-80) REVERT: G 350 MET cc_start: 0.8976 (mmt) cc_final: 0.8640 (mmt) REVERT: G 452 MET cc_start: 0.5706 (ttm) cc_final: 0.4372 (ptp) REVERT: I 452 MET cc_start: 0.6839 (ttt) cc_final: 0.6166 (ttp) REVERT: J 452 MET cc_start: 0.5528 (OUTLIER) cc_final: 0.4641 (ttt) REVERT: L 399 MET cc_start: 0.5867 (mmt) cc_final: 0.5617 (tmm) REVERT: L 417 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8369 (t70) outliers start: 50 outliers final: 30 residues processed: 371 average time/residue: 0.6019 time to fit residues: 260.3774 Evaluate side-chains 349 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 316 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain H residue 459 ASP Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 419 THR Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 427 THR Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 460 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 222 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 213 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 324 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 293 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN C 278 HIS D 268 ASN D 361 ASN F 240 ASN F 336 ASN I 474 HIS K 477 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117104 restraints weight = 34935.669| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.17 r_work: 0.3250 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28346 Z= 0.107 Angle : 0.476 9.092 38690 Z= 0.254 Chirality : 0.040 0.152 4415 Planarity : 0.005 0.073 4764 Dihedral : 9.577 133.714 3989 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.38 % Favored : 97.27 % Rotamer: Outliers : 2.23 % Allowed : 11.76 % Favored : 86.02 % 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 aren not related in a simple way. whole: 1.05 (0.15), residues: 3443 helix: 1.05 (0.13), residues: 1778 sheet: 2.70 (0.30), residues: 300 loop : -0.15 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 394 TYR 0.013 0.001 TYR K 475 PHE 0.010 0.001 PHE C 358 TRP 0.023 0.001 TRP E 466 HIS 0.004 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00256 (28346) covalent geometry : angle 0.47631 (38690) hydrogen bonds : bond 0.03931 ( 1217) hydrogen bonds : angle 3.77419 ( 3486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 320 time to evaluate : 1.115 Fit side-chains REVERT: A 476 GLU cc_start: 0.7813 (mp0) cc_final: 0.7464 (mp0) REVERT: A 481 ASN cc_start: 0.7607 (m110) cc_final: 0.7141 (m110) REVERT: B 225 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7917 (tp30) REVERT: B 452 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.4831 (ttt) REVERT: D 300 ASN cc_start: 0.6056 (t0) cc_final: 0.5487 (m-40) REVERT: D 433 LYS cc_start: 0.8322 (tptt) cc_final: 0.7827 (tptp) REVERT: E 399 MET cc_start: 0.5493 (ptt) cc_final: 0.5248 (mmm) REVERT: F 225 GLU cc_start: 0.7990 (tt0) cc_final: 0.7765 (tt0) REVERT: F 447 ARG cc_start: 0.7807 (ptm160) cc_final: 0.7474 (ptm160) REVERT: G 452 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.4424 (ptp) REVERT: H 439 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8416 (mtm) REVERT: I 452 MET cc_start: 0.6850 (ttt) cc_final: 0.6182 (ttp) REVERT: J 452 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.4666 (ttt) REVERT: L 399 MET cc_start: 0.5870 (mmt) cc_final: 0.5610 (ttp) REVERT: L 417 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8379 (t70) outliers start: 67 outliers final: 36 residues processed: 368 average time/residue: 0.5835 time to fit residues: 250.0795 Evaluate side-chains 353 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 312 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 350 MET Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 439 MET Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain H residue 459 ASP Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 419 THR Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 427 THR Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 459 ASP Chi-restraints excluded: chain L residue 460 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 243 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 50 optimal weight: 0.0000 chunk 167 optimal weight: 0.0870 chunk 171 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 232 optimal weight: 10.0000 chunk 297 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN B 361 ASN C 278 HIS D 268 ASN D 361 ASN F 240 ASN F 336 ASN I 308 GLN I 474 HIS K 477 ASN L 299 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121259 restraints weight = 35025.716| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.14 