Starting phenix.real_space_refine on Mon Aug 25 09:54:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kbj_62227/08_2025/9kbj_62227.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kbj_62227/08_2025/9kbj_62227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kbj_62227/08_2025/9kbj_62227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kbj_62227/08_2025/9kbj_62227.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kbj_62227/08_2025/9kbj_62227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kbj_62227/08_2025/9kbj_62227.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 33 5.49 5 Mg 11 5.21 5 S 147 5.16 5 C 17539 2.51 5 N 4582 2.21 5 O 5054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s 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: 27366 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2243 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2246 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2261 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2251 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2253 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2243 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2261 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2240 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2256 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2268 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 275} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2246 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2246 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 3 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: "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: "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: "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: "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} Time building chain proxies: 6.42, per 1000 atoms: 0.23 Number of scatterers: 27366 At special positions: 0 Unit cell: (134.2, 149.6, 157.3, 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 147 16.00 P 33 15.00 Mg 11 11.99 O 5054 8.00 N 4582 7.00 C 17539 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: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6454 Finding SS restraints... Secondary structure from input PDB file: 183 helices and 24 sheets defined 54.5% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 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: 3.621A pdb=" N TYR A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 268 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.678A pdb=" N ASP A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.572A pdb=" N LEU A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 431 through 438 removed outlier: 3.756A pdb=" N ARG A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.619A pdb=" N GLY A 453 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 removed outlier: 3.749A pdb=" N GLN A 470 " --> pdb=" O TRP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 480 Processing helix chain 'A' and resid 495 through 499 Processing helix chain 'C' and resid 210 through 225 Processing helix chain 'C' and resid 230 through 238 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.527A pdb=" N TYR C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 268 removed outlier: 3.573A pdb=" N GLN C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 removed outlier: 4.028A pdb=" N PHE C 275 " --> pdb=" O PRO C 271 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) 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 removed outlier: 3.522A pdb=" N LYS C 312 " --> pdb=" O GLN C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' Processing helix chain 'C' and resid 380 through 389 removed outlier: 3.655A pdb=" N ALA C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 399 Processing helix chain 'C' and resid 431 through 437 Processing helix chain 'C' and resid 449 through 453 Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.658A pdb=" N ALA C 469 " --> pdb=" O THR C 465 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 470 " --> pdb=" O TRP C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 480 Processing helix chain 'C' and resid 495 through 499 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: 3.848A pdb=" N TYR D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 268 removed outlier: 3.802A pdb=" N GLN D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 286 through 289 Processing helix chain 'D' and resid 290 through 299 Processing helix chain 'D' and resid 302 through 315 removed outlier: 3.782A pdb=" N GLY D 307 " --> pdb=" O PRO D 303 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D 312 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 377 through 379 No H-bonds generated for 'chain 'D' and resid 377 through 379' Processing helix chain 'D' and resid 380 through 389 removed outlier: 3.882A pdb=" N ALA D 386 " --> pdb=" O GLU D 382 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 399 Processing helix chain 'D' and resid 431 through 437 removed outlier: 3.543A pdb=" N LYS D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D 437 " --> pdb=" O LYS D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 453 removed outlier: 4.288A pdb=" N GLY D 453 " --> pdb=" O PRO D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 470 removed outlier: 3.544A pdb=" N VAL D 460 " --> pdb=" O THR D 456 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA D 469 " --> pdb=" O THR D 465 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN D 470 " --> pdb=" O TRP D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 478 through 481 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: 3.537A pdb=" N TYR E 242 " --> pdb=" O ASP E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 266 removed outlier: 4.311A pdb=" N GLN E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 removed outlier: 4.402A pdb=" N PHE E 275 " --> pdb=" O PRO E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 289 Processing helix chain 'E' and resid 290 through 299 removed outlier: 3.796A pdb=" N LYS E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 314 removed outlier: 3.712A pdb=" N LYS E 312 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 345 Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 380 through 389 removed outlier: 3.860A pdb=" N ALA E 386 " --> pdb=" O GLU E 382 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 399 Processing helix chain 'E' and resid 431 through 437 Processing helix chain 'E' and resid 449 through 453 removed outlier: 4.695A pdb=" N GLY E 453 " --> pdb=" O PRO E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 470 removed outlier: 3.645A pdb=" N GLN E 470 " --> pdb=" O TRP E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 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 Processing helix chain 'F' and resid 248 through 268 removed outlier: 3.647A pdb=" N GLN F 254 " --> pdb=" O SER F 250 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU F 259 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS F 260 " --> pdb=" O GLN F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 277 removed outlier: 3.510A pdb=" N LEU F 276 " --> pdb=" O THR F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 289 Processing helix chain 'F' and resid 290 through 299 Processing helix chain 'F' and resid 302 through 315 removed outlier: 3.611A pdb=" N LYS F 312 " --> pdb=" O GLN