r_work: 0.3262 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 28346 Z= 0.102 Angle : 0.472 9.938 38690 Z= 0.251 Chirality : 0.039 0.147 4415 Planarity : 0.005 0.073 4764 Dihedral : 9.555 135.016 3989 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.50 % Favored : 97.21 % Rotamer: Outliers : 1.99 % Allowed : 12.35 % Favored : 85.65 % 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 aren not related in a simple way. whole: 1.09 (0.15), residues: 3443 helix: 1.07 (0.13), residues: 1778 sheet: 2.68 (0.30), residues: 300 loop : -0.11 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 394 TYR 0.013 0.001 TYR H 327 PHE 0.010 0.001 PHE C 358 TRP 0.026 0.001 TRP E 466 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00240 (28346) covalent geometry : angle 0.47182 (38690) hydrogen bonds : bond 0.03748 ( 1217) hydrogen bonds : angle 3.72730 ( 3486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 325 time to evaluate : 0.826 Fit side-chains REVERT: A 476 GLU cc_start: 0.7789 (mp0) cc_final: 0.7383 (mp0) REVERT: A 481 ASN cc_start: 0.7623 (m110) cc_final: 0.7148 (m110) REVERT: A 497 ASP cc_start: 0.7544 (t70) cc_final: 0.7318 (t70) REVERT: B 225 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7902 (tp30) REVERT: B 452 MET cc_start: 0.5724 (OUTLIER) cc_final: 0.4848 (ttt) REVERT: D 433 LYS cc_start: 0.8332 (tptt) cc_final: 0.7839 (tptp) REVERT: F 225 GLU cc_start: 0.7970 (tt0) cc_final: 0.7747 (tt0) REVERT: F 447 ARG cc_start: 0.7799 (ptm160) cc_final: 0.7480 (ptm160) REVERT: G 452 MET cc_start: 0.5610 (ttm) cc_final: 0.4356 (ptp) REVERT: H 373 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7963 (mm-30) REVERT: H 439 MET cc_start: 0.8706 (mtp) cc_final: 0.8441 (mtm) REVERT: I 289 ASP cc_start: 0.6573 (t0) cc_final: 0.6277 (t70) REVERT: I 452 MET cc_start: 0.6922 (ttt) cc_final: 0.6326 (ttp) REVERT: J 444 PHE cc_start: 0.7357 (m-10) cc_final: 0.7131 (m-10) REVERT: J 452 MET cc_start: 0.5502 (OUTLIER) cc_final: 0.4631 (ttt) REVERT: L 399 MET cc_start: 0.5891 (mmt) cc_final: 0.5612 (ttp) REVERT: L 417 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8331 (t70) outliers start: 60 outliers final: 35 residues processed: 365 average time/residue: 0.6401 time to fit residues: 270.8376 Evaluate side-chains 356 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 318 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 336 ASN Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain H residue 459 ASP Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 427 THR Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 459 ASP Chi-restraints excluded: chain L residue 460 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 183 optimal weight: 0.7980 chunk 230 optimal weight: 0.0000 chunk 179 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 227 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN B 300 ASN B 361 ASN C 278 HIS D 256 GLN D 361 ASN F 240 ASN I 256 GLN I 308 GLN I 474 HIS K 477 ASN L 240 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121348 restraints weight = 34835.473| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.13 r_work: 0.3267 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 28346 Z= 0.103 Angle : 0.476 10.345 38690 Z= 0.252 Chirality : 0.040 0.156 4415 Planarity : 0.004 0.072 4764 Dihedral : 9.551 138.103 3989 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.53 % Favored : 97.12 % Rotamer: Outliers : 1.69 % Allowed : 13.09 % Favored : 85.22 % 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 aren not related in a simple way. whole: 1.11 (0.15), residues: 3443 helix: 1.10 (0.12), residues: 1778 sheet: 2.67 (0.30), residues: 300 loop : -0.10 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 227 TYR 0.013 0.001 TYR K 475 PHE 0.010 0.001 PHE C 358 TRP 0.030 0.001 TRP E 466 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00243 (28346) covalent geometry : angle 0.47581 (38690) hydrogen bonds : bond 0.03765 ( 1217) hydrogen bonds : angle 3.72166 ( 3486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 328 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 476 GLU cc_start: 0.7781 (mp0) cc_final: 0.7297 (mp0) REVERT: A 481 ASN cc_start: 0.7675 (m110) cc_final: 0.7210 (m110) REVERT: A 497 ASP cc_start: 0.7509 (t70) cc_final: 0.7243 (t70) REVERT: B 225 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7893 (tp30) REVERT: D 433 LYS cc_start: 0.8363 (tptt) cc_final: 0.7861 (tptp) REVERT: F 225 GLU cc_start: 0.7982 (tt0) cc_final: 0.7756 (tt0) REVERT: F 447 ARG cc_start: 0.7817 (ptm160) cc_final: 0.7509 (ptm160) REVERT: G 452 MET cc_start: 0.5604 (ttm) cc_final: 0.4328 (ptp) REVERT: H 373 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7962 (mm-30) REVERT: H 439 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8438 (mtm) REVERT: I 403 VAL cc_start: 0.3385 (OUTLIER) cc_final: 0.3156 (t) REVERT: I 419 THR cc_start: 0.7016 (OUTLIER) cc_final: 0.6720 (m) REVERT: I 452 MET cc_start: 0.6846 (ttt) cc_final: 0.6264 (ttp) REVERT: J 452 MET cc_start: 0.5426 (OUTLIER) cc_final: 0.4599 (ttt) REVERT: L 399 MET cc_start: 0.5876 (mmt) cc_final: 0.5602 (ttp) REVERT: L 417 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8338 (t70) outliers start: 51 outliers final: 34 residues processed: 362 average time/residue: 0.5820 time to fit residues: 244.8127 Evaluate side-chains 354 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 315 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 439 MET Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain H residue 459 ASP Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 403 VAL Chi-restraints excluded: chain I residue 419 THR Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 461 GLN Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 427 THR Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain L residue 379 THR Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 459 ASP Chi-restraints excluded: chain L residue 460 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 272 optimal weight: 7.9990 chunk 191 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS B 300 ASN B 361 ASN C 278 HIS D 256 GLN D 361 ASN G 470 GLN I 308 GLN I 474 HIS K 477 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112941 restraints weight = 34934.579| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.16 r_work: 0.3201 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28346 Z= 0.169 Angle : 0.559 10.828 38690 Z= 0.297 Chirality : 0.043 0.181 4415 Planarity : 0.005 0.069 4764 Dihedral : 9.798 141.123 3989 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.76 % Favored : 96.89 % Rotamer: Outliers : 2.09 % Allowed : 12.92 % Favored : 84.99 % 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 aren not related in a simple way. whole: 0.77 (0.14), residues: 3443 helix: 0.83 (0.12), residues: 1778 sheet: 2.49 (0.30), residues: 300 loop : -0.27 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 227 TYR 0.018 0.002 TYR K 475 PHE 0.010 0.001 PHE C 444 TRP 0.040 0.002 TRP E 466 HIS 0.006 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00419 (28346) covalent geometry : angle 0.55914 (38690) hydrogen bonds : bond 0.05375 ( 1217) hydrogen bonds : angle 4.04533 ( 3486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 326 time to evaluate : 0.957 Fit side-chains REVERT: A 476 GLU cc_start: 0.7818 (mp0) cc_final: 0.7302 (mp0) REVERT: A 497 ASP cc_start: 0.7409 (t70) cc_final: 0.7153 (t70) REVERT: B 211 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7607 (mmmt) REVERT: B 225 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8001 (tp30) REVERT: D 300 ASN cc_start: 0.6065 (t0) cc_final: 0.5348 (m110) REVERT: D 433 LYS cc_start: 0.8336 (tptt) cc_final: 0.7810 (tptp) REVERT: D 452 MET cc_start: 0.3860 (ttp) cc_final: 0.3414 (ttt) REVERT: E 399 MET cc_start: 0.6468 (tmt) cc_final: 0.5666 (mmm) REVERT: F 225 GLU cc_start: 0.8109 (tt0) cc_final: 0.7888 (tt0) REVERT: F 447 ARG cc_start: 0.7850 (ptm160) cc_final: 0.7487 (ptm160) REVERT: G 452 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.4198 (ptp) REVERT: H 373 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7975 (mm-30) REVERT: H 439 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8520 (mtm) REVERT: I 452 MET cc_start: 0.6888 (ttt) cc_final: 0.6402 (ttp) REVERT: J 452 MET cc_start: 0.5344 (OUTLIER) cc_final: 0.4575 (ttt) REVERT: L 399 MET cc_start: 0.5935 (mmt) cc_final: 0.5604 (ttp) REVERT: L 417 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8456 (t70) outliers start: 63 outliers final: 35 residues processed: 368 average time/residue: 0.6289 time to fit residues: 268.1441 Evaluate side-chains 357 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 317 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 211 LYS Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain F residue 481 ASN Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 439 MET Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain H residue 459 ASP Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 419 THR Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 427 THR Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 459 ASP Chi-restraints excluded: chain L residue 