F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 345 removed outlier: 3.506A pdb=" N VAL F 345 " --> pdb=" O ILE F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 354 No H-bonds generated for 'chain 'F' and resid 352 through 354' Processing helix chain 'F' and resid 380 through 389 removed outlier: 3.601A pdb=" N ALA F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 400 Processing helix chain 'F' and resid 431 through 437 removed outlier: 3.587A pdb=" N GLU F 437 " --> pdb=" O LYS F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 453 removed outlier: 4.388A pdb=" N GLY F 453 " --> pdb=" O PRO F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 470 Processing helix chain 'F' and resid 472 through 480 removed outlier: 3.500A pdb=" N GLU F 476 " --> pdb=" O TRP F 472 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN F 477 " --> pdb=" O ASP F 473 " (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: 3.556A pdb=" N TYR G 242 " --> pdb=" O ASP G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 268 removed outlier: 4.061A pdb=" N GLN G 254 " --> pdb=" O SER G 250 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN G 256 " --> pdb=" O SER G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 277 Processing helix chain 'G' and resid 290 through 299 Processing helix chain 'G' and resid 302 through 315 removed outlier: 3.517A pdb=" N LYS G 312 " --> pdb=" O GLN G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 345 removed outlier: 3.512A pdb=" N SER G 344 " --> pdb=" O ALA G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 389 removed outlier: 4.005A pdb=" N ALA G 386 " --> pdb=" O GLU G 382 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE G 387 " --> pdb=" O ALA G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 393 through 399 Processing helix chain 'G' and resid 431 through 437 Processing helix chain 'G' and resid 456 through 470 Processing helix chain 'G' and resid 472 through 481 removed outlier: 3.503A pdb=" N ASN G 477 " --> pdb=" O ASP G 473 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP G 478 " --> pdb=" O HIS G 474 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN G 481 " --> pdb=" O ASN G 477 " (cutoff:3.500A) 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: 3.614A pdb=" N TYR H 242 " --> pdb=" O ASP H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 268 removed outlier: 4.151A pdb=" N GLN H 254 " --> pdb=" O SER H 250 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN H 256 " --> pdb=" O SER H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 277 removed outlier: 4.385A pdb=" N PHE H 275 " --> pdb=" O PRO H 271 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU H 276 " --> pdb=" O THR H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 289 Processing helix chain 'H' and resid 290 through 299 Processing helix chain 'H' and resid 302 through 314 Processing helix chain 'H' and resid 334 through 345 removed outlier: 3.505A pdb=" N SER H 344 " --> pdb=" O ALA H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 389 removed outlier: 3.663A pdb=" N ALA H 386 " --> pdb=" O GLU H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 393 through 399 Processing helix chain 'H' and resid 431 through 437 Processing helix chain 'H' and resid 449 through 453 Processing helix chain 'H' and resid 456 through 470 removed outlier: 3.662A pdb=" N GLN H 470 " --> pdb=" O TRP H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 472 through 480 removed outlier: 3.576A pdb=" N ASN H 477 " --> pdb=" O ASP H 473 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TRP H 478 " --> pdb=" O HIS H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 499 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: 3.734A pdb=" N TYR I 242 " --> pdb=" O ASP I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 269 removed outlier: 4.221A pdb=" N GLN I 254 " --> pdb=" O SER I 250 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN I 256 " --> pdb=" O SER I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 276 removed outlier: 3.956A pdb=" N PHE I 275 " --> pdb=" O PRO I 271 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU I 276 " --> pdb=" O THR I 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 271 through 276' Processing helix chain 'I' and resid 290 through 299 Processing helix chain 'I' and resid 302 through 315 removed outlier: 3.514A pdb=" N GLN I 308 " --> pdb=" O LEU I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 345 removed outlier: 3.524A pdb=" N SER I 344 " --> pdb=" O ALA I 340 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL I 345 " --> pdb=" O ILE I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 389 removed outlier: 3.640A pdb=" N ALA I 386 " --> pdb=" O GLU I 382 " (cutoff:3.500A) Processing helix chain 'I' and resid 393 through 399 Processing helix chain 'I' and resid 431 through 437 Processing helix chain 'I' and resid 449 through 453 removed outlier: 3.761A pdb=" N GLY I 453 " --> pdb=" O PRO I 450 " (cutoff:3.500A) Processing helix chain 'I' and resid 456 through 470 removed outlier: 3.772A pdb=" N VAL I 460 " --> pdb=" O THR I 456 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 479 removed outlier: 3.848A pdb=" N TRP I 478 " --> pdb=" O HIS I 474 " (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 Processing helix chain 'J' and resid 248 through 268 removed outlier: 4.245A pdb=" N GLN J 254 " --> pdb=" O SER J 250 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN J 256 " --> pdb=" O SER J 252 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU J 259 " --> pdb=" O ILE J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 276 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 314 removed outlier: 3.514A pdb=" N LYS J 312 " --> pdb=" O GLN J 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 333 through 343 Processing helix chain 'J' and resid 380 through 389 Processing helix chain 'J' and resid 393 through 399 Processing helix chain 'J' and resid 431 through 437 Processing helix chain 'J' and resid 449 through 453 removed outlier: 4.309A pdb=" N GLY J 453 " --> pdb=" O PRO J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 469 Processing helix chain 'J' and resid 472 through 480 removed outlier: 3.594A pdb=" N TRP J 478 " --> pdb=" O HIS J 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 227 removed outlier: 3.567A pdb=" N CYS K 224 " --> pdb=" O VAL K 220 " (cutoff:3.500A) Processing helix chain 'K' and resid 230 through 246 removed outlier: 7.388A pdb=" N ASN K 240 " --> pdb=" O LEU K 236 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLN K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 268 removed outlier: 3.653A pdb=" N GLN K 254 " --> pdb=" O SER K 250 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE K 255 " --> pdb=" O GLY K 251 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN K 256 " --> pdb=" O SER K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 277 removed outlier: 3.533A pdb=" N LEU K 276 " --> pdb=" O THR K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 299 Processing helix chain 'K' and resid 302 through 315 Processing helix chain 'K' and resid 333 through 343 Processing helix chain 'K' and resid 352 through 354 No H-bonds generated for 'chain 'K' and resid 352 through 354' Processing helix chain 'K' and resid 380 through 389 removed outlier: 3.587A pdb=" N ALA K 386 " --> pdb=" O GLU K 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 400 Processing helix chain 'K' and resid 431 through 437 Processing helix chain 'K' and resid 449 through 453 removed outlier: 3.612A pdb=" N GLY K 453 " --> pdb=" O PRO K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 456 through 469 removed outlier: 3.556A pdb=" N VAL K 460 " --> pdb=" O THR K 456 " (cutoff:3.500A) Processing helix chain 'K' and resid 472 through 480 removed outlier: 4.050A pdb=" N TRP K 478 " --> pdb=" O HIS K 474 " (cutoff:3.500A) removed outlier: 3.772A 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: 3.654A pdb=" N TYR L 242 " --> pdb=" O ASP L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 248 through 269 removed outlier: 4.432A pdb=" N GLN L 254 " --> pdb=" O SER L 250 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN L 256 " --> pdb=" O SER L 252 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU L 269 " --> pdb=" O LYS L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 277 removed outlier: 3.600A pdb=" N LEU L 276 " --> pdb=" O THR L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 289 Processing helix chain 'L' and resid 290 through 299 Processing helix chain 'L' and resid 302 through 315 removed outlier: 3.518A pdb=" N ASP L 315 " --> pdb=" O LEU L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 333 through 344 Processing helix chain 'L' and resid 377 through 379 No H-bonds generated for 'chain 'L' and resid 377 through 379' Processing helix chain 'L' and resid 380 through 389 removed outlier: 3.620A pdb=" N ALA L 386 " --> pdb=" O GLU L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 393 through 400 Processing helix chain 'L' and resid 431 through 437 Processing helix chain 'L' and resid 449 through 453 Processing helix chain 'L' and resid 456 through 470 removed outlier: 3.747A pdb=" N VAL L 460 " --> pdb=" O THR L 456 " (cutoff:3.500A) Processing helix chain 'L' and resid 472 through 480 removed outlier: 3.650A pdb=" N GLU L 476 " --> pdb=" O TRP L 472 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN L 477 " --> pdb=" O ASP L 473 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP L 478 " --> pdb=" O HIS L 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 226 removed outlier: 3.506A pdb=" N GLN B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 248 through 268 removed outlier: 3.956A pdb=" N GLN B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 removed outlier: 3.691A pdb=" N LEU B 276 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.509A pdb=" N VAL B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 389 removed outlier: 4.015A pdb=" N ALA B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 400 Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 456 through 470 removed outlier: 3.526A pdb=" N GLN B 470 " --> pdb=" O TRP B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 480 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 'C' and resid 348 through 350 removed outlier: 6.537A pdb=" N GLY C 349 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ASP C 372 " --> pdb=" O GLY C 349 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL C 369 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR C 413 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TRP C 371 " --> pdb=" O THR C 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 421 through 423 Processing sheet with id=AA5, first strand: chain 'D' and resid 348 through 350 Processing sheet with id=AA6, first strand: chain 'D' and resid 421 through 423 Processing sheet with id=AA7, first strand: chain 'E' and resid 348 through 350 Processing sheet with id=AA8, first strand: chain 'E' and resid 421 through 422 Processing sheet with id=AA9, first strand: chain 'F' and resid 348 through 350 removed outlier: 6.432A pdb=" N VAL F 369 " --> pdb=" O VAL F 411 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR F 413 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP F 371 " --> pdb=" O THR F 413 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 421 through 423 Processing sheet with id=AB2, first strand: chain 'G' and resid 348 through 350 removed outlier: 6.792A pdb=" N GLY G 349 " --> pdb=" O VAL G 370 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP G 372 " --> pdb=" O GLY G 349 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 421 through 422 Processing sheet with id=AB4, first strand: chain 'H' and resid 348 through 350 removed outlier: 6.218A pdb=" N LEU H 324 " --> pdb=" O ILE H 412 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N SER H 414 " --> pdb=" O LEU H 324 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE H 326 " --> pdb=" O SER H 414 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 421 through 423 Processing sheet with id=AB6, first strand: chain 'I' and resid 348 through 350 removed outlier: 6.667A pdb=" N GLY I 349 " --> pdb=" O VAL I 370 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASP I 372 " --> pdb=" O GLY I 349 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU I 324 " --> pdb=" O ILE I 412 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N SER I 414 " --> pdb=" O LEU I 324 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N PHE I 326 " --> pdb=" O SER I 414 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 421 through 422 Processing sheet with id=AB8, first strand: chain 'J' and resid 348 through 350 removed outlier: 6.716A pdb=" N GLY J 349 " --> pdb=" O VAL J 370 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ASP J 372 " --> pdb=" O GLY J 349 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL J 369 " --> pdb=" O VAL J 411 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N THR J 413 " --> pdb=" O VAL J 369 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP J 371 " --> pdb=" O THR J 413 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 421 through 422 Processing sheet with id=AC1, first strand: chain 'K' and resid 348 through 350 removed outlier: 6.511A pdb=" N GLY K 349 " --> pdb=" O VAL K 370 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASP K 372 " --> pdb=" O GLY K 349 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL K 369 " --> pdb=" O VAL K 411 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N THR K 413 " --> pdb=" O VAL K 369 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP K 371 " --> pdb=" O THR K 413 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 421 through 422 Processing sheet with id=AC3, first strand: chain 'L' and resid 348 through 350 Processing sheet with id=AC4, first strand: chain 'L' and resid 421 through 423 Processing sheet with id=AC5, first strand: chain 'B' and resid 349 through 350 removed outlier: 6.955A pdb=" N GLY B 349 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ASP B 372 " --> pdb=" O GLY B 349 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 421 through 422 1205 hydrogen bonds defined for protein. 