460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 185 optimal weight: 7.9990 chunk 147 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 298 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 330 optimal weight: 2.9990 chunk 258 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 268 optimal weight: 6.9990 chunk 263 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN C 278 HIS D 256 GLN D 361 ASN G 490 ASN H 462 GLN I 256 GLN I 308 GLN I 474 HIS K 477 ASN L 240 ASN L 256 GLN L 474 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.155144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117225 restraints weight = 34929.776| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.16 r_work: 0.3250 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 28346 Z= 0.100 Angle : 0.483 11.911 38690 Z= 0.256 Chirality : 0.040 0.203 4415 Planarity : 0.005 0.075 4764 Dihedral : 9.610 139.620 3989 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.47 % Favored : 97.24 % Rotamer: Outliers : 1.63 % Allowed : 13.38 % Favored : 84.99 % 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 aren not related in a simple way. whole: 1.04 (0.14), residues: 3443 helix: 1.11 (0.13), residues: 1745 sheet: 2.57 (0.30), residues: 300 loop : -0.18 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 227 TYR 0.012 0.001 TYR H 327 PHE 0.011 0.001 PHE C 358 TRP 0.043 0.001 TRP E 466 HIS 0.003 0.001 HIS I 249 Details of bonding type rmsd covalent geometry : bond 0.00234 (28346) covalent geometry : angle 0.48300 (38690) hydrogen bonds : bond 0.03578 ( 1217) hydrogen bonds : angle 3.73723 ( 3486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 323 time to evaluate : 1.010 Fit side-chains REVERT: A 476 GLU cc_start: 0.7791 (mp0) cc_final: 0.7187 (mp0) REVERT: A 481 ASN cc_start: 0.7595 (m110) cc_final: 0.7140 (m110) REVERT: A 497 ASP cc_start: 0.7501 (t70) cc_final: 0.7181 (t70) REVERT: B 211 LYS cc_start: 0.7938 (mttt) cc_final: 0.7434 (mmmt) REVERT: B 225 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7867 (tp30) REVERT: B 452 MET cc_start: 0.5643 (ttt) cc_final: 0.4897 (ttt) REVERT: D 433 LYS cc_start: 0.8331 (tptt) cc_final: 0.7841 (tptp) REVERT: D 439 MET cc_start: 0.8831 (mtp) cc_final: 0.8569 (mtp) REVERT: D 452 MET cc_start: 0.3640 (ttp) cc_final: 0.3174 (ttt) REVERT: E 399 MET cc_start: 0.6429 (tmt) cc_final: 0.5660 (mmm) REVERT: F 225 GLU cc_start: 0.7988 (tt0) cc_final: 0.7760 (tt0) REVERT: F 447 ARG cc_start: 0.7793 (ptm160) cc_final: 0.7469 (ptm160) REVERT: G 452 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.4089 (ptp) REVERT: H 439 MET cc_start: 0.8691 (mtp) cc_final: 0.8406 (mtm) REVERT: I 452 MET cc_start: 0.6857 (ttt) cc_final: 0.6348 (ttp) REVERT: J 452 MET cc_start: 0.4925 (OUTLIER) cc_final: 0.4421 (ttt) REVERT: L 399 MET cc_start: 0.5871 (mmt) cc_final: 0.5620 (tmm) REVERT: L 417 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8479 (t70) outliers start: 49 outliers final: 35 residues processed: 354 average time/residue: 0.6567 time to fit residues: 269.3766 Evaluate side-chains 357 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 319 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain H residue 459 ASP Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 419 THR Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 427 THR Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 459 ASP Chi-restraints excluded: chain L residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 9 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 230 optimal weight: 0.2980 chunk 297 optimal weight: 0.8980 chunk 294 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 346 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN C 278 HIS D 361 ASN H 462 GLN I 474 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.155244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.117320 restraints weight = 35070.146| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.17 r_work: 0.3260 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 28346 Z= 0.101 Angle : 0.483 12.048 38690 Z= 0.257 Chirality : 0.040 0.235 4415 Planarity : 0.005 0.072 4764 Dihedral : 9.593 139.087 3989 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.67 % Favored : 97.01 % Rotamer: Outliers : 1.49 % Allowed : 13.82 % Favored : 84.69 % 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 aren not related in a simple way. whole: 1.13 (0.14), residues: 3443 helix: 1.18 (0.13), residues: 1745 sheet: 2.61 (0.31), residues: 300 loop : -0.13 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 394 TYR 0.021 0.001 TYR B 301 PHE 0.010 0.001 PHE C 358 TRP 0.060 0.001 TRP E 466 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00235 (28346) covalent geometry : angle 0.48282 (38690) hydrogen bonds : bond 0.03629 ( 1217) hydrogen bonds : angle 3.70369 ( 3486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6886 Ramachandran restraints generated. 