3465 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: 4.73 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8501 1.34 - 1.46: 6722 1.46 - 1.58: 12538 1.58 - 1.70: 54 1.70 - 1.82: 222 Bond restraints: 28037 Sorted by residual: bond pdb=" O3A ANP A 602 " pdb=" PB ANP A 602 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP B 602 " pdb=" PB ANP B 602 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" O3A ANP F 602 " pdb=" PB ANP F 602 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" O3A ANP D 602 " pdb=" PB ANP D 602 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" O3A ANP C 602 " pdb=" PB ANP C 602 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 ... (remaining 28032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.82: 38060 3.82 - 7.64: 103 7.64 - 11.46: 41 11.46 - 15.29: 0 15.29 - 19.11: 11 Bond angle restraints: 38215 Sorted by residual: angle pdb=" PB ANP A 602 " pdb=" N3B ANP A 602 " pdb=" PG ANP A 602 " ideal model delta sigma weight residual 126.95 107.84 19.11 3.00e+00 1.11e-01 4.06e+01 angle pdb=" PB ANP K 602 " pdb=" N3B ANP K 602 " pdb=" PG ANP K 602 " ideal model delta sigma weight residual 126.95 107.94 19.01 3.00e+00 1.11e-01 4.01e+01 angle pdb=" PB ANP E 602 " pdb=" N3B ANP E 602 " pdb=" PG ANP E 602 " ideal model delta sigma weight residual 126.95 108.05 18.90 3.00e+00 1.11e-01 3.97e+01 angle pdb=" PB ANP G 602 " pdb=" N3B ANP G 602 " pdb=" PG ANP G 602 " ideal model delta sigma weight residual 126.95 108.12 18.83 3.00e+00 1.11e-01 3.94e+01 angle pdb=" PB ANP F 602 " pdb=" N3B ANP F 602 " pdb=" PG ANP F 602 " ideal model delta sigma weight residual 126.95 108.13 18.82 3.00e+00 1.11e-01 3.94e+01 ... (remaining 38210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.83: 15846 26.83 - 53.65: 573 53.65 - 80.48: 168 80.48 - 107.30: 18 107.30 - 134.13: 9 Dihedral angle restraints: 16614 sinusoidal: 6683 harmonic: 9931 Sorted by residual: dihedral pdb=" O1A ANP J 602 " pdb=" O3A ANP J 602 " pdb=" PA ANP J 602 " pdb=" PB ANP J 602 " ideal model delta sinusoidal sigma weight residual 83.11 -51.02 134.13 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" CA TRP F 472 " pdb=" C TRP F 472 " pdb=" N ASP F 473 " pdb=" CA ASP F 473 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" O1A ANP C 602 " pdb=" O3A ANP C 602 " pdb=" PA ANP C 602 " pdb=" PB ANP C 602 " ideal model delta sinusoidal sigma weight residual 83.11 -46.78 129.89 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 16611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3758 0.056 - 0.111: 535 0.111 - 0.167: 41 0.167 - 0.222: 0 0.222 - 0.278: 11 Chirality restraints: 4345 Sorted by residual: chirality pdb=" C3' ANP K 602 " pdb=" C2' ANP K 602 " pdb=" C4' ANP K 602 " pdb=" O3' ANP K 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' ANP L 602 " pdb=" C2' ANP L 602 " pdb=" C4' ANP L 602 " pdb=" O3' ANP L 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' ANP F 602 " pdb=" C2' ANP F 602 " pdb=" C4' ANP F 602 " pdb=" O3' ANP F 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 4342 not shown) Planarity restraints: 4695 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS K 495 " 0.044 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO K 496 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO K 496 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO K 496 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 449 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO E 450 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 450 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 450 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 203 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.67e+00 pdb=" N PRO H 204 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO H 204 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 204 " -0.023 5.00e-02 4.00e+02 ... (remaining 4692 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 216 2.61 - 3.18: 23680 3.18 - 3.76: 40983 3.76 - 4.33: 59279 4.33 - 4.90: 96399 Nonbonded interactions: 220557 Sorted by model distance: nonbonded pdb="MG MG E 601 " pdb=" O3G ANP E 602 " model vdw 2.040 2.170 nonbonded pdb="MG MG G 601 " pdb=" O3G ANP G 602 " model vdw 2.041 2.170 nonbonded pdb="MG MG A 601 " pdb=" O3G ANP A 602 " model vdw 2.054 2.170 nonbonded pdb="MG MG H 601 " pdb=" O2B ANP H 602 " model vdw 2.065 2.170 nonbonded pdb=" OG1 THR F 335 " pdb="MG MG F 601 " model vdw 2.068 2.170 ... (remaining 220552 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 395 or (resid 396 and (name N or name CA or na \ me C or name O or name CB )) or resid 397 through 400 or resid 408 through 449 o \ r resid 451 through 499)) selection = (chain 'B' and (resid 202 through 277 or resid 286 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 400 o \ r resid 408 through 499)) selection = (chain 'C' and (resid 202 through 277 or resid 286 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 400 o \ r resid 408 through 449 or resid 451 through 499)) selection = (chain 'D' and (resid 202 through 277 or resid 286 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 400 o \ r resid 408 through 449 or resid 451 through 499)) selection = (chain 'E' and (resid 202 through 277 or resid 286 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 400 o \ r resid 408 through 449 or resid 451 through 499)) selection = (chain 'F' and (resid 202 through 277 or resid 286 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 400 o \ r resid 408 through 449 or resid 451 through 499)) selection = (chain 'G' and (resid 202 through 395 or (resid 396 and (name N or name CA or na \ me C or name O or name CB )) or resid 397 through 400 or resid 408 through 449 o \ r resid 451 through 499)) selection = (chain 'H' and (resid 202 through 277 or resid 286 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 400 o \ r resid 408 through 449 or resid 451 through 499)) selection = (chain 'I' and (resid 202 through 400 or resid 408 through 449 or resid 451 thro \ ugh 499)) selection = (chain 'J' and (resid 202 through 277 or resid 286 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 449 o \ r resid 451 through 499)) selection = (chain 'K' and (resid 202 through 277 or resid 286 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 400 o \ r resid 408 through 449 or resid 451 through 499)) selection = (chain 'L' and (resid 202 through 277 or resid 286 through 395 or (resid 396 and \ (name N or name CA or name C or name O or name CB )) or resid 397 through 400 o \ r resid 408 through 449 or resid 451 through 499)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.280 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 23.880 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.005 0.144 28037 Z= 0.248 Angle : 0.730 19.107 38215 Z= 0.337 Chirality : 0.040 0.278 4345 Planarity : 0.004 0.067 4695 Dihedral : 15.924 134.127 10160 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.03 % Allowed : 0.20 % Favored : 99.77 % 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: 0.60 (0.15), residues: 3356 helix: 0.03 (0.12), residues: 1667 sheet: 1.47 (0.30), residues: 364 loop : 0.87 (0.18), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 438 TYR 0.023 0.001 TYR H 327 PHE 0.007 0.001 PHE L 360 TRP 0.024 0.001 TRP G 478 HIS 0.004 0.001 HIS A 474 Details of bonding type rmsd covalent geometry : bond 0.00492 (28037) covalent geometry : angle 0.72952 (38215) hydrogen bonds : bond 0.25331 ( 1205) hydrogen bonds : angle 6.73308 ( 3465) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 475 TYR cc_start: 0.7941 (t80) cc_final: 0.7087 (t80) REVERT: C 375 ILE cc_start: 0.8761 (mm) cc_final: 0.8215 (pt) REVERT: D 287 ILE cc_start: 0.7145 (tp) cc_final: 0.6924 (tp) REVERT: D 466 TRP cc_start: 0.8079 (t60) cc_final: 0.7772 (t60) REVERT: E 459 ASP cc_start: 0.7700 (m-30) cc_final: 0.7458 (m-30) REVERT: F 339 MET cc_start: 0.8482 (mmt) cc_final: 0.8129 (mmp) REVERT: H 417 ASP cc_start: 0.8262 (t0) cc_final: 0.7991 (t0) REVERT: I 462 GLN cc_start: 0.7427 (mt0) cc_final: 0.7051 (mm-40) REVERT: K 219 MET cc_start: 0.8610 (ttp) cc_final: 0.8356 (ttm) REVERT: L 278 HIS cc_start: 0.5383 (t-90) cc_final: 0.5071 (t70) outliers start: 1 outliers final: 0 residues processed: 390 average time/residue: 0.1617 time to fit residues: 98.9301 Evaluate side-chains 307 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 217 GLN C 431 HIS D 217 GLN E 226 ASN E 290 ASN E 468 ASN E 481 ASN F 322 ASN F 425 ASN G 361 ASN B 361 ASN B 391 GLN B 415 ASN B 477 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.094589 restraints weight = 47323.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097385 restraints weight = 28969.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099206 restraints weight = 21089.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100427 restraints weight = 17246.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.101228 restraints weight = 15073.068| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 28037 Z= 0.118 Angle : 0.494 6.372 38215 Z= 0.259 Chirality : 0.041 0.138 4345 Planarity : 0.004 0.044 4695 Dihedral : 12.278 148.648 3877 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.70 % Allowed : 5.07 % Favored : 94.23 % 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: 1.08 (0.15), residues: 3356 helix: 0.57 (0.12), residues: 1716 sheet: 1.56 (0.29), residues: 371 loop : 0.95 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 447 TYR 0.016 0.001 TYR B 475 PHE 0.011 0.001 PHE L 360 TRP 0.017 0.001 TRP H 472 HIS 0.004 0.001 HIS B 495 Details of bonding type rmsd covalent geometry : bond 0.00260 (28037) covalent geometry : angle 0.49443 (38215) hydrogen bonds : bond 0.04468 ( 1205) hydrogen bonds : angle 4.30145 ( 3465) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 351 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 475 TYR cc_start: 0.8048 (t80) cc_final: 0.7107 (t80) REVERT: D 301 TYR cc_start: 0.7627 (m-80) cc_final: 0.7319 (m-80) REVERT: D 361 ASN cc_start: 0.7423 (t0) cc_final: 0.7218 (t0) REVERT: E 355 ASN cc_start: 0.8305 (p0) cc_final: 0.8038 (p0) REVERT: E 436 LYS cc_start: 0.8834 (mttt) cc_final: 0.8229 (mtmm) REVERT: F 478 TRP cc_start: 0.7421 (t60) cc_final: 0.7200 (t60) REVERT: I 358 PHE cc_start: 0.7363 (m-80) cc_final: 0.7131 (m-80) REVERT: K 426 THR cc_start: 0.8939 (m) cc_final: 0.8477 (p) REVERT: K 496 PRO cc_start: 0.8084 (Cg_endo) cc_final: 0.7857 (Cg_exo) REVERT: L 278 HIS cc_start: 0.5451 (t-90) cc_final: 0.5084 (t70) outliers start: 21 outliers final: 11 residues processed: 357 average time/residue: 0.1811 time to fit residues: 101.2528 Evaluate side-chains 310 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 299 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain F residue 350 MET Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain K residue 459 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 187 optimal weight: 0.0670 chunk 298 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 111 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 ASN D 425 ASN B 361 ASN B 495 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.121146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095429 restraints weight = 47375.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098246 restraints weight = 28731.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100110 restraints weight = 20816.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101342 restraints weight = 16931.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.102131 restraints weight = 14752.014| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28037 Z= 0.091 Angle : 0.436 8.719 38215 Z= 0.228 Chirality : 0.039 0.135 4345 Planarity : 0.003 0.037 4695 Dihedral : 9.772 141.054 3877 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.03 % Allowed : 7.61 % Favored : 91.36 % 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: 1.37 (0.15), residues: 3356 helix: 0.91 (0.12), residues: 1722 sheet: 1.52 (0.29), residues: 373 loop : 0.99 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 447 TYR 0.013 0.001 TYR B 475 PHE 0.009 0.001 PHE L 360 TRP 0.017 0.001 TRP H 472 HIS 0.005 0.001 HIS B 495 Details of bonding type rmsd covalent geometry : bond 0.00198 (28037) covalent geometry : angle 0.43581 (38215) hydrogen bonds : bond 0.03678 ( 1205) hydrogen bonds : angle 3.83502 ( 3465) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 336 time to evaluate : 1.086 Fit side-chains REVERT: A 475 TYR cc_start: 0.8057 (t80) cc_final: 0.7117 (t80) REVERT: D 268 ASN cc_start: 0.9047 (m-40) cc_final: 0.8814 (m-40) REVERT: D 301 TYR cc_start: 0.7697 (m-80) cc_final: 0.7284 (m-80) REVERT: E 291 LYS cc_start: 0.6982 (mtmt) cc_final: 0.6722 (ptpt) REVERT: E 436 LYS cc_start: 0.8796 (mttt) cc_final: 0.8208 (mtmm) REVERT: F 478 TRP cc_start: 0.7457 (t60) cc_final: 0.7170 (t60) REVERT: G 232 ASP cc_start: 0.8218 (m-30) cc_final: 0.8016 (m-30) REVERT: H 452 MET cc_start: 0.5970 (mmp) cc_final: 0.5488 (ttm) REVERT: J 304 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7718 (mt) REVERT: K 426 THR cc_start: 0.8894 (m) cc_final: 0.8476 (p) REVERT: B 225 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 466 TRP cc_start: 0.7748 (t60) cc_final: 0.7122 (t60) outliers start: 31 outliers final: 16 residues processed: 353 average time/residue: 0.1908 time to fit residues: 106.2056 Evaluate side-chains 320 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 303 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 231 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain K residue 459 ASP Chi-restraints excluded: chain L residue 249 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 296 optimal weight: 4.9990 chunk 271 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 147 optimal weight: 0.0000 chunk 194 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 269 optimal weight: 0.7980 chunk 184 optimal weight: 5.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.094420 restraints weight = 47360.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097169 restraints weight = 28896.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098983 restraints weight = 21028.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100183 restraints weight = 17124.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100855 restraints weight = 14983.404| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 28037 Z= 0.108 Angle : 0.434 7.359 38215 Z= 0.229 Chirality : 0.039 0.135 4345 Planarity : 0.003 0.037 4695 Dihedral : 9.328 135.231 3877 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.10 % Allowed : 8.94 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.15), residues: 3356 helix: 1.01 (0.12), residues: 1723 sheet: 1.47 (0.29), residues: 375 loop : 1.01 (0.18), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 394 TYR 0.014 0.001 TYR B 475 PHE 0.010 0.001 PHE L 360 TRP 0.016 0.001 TRP H 472 HIS 0.003 0.001 HIS L 309 Details of bonding type rmsd covalent geometry : bond 0.00249 (28037) covalent geometry : angle 0.43364 (38215) hydrogen bonds : bond 0.03597 ( 1205) hydrogen bonds : angle 3.71798 ( 3465) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 317 time to evaluate : 1.025 Fit side-chains REVERT: A 387 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8629 (mm) REVERT: A 475 TYR cc_start: 0.8113 (t80) cc_final: 0.7167 (t80) REVERT: D 301 TYR cc_start: 0.7778 (m-80) cc_final: 0.7373 (m-80) REVERT: E 436 LYS cc_start: 0.8790 (mttt) cc_final: 0.8190 (mtmm) REVERT: F 478 TRP cc_start: 0.7473 (t60) cc_final: 0.7151 (t60) REVERT: H 452 MET cc_start: 0.6084 (mmp) cc_final: 0.5566 (ttm) REVERT: K 426 THR cc_start: 0.8988 (m) cc_final: 0.8620 (p) REVERT: B 225 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 466 TRP cc_start: 0.7716 (t60) cc_final: 0.7009 (t60) REVERT: B 475 TYR cc_start: 0.7003 (t80) cc_final: 0.6591 (t80) outliers start: 33 outliers final: 22 residues processed: 339 average time/residue: 0.1757 time to fit residues: 93.5679 Evaluate side-chains 326 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 437 GLU Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 219 MET Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain K residue 459 ASP Chi-restraints excluded: chain L residue 249 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 275 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 245 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 267 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093682 restraints weight = 47540.