3443 Oldfield, 0 Emsley, 3443 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 321 time to evaluate : 0.957 Fit side-chains REVERT: A 476 GLU cc_start: 0.7788 (mp0) cc_final: 0.7183 (mp0) REVERT: A 481 ASN cc_start: 0.7586 (m110) cc_final: 0.7128 (m110) REVERT: A 497 ASP cc_start: 0.7464 (t70) cc_final: 0.7174 (t70) REVERT: B 211 LYS cc_start: 0.7984 (mttt) cc_final: 0.7481 (mmmt) REVERT: B 225 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7876 (tp30) REVERT: B 452 MET cc_start: 0.5623 (ttt) cc_final: 0.4873 (ttt) REVERT: D 300 ASN cc_start: 0.5803 (t0) cc_final: 0.4948 (m110) REVERT: D 433 LYS cc_start: 0.8331 (tptt) cc_final: 0.7842 (tptp) REVERT: D 439 MET cc_start: 0.8817 (mtp) cc_final: 0.8537 (mtp) REVERT: D 452 MET cc_start: 0.3644 (ttp) cc_final: 0.3150 (ttt) REVERT: E 399 MET cc_start: 0.6450 (tmt) cc_final: 0.5650 (mmm) REVERT: E 433 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7593 (tttt) REVERT: F 225 GLU cc_start: 0.7991 (tt0) cc_final: 0.7767 (tt0) REVERT: F 447 ARG cc_start: 0.7801 (ptm160) cc_final: 0.7490 (ptm160) REVERT: G 452 MET cc_start: 0.5437 (OUTLIER) cc_final: 0.4040 (ptp) REVERT: H 439 MET cc_start: 0.8692 (mtp) cc_final: 0.8434 (mtm) REVERT: I 452 MET cc_start: 0.6817 (ttt) cc_final: 0.6329 (ttp) REVERT: J 444 PHE cc_start: 0.7359 (m-10) cc_final: 0.7121 (m-10) REVERT: J 452 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4394 (ttt) REVERT: L 399 MET cc_start: 0.5890 (mmt) cc_final: 0.5643 (tmm) REVERT: L 417 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8435 (t70) outliers start: 45 outliers final: 37 residues processed: 350 average time/residue: 0.6256 time to fit residues: 252.8597 Evaluate side-chains 358 residues out of total 3047 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 317 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain E residue 433 LYS Chi-restraints excluded: chain E residue 456 THR Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 403 VAL Chi-restraints excluded: chain F residue 427 THR Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain F residue 494 LEU Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 452 MET Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 456 THR Chi-restraints excluded: chain H residue 459 ASP Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain I residue 203 VAL Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 419 THR Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain I residue 494 LEU Chi-restraints excluded: chain J residue 228 VAL Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 305 LEU Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 427 THR Chi-restraints excluded: chain J residue 452 MET Chi-restraints excluded: chain L residue 417 ASP Chi-restraints excluded: chain L residue 459 ASP Chi-restraints excluded: chain L residue 460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 1 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 325 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 260 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 300 ASN C 278 HIS ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 ASN H 462 GLN I 474 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.155565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121471 restraints weight = 34956.898| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.12 r_work: 0.3258 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 28346 Z= 0.102 Angle : 0.486 10.972 38690 Z= 0.258 Chirality : 0.040 0.238 4415 Planarity : 0.004 0.071 4764 Dihedral : 9.570 138.774 3989 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.85 % Favored : 96.89 % Rotamer: Outliers : 1.73 % Allowed : 13.68 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.14), residues: 3443 helix: 1.21 (0.13), residues: 1745 sheet: 2.62 (0.31), residues: 300 loop : -0.12 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 394 TYR 0.012 0.001 TYR K 475 PHE 0.011 0.001 PHE C 358 TRP 0.067 0.001 TRP E 466 HIS 0.003 0.001 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00236 (28346) covalent geometry : angle 0.48612 (38690) hydrogen bonds : bond 0.03638 ( 1217) hydrogen bonds : angle 3.68188 ( 3486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9886.48 seconds wall clock time: 168 minutes 59.74 seconds (10139.74 seconds total)