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.096414 restraints weight = 29038.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098222 restraints weight = 21180.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099423 restraints weight = 17252.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100181 restraints weight = 15081.131| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 28037 Z= 0.122 Angle : 0.451 10.126 38215 Z= 0.236 Chirality : 0.039 0.136 4345 Planarity : 0.003 0.035 4695 Dihedral : 9.199 131.906 3877 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.30 % Allowed : 10.01 % Favored : 88.69 % 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: 1.45 (0.15), residues: 3356 helix: 1.03 (0.13), residues: 1724 sheet: 1.45 (0.29), residues: 375 loop : 0.96 (0.18), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 447 TYR 0.014 0.001 TYR F 475 PHE 0.009 0.001 PHE L 360 TRP 0.019 0.001 TRP D 466 HIS 0.004 0.001 HIS L 309 Details of bonding type rmsd covalent geometry : bond 0.00285 (28037) covalent geometry : angle 0.45064 (38215) hydrogen bonds : bond 0.03649 ( 1205) hydrogen bonds : angle 3.69867 ( 3465) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 319 time to evaluate : 1.137 Fit side-chains REVERT: A 387 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8651 (mm) REVERT: D 301 TYR cc_start: 0.7870 (m-80) cc_final: 0.7447 (m-80) REVERT: E 291 LYS cc_start: 0.7101 (mtmt) cc_final: 0.6879 (ptpt) REVERT: E 436 LYS cc_start: 0.8794 (mttt) cc_final: 0.8185 (mtmm) REVERT: F 478 TRP cc_start: 0.7532 (t60) cc_final: 0.7191 (t60) REVERT: G 249 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6804 (t-90) REVERT: H 452 MET cc_start: 0.6066 (mmp) cc_final: 0.5628 (ttm) REVERT: K 426 THR cc_start: 0.8990 (m) cc_final: 0.8621 (p) REVERT: B 225 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7716 (tm-30) REVERT: B 466 TRP cc_start: 0.7736 (t60) cc_final: 0.6953 (t60) REVERT: B 475 TYR cc_start: 0.7235 (t80) cc_final: 0.6718 (t80) outliers start: 39 outliers final: 29 residues processed: 342 average time/residue: 0.1875 time to fit residues: 101.5090 Evaluate side-chains 338 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 372 ASP Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain K residue 459 ASP Chi-restraints excluded: chain L residue 249 HIS Chi-restraints excluded: chain L residue 411 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 489 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 216 optimal weight: 0.1980 chunk 193 optimal weight: 8.9990 chunk 112 optimal weight: 0.0870 chunk 249 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 301 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 191 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 481 ASN B 431 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.120664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095105 restraints weight = 47606.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097870 restraints weight = 28865.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099717 restraints weight = 20990.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.100934 restraints weight = 17049.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101722 restraints weight = 14859.164| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 28037 Z= 0.089 Angle : 0.417 7.321 38215 Z= 0.221 Chirality : 0.039 0.140 4345 Planarity : 0.003 0.040 4695 Dihedral : 9.002 129.551 3877 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.33 % Allowed : 10.28 % Favored : 88.39 % 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: 1.59 (0.15), residues: 3356 helix: 1.14 (0.13), residues: 1729 sheet: 1.61 (0.29), residues: 372 loop : 1.01 (0.18), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 447 TYR 0.013 0.001 TYR D 348 PHE 0.009 0.001 PHE L 360 TRP 0.020 0.001 TRP D 466 HIS 0.004 0.000 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00199 (28037) covalent geometry : angle 0.41721 (38215) hydrogen bonds : bond 0.03200 ( 1205) hydrogen bonds : angle 3.53927 ( 3465) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 334 time to evaluate : 1.142 Fit side-chains REVERT: C 256 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7420 (mm-40) REVERT: D 301 TYR cc_start: 0.7855 (m-80) cc_final: 0.7490 (m-80) REVERT: E 436 LYS cc_start: 0.8798 (mttt) cc_final: 0.8198 (mtmm) REVERT: F 236 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8551 (mm) REVERT: F 478 TRP cc_start: 0.7404 (t60) cc_final: 0.7025 (t60) REVERT: G 249 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6760 (t-90) REVERT: H 452 MET cc_start: 0.6083 (mmp) cc_final: 0.5636 (ttm) REVERT: J 304 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7737 (mt) REVERT: K 285 MET cc_start: 0.5694 (tpt) cc_final: 0.5464 (tpt) REVERT: K 426 THR cc_start: 0.8948 (m) cc_final: 0.8564 (p) REVERT: L 268 ASN cc_start: 0.8303 (m-40) cc_final: 0.8047 (m-40) REVERT: B 225 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7731 (tm-30) REVERT: B 466 TRP cc_start: 0.7592 (t60) cc_final: 0.6940 (t60) outliers start: 40 outliers final: 28 residues processed: 358 average time/residue: 0.1763 time to fit residues: 99.5493 Evaluate side-chains 345 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 314 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain F residue 225 GLU Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 437 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain K residue 457 GLU Chi-restraints excluded: chain K residue 459 ASP Chi-restraints excluded: chain L residue 249 HIS Chi-restraints excluded: chain L residue 411 VAL Chi-restraints excluded: chain B residue 350 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 269 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 253 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 329 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS G 495 HIS H 495 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.119964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094393 restraints weight = 47165.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097137 restraints weight = 28831.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098935 restraints weight = 20969.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100127 restraints weight = 17142.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100844 restraints weight = 14987.525| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 28037 Z= 0.106 Angle : 0.437 11.921 38215 Z= 0.228 Chirality : 0.039 0.139 4345 Planarity : 0.003 0.037 4695 Dihedral : 8.989 127.935 3877 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.53 % Allowed : 10.74 % Favored : 87.72 % 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: 1.59 (0.15), residues: 3356 helix: 1.16 (0.13), residues: 1727 sheet: 1.60 (0.29), residues: 373 loop : 0.98 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 447 TYR 0.017 0.001 TYR B 475 PHE 0.009 0.001 PHE H 358 TRP 0.019 0.001 TRP D 466 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00245 (28037) covalent geometry : angle 0.43673 (38215) hydrogen bonds : bond 0.03398 ( 1205) hydrogen bonds : angle 3.55815 ( 3465) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 329 time to evaluate : 0.825 Fit side-chains REVERT: A 464 LEU cc_start: 0.8754 (mm) cc_final: 0.8419 (mm) REVERT: C 256 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7405 (mm-40) REVERT: D 225 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7498 (tt0) REVERT: D 301 TYR cc_start: 0.7890 (m-80) cc_final: 0.7500 (m-80) REVERT: E 436 LYS cc_start: 0.8795 (mttt) cc_final: 0.8194 (mtmm) REVERT: F 236 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8543 (mm) REVERT: F 478 TRP cc_start: 0.7275 (t60) cc_final: 0.6954 (t60) REVERT: G 249 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6791 (t-90) REVERT: H 452 MET cc_start: 0.6107 (mmp) cc_final: 0.5653 (ttm) REVERT: J 304 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7748 (mt) REVERT: L 268 ASN cc_start: 0.8273 (m-40) cc_final: 0.8006 (m-40) REVERT: L 427 THR cc_start: 0.7307 (m) cc_final: 0.7063 (t) REVERT: B 225 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7739 (tm-30) REVERT: B 466 TRP cc_start: 0.7587 (t60) cc_final: 0.6945 (t60) REVERT: B 475 TYR cc_start: 0.6901 (t80) cc_final: 0.6521 (t80) outliers start: 46 outliers final: 34 residues processed: 355 average time/residue: 0.1644 time to fit residues: 91.8423 Evaluate side-chains 354 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 317 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 483 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 358 PHE Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain J residue 219 MET Chi-restraints excluded: chain J residue 304 LEU Chi-restraints excluded: chain K residue 457 GLU Chi-restraints excluded: chain K residue 459 ASP Chi-restraints excluded: chain K residue 480 ILE Chi-restraints excluded: chain L residue 249 HIS Chi-restraints excluded: chain L residue 411 VAL Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 426 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 209 optimal weight: 0.4980 chunk 102 optimal weight: 0.5980 chunk 284 optimal weight: 4.9990 chunk 15 optimal weight: 0.0070 chunk 157 optimal weight: 0.9990 chunk 330 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 499 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096176 restraints weight = 47243.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.098952 restraints weight = 28577.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100796 restraints weight = 20724.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101980 restraints weight = 16813.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102789 restraints weight = 14712.902| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28037 Z= 0.081 Angle : 0.410 10.050 38215 Z= 0.216 Chirality : 0.038 0.142 4345 Planarity : 0.003 0.036 4695 Dihedral : 8.816 126.130 3877 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.10 % Allowed : 11.21 % Favored : 87.69 % 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: 1.72 (0.15), residues: 3356 helix: 1.27 (0.13), residues: 1734 sheet: 1.74 (0.29), residues: 371 loop : 0.98 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 394 TYR 0.021 0.001 TYR F 475 PHE 0.013 0.001 PHE H 358 TRP 0.020 0.001 TRP H 466 HIS 0.003 0.000 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00177 (28037) covalent geometry : angle 0.41020 (38215) hydrogen bonds : bond 0.02999 ( 1205) hydrogen bonds : angle 3.42329 ( 3465) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 344 time to evaluate : 0.882 Fit side-chains REVERT: A 464 LEU cc_start: 0.8765 (mm) cc_final: 0.8398 (mm) REVERT: A 475 TYR cc_start: 0.8063 (t80) cc_final: 0.7086 (t80) REVERT: D 225 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7508 (tt0) REVERT: D 301 TYR cc_start: 0.7855 (m-80) cc_final: 0.7454 (m-80) REVERT: E 436 LYS cc_start: 0.8767 (mttt) cc_final: 0.8175 (mtmm) REVERT: F 236 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8569 (mm) REVERT: F 478 TRP cc_start: 0.7169 (t60) cc_final: 0.6850 (t60) REVERT: H 301 TYR cc_start: 0.7617 (m-80) cc_final: 0.7286 (m-80) REVERT: H 452 MET cc_start: 0.6362 (mmp) cc_final: 0.5901 (ttm) REVERT: H 478 TRP cc_start: 0.7230 (t60) cc_final: 0.7013 (t60) REVERT: L 268 ASN cc_start: 0.8265 (m-40) cc_final: 0.8002 (m-40) REVERT: L 427 THR cc_start: 0.7153 (m) cc_final: 0.6919 (t) REVERT: B 225 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7748 (tm-30) REVERT: B 466 TRP cc_start: 0.7601 (t60) cc_final: 0.7025 (t60) REVERT: B 475 TYR cc_start: 0.6898 (t80) cc_final: 0.6670 (t80) outliers start: 33 outliers final: 27 residues processed: 363 average time/residue: 0.1628 time to fit residues: 92.6664 Evaluate side-chains 348 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 320 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 439 MET Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain H residue 437 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 219 MET Chi-restraints excluded: chain K residue 457 GLU Chi-restraints excluded: chain K residue 459 ASP Chi-restraints excluded: chain K residue 480 ILE Chi-restraints excluded: chain L residue 249 HIS Chi-restraints excluded: chain L residue 411 VAL Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 489 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 311 optimal weight: 0.9980 chunk 112 optimal weight: 0.0870 chunk 243 optimal weight: 0.3980 chunk 275 optimal weight: 0.7980 chunk 326 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 200 optimal weight: 1.9990 chunk 154 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS C 217 GLN E 468 ASN ** G 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.122018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.096717 restraints weight = 47374.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099498 restraints weight = 28464.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101348 restraints weight = 20599.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102569 restraints weight = 16685.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103246 restraints weight = 14512.955| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 28037 Z= 0.081 Angle : 0.418 12.086 38215 Z= 0.218 Chirality : 0.038 0.141 4345 Planarity : 0.003 0.036 4695 Dihedral : 8.716 125.048 3877 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.17 % Allowed : 11.48 % Favored : 87.35 % 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: 1.82 (0.15), residues: 3356 helix: 1.36 (0.13), residues: 1743 sheet: 1.84 (0.29), residues: 371 loop : 0.99 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 447 TYR 0.020 0.001 TYR F 475 PHE 0.008 0.001 PHE L 360 TRP 0.020 0.001 TRP H 466 HIS 0.003 0.000 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00178 (28037) covalent geometry : angle 0.41758 (38215) hydrogen bonds : bond 0.02881 ( 1205) hydrogen bonds : angle 3.35700 ( 3465) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 339 time to evaluate : 0.892 Fit side-chains REVERT: A 464 LEU cc_start: 0.8777 (mm) cc_final: 0.8405 (mm) REVERT: A 475 TYR cc_start: 0.8002 (t80) cc_final: 0.7154 (t80) REVERT: D 225 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7490 (tt0) REVERT: D 296 LEU cc_start: 0.7895 (mm) cc_final: 0.7666 (mm) REVERT: D 301 TYR cc_start: 0.7860 (m-80) cc_final: 0.7496 (m-80) REVERT: E 436 LYS cc_start: 0.8752 (mttt) cc_final: 0.8200 (mtmm) REVERT: F 339 MET cc_start: 0.8708 (mmt) cc_final: 0.8278 (mmp) REVERT: F 478 TRP cc_start: 0.7248 (t60) cc_final: 0.6955 (t60) REVERT: G 249 HIS cc_start: 0.6910 (OUTLIER) cc_final: 0.6623 (t-90) REVERT: H 301 TYR cc_start: 0.7600 (m-80) cc_final: 0.7276 (m-80) REVERT: H 452 MET cc_start: 0.6325 (mmp) cc_final: 0.5901 (ttm) REVERT: H 472 TRP cc_start: 0.6698 (m100) cc_final: 0.6379 (m-90) REVERT: H 478 TRP cc_start: 0.7271 (t60) cc_final: 0.7011 (t60) REVERT: L 268 ASN cc_start: 0.8221 (m-40) cc_final: 0.7979 (m-40) REVERT: L 427 THR cc_start: 0.7171 (m) cc_final: 0.6847 (t) REVERT: B 225 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7757 (tm-30) REVERT: B 350 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8144 (mtp) REVERT: B 444 PHE cc_start: 0.7789 (m-10) cc_final: 0.7524 (m-80) REVERT: B 475 TYR cc_start: 0.6931 (t80) cc_final: 0.6710 (t80) outliers start: 35 outliers final: 28 residues processed: 361 average time/residue: 0.1582 time to fit residues: 90.4131 Evaluate side-chains 353 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 323 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 457 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 219 MET Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 457 GLU Chi-restraints excluded: chain K residue 459 ASP Chi-restraints excluded: chain L residue 249 HIS Chi-restraints excluded: chain L residue 411 VAL Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 168 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 290 optimal weight: 0.0770 chunk 156 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS ** G 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 474 HIS L 461 GLN B 391 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.117980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092293 restraints weight = 47718.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.094920 restraints weight = 29167.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.096678 restraints weight = 21395.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.097837 restraints weight = 17520.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.098573 restraints weight = 15362.429| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28037 Z= 0.168 Angle : 0.502 9.371 38215 Z= 0.263 Chirality : 0.041 0.153 4345 Planarity : 0.004 0.042 4695 Dihedral : 9.104 129.127 3877 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.23 % Allowed : 11.51 % Favored : 87.25 % 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: 1.55 (0.15), residues: 3356 helix: 1.16 (0.13), residues: 1725 sheet: 1.61 (0.29), residues: 359 loop : 0.90 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 447 TYR 0.019 0.002 TYR A 475 PHE 0.023 0.001 PHE H 358 TRP 0.019 0.001 TRP H 466 HIS 0.005 0.001 HIS L 309 Details of bonding type rmsd covalent geometry : bond 0.00401 (28037) covalent geometry : angle 0.50168 (38215) hydrogen bonds : bond 0.04015 ( 1205) hydrogen bonds : angle 3.71751 ( 3465) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6712 Ramachandran restraints generated. 3356 Oldfield, 0 Emsley, 3356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 319 time to evaluate : 1.067 Fit side-chains REVERT: A 464 LEU cc_start: 0.8758 (mm) cc_final: 0.8438 (mm) REVERT: A 475 TYR cc_start: 0.8101 (t80) cc_final: 0.7113 (t80) REVERT: D 225 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7491 (tt0) REVERT: D 301 TYR cc_start: 0.7978 (m-80) cc_final: 0.7564 (m-80) REVERT: E 436 LYS cc_start: 0.8800 (mttt) cc_final: 0.8243 (mtmm) REVERT: F 478 TRP cc_start: 0.7262 (t60) cc_final: 0.6958 (t60) REVERT: G 249 HIS cc_start: 0.7150 (OUTLIER) cc_final: 0.6899 (t-90) REVERT: G 358 PHE cc_start: 0.7617 (m-80) cc_final: 0.7348 (m-80) REVERT: H 452 MET cc_start: 0.6054 (mmp) cc_final: 0.5682 (ttm) REVERT: I 447 ARG cc_start: 0.7034 (ttt90) cc_final: 0.6629 (tpt-90) REVERT: K 373 GLU cc_start: 0.7903 (pt0) cc_final: 0.7624 (pt0) REVERT: L 268 ASN cc_start: 0.8294 (m-40) cc_final: 0.8033 (m-40) REVERT: L 427 THR cc_start: 0.7511 (m) cc_final: 0.7209 (t) REVERT: B 444 PHE cc_start: 0.7826 (m-10) cc_final: 0.7483 (m-80) REVERT: B 466 TRP cc_start: 0.7451 (t-100) cc_final: 0.6994 (t60) REVERT: B 475 TYR cc_start: 0.7212 (t80) cc_final: 0.6697 (t80) outliers start: 37 outliers final: 31 residues processed: 343 average time/residue: 0.1648 time to fit residues: 89.9906 Evaluate side-chains 346 residues out of total 3010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 314 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 275 PHE Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 411 VAL Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain G residue 427 THR Chi-restraints excluded: chain G residue 485 ASP Chi-restraints excluded: chain H residue 224 CYS Chi-restraints excluded: chain H residue 304 LEU Chi-restraints excluded: chain H residue 429 THR Chi-restraints excluded: chain I residue 427 THR Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 305 LEU Chi-restraints excluded: chain K residue 457 GLU Chi-restraints excluded: chain K residue 459 ASP Chi-restraints excluded: chain K residue 480 ILE Chi-restraints excluded: chain L residue 249 HIS Chi-restraints excluded: chain L residue 411 VAL Chi-restraints excluded: chain B residue 350 MET Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 489 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 333 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 293 optimal weight: 0.7980 chunk 315 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 131 optimal weight: 0.0870 chunk 63 optimal weight: 7.9990 chunk 209 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 322 ASN B 391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.120885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.095444 restraints weight = 47148.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098195 restraints weight = 28543.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.100011 restraints weight = 20736.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101210 restraints weight = 16882.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.101884 restraints weight = 14724.670| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28037 Z= 0.088 Angle : 0.439 12.779 38215 Z= 0.230 Chirality : 0.039 0.182 4345 Planarity : 0.003 0.039 4695 Dihedral : 8.822 124.749 3877 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.10 % Allowed : 11.88 % Favored : 87.02 % 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: 1.70 (0.15), residues: 3356 helix: 1.29 (0.13), residues: 1739 sheet: 1.72 (0.29), residues: 365 loop : 0.93 (0.18), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 394 TYR 0.019 0.001 TYR F 475 PHE 0.007 0.001 PHE L 360 TRP 0.022 0.001 TRP H 466 HIS 0.004 0.000 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00195 (28037) covalent geometry : angle 0.43869 (38215) hydrogen bonds : bond 0.03093 ( 1205) hydrogen bonds : angle 3.47041 ( 3465) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3935.61 seconds wall clock time: 69 minutes 8.86 seconds (4148.86 seconds total)