Starting phenix.real_space_refine on Fri Jul 3 23:54:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7apd_11852/07_2026/7apd_11852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7apd_11852/07_2026/7apd_11852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7apd_11852/07_2026/7apd_11852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7apd_11852/07_2026/7apd_11852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7apd_11852/07_2026/7apd_11852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7apd_11852/07_2026/7apd_11852.map" } resolution = 3.9 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= 0.048 sd= 0.782 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 76 5.49 5 S 78 5.16 5 C 10876 2.51 5 N 3005 2.21 5 O 3261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17296 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1201 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 146} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2238 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 279} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2228 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2228 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "E" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2232 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2229 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 276} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2213 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "H" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1184 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "P" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 805 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N GLY H 156 " occ=0.60 ... (2 atoms not shown) pdb=" O GLY H 156 " occ=0.60 residue: pdb=" N SER H 157 " occ=0.60 ... (4 atoms not shown) pdb=" OG SER H 157 " occ=0.60 residue: pdb=" N ARG H 158 " occ=0.60 ... (9 atoms not shown) pdb=" NH2 ARG H 158 " occ=0.60 Time building chain proxies: 3.28, per 1000 atoms: 0.19 Number of scatterers: 17296 At special positions: 0 Unit cell: (135.625, 157.325, 116.095, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 76 15.00 O 3261 8.00 N 3005 7.00 C 10876 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 636.0 milliseconds 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 13 sheets defined 53.3% alpha, 8.2% beta 15 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'G' and resid 160 through 172 Processing helix chain 'G' and resid 200 through 212 Processing helix chain 'G' and resid 242 through 254 Processing helix chain 'G' and resid 271 through 281 removed outlier: 4.818A pdb=" N TRP G 277 " --> pdb=" O ALA G 273 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 342 through 351 removed outlier: 3.518A pdb=" N THR B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 376 removed outlier: 4.211A pdb=" N LEU B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 388 Processing helix chain 'B' and resid 395 through 405 Processing helix chain 'B' and resid 408 through 421 removed outlier: 4.056A pdb=" N PHE B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 418 " --> pdb=" O ASN B 414 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 451 removed outlier: 3.797A pdb=" N LEU B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 removed outlier: 4.046A pdb=" N HIS B 463 " --> pdb=" O HIS B 460 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 464 " --> pdb=" O LYS B 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 464' Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 481 through 491 Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.676A pdb=" N LEU B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 532 through 537 removed outlier: 4.622A pdb=" N SER B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 571 Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 591 through 595 removed outlier: 4.158A pdb=" N PHE B 594 " --> pdb=" O MET B 591 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 595 " --> pdb=" O ARG B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 591 through 595' Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 327 through 339 Processing helix chain 'C' and resid 342 through 350 removed outlier: 3.776A pdb=" N ALA C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 374 Processing helix chain 'C' and resid 377 through 389 Processing helix chain 'C' and resid 395 through 405 Processing helix chain 'C' and resid 408 through 420 removed outlier: 3.927A pdb=" N PHE C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'C' and resid 456 through 471 removed outlier: 3.774A pdb=" N ASN C 459 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS C 461 " --> pdb=" O ALA C 458 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS C 463 " --> pdb=" O HIS C 460 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE C 464 " --> pdb=" O LYS C 461 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 466 " --> pdb=" O HIS C 463 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER C 468 " --> pdb=" O TRP C 465 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 470 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 491 Processing helix chain 'C' and resid 492 through 498 Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'C' and resid 560 through 571 removed outlier: 3.990A pdb=" N TRP C 564 " --> pdb=" O THR C 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.639A pdb=" N MET D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 338 Processing helix chain 'D' and resid 342 through 350 removed outlier: 4.080A pdb=" N ALA D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 376 Processing helix chain 'D' and resid 377 through 387 Processing helix chain 'D' and resid 395 through 405 removed outlier: 3.570A pdb=" N LEU D 399 " --> pdb=" O TRP D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 422 removed outlier: 3.981A pdb=" N PHE D 412 " --> pdb=" O GLU D 408 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU D 418 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS D 421 " --> pdb=" O LYS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 450 Processing helix chain 'D' and resid 456 through 460 removed outlier: 4.053A pdb=" N ASN D 459 " --> pdb=" O SER D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 471 removed outlier: 4.120A pdb=" N LEU D 466 " --> pdb=" O HIS D 463 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER D 468 " --> pdb=" O TRP D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 491 Processing helix chain 'D' and resid 492 through 498 Processing helix chain 'D' and resid 529 through 533 removed outlier: 3.551A pdb=" N LEU D 533 " --> pdb=" O ASP D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 571 Processing helix chain 'E' and resid 312 through 324 removed outlier: 3.592A pdb=" N MET E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 339 Processing helix chain 'E' and resid 342 through 349 Processing helix chain 'E' and resid 353 through 374 Processing helix chain 'E' and resid 377 through 389 Processing helix chain 'E' and resid 395 through 406 removed outlier: 4.815A pdb=" N PHE E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 422 removed outlier: 3.991A pdb=" N PHE E 412 " --> pdb=" O GLU E 408 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU E 418 " --> pdb=" O ASN E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 450 Processing helix chain 'E' and resid 456 through 471 removed outlier: 3.675A pdb=" N ASN E 459 " --> pdb=" O SER E 456 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS E 461 " --> pdb=" O ALA E 458 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS E 463 " --> pdb=" O HIS E 460 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE E 464 " --> pdb=" O LYS E 461 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU E 466 " --> pdb=" O HIS E 463 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER E 468 " --> pdb=" O TRP E 465 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP E 471 " --> pdb=" O SER E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 481 through 491 Processing helix chain 'E' and resid 492 through 498 removed outlier: 3.684A pdb=" N LEU E 496 " --> pdb=" O LEU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 removed outlier: 3.582A pdb=" N HIS E 536 " --> pdb=" O LEU E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 571 removed outlier: 4.049A pdb=" N TRP E 564 " --> pdb=" O THR E 560 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 324 removed outlier: 3.522A pdb=" N MET F 316 " --> pdb=" O ASP F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 339 Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 353 through 375 Processing helix chain 'F' and resid 377 through 389 removed outlier: 3.715A pdb=" N LEU F 388 " --> pdb=" O ALA F 384 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 405 Processing helix chain 'F' and resid 408 through 422 removed outlier: 3.804A pdb=" N PHE F 412 " --> pdb=" O GLU F 408 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU F 418 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS F 421 " --> pdb=" O LYS F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 450 Processing helix chain 'F' and resid 456 through 462 removed outlier: 3.601A pdb=" N ASN F 459 " --> pdb=" O SER F 456 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS F 461 " --> pdb=" O ALA F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'F' and resid 481 through 492 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 532 through 538 removed outlier: 3.556A pdb=" N HIS F 536 " --> pdb=" O LEU F 533 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER F 537 " --> pdb=" O TYR F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 571 removed outlier: 3.595A pdb=" N TRP F 564 " --> pdb=" O THR F 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.645A pdb=" N ALA A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 376 Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.671A pdb=" N PHE A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 450 Processing helix chain 'A' and resid 456 through 460 removed outlier: 3.757A pdb=" N ASN A 459 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 removed outlier: 3.749A pdb=" N ALA A 470 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 491 Processing helix chain 'A' and resid 493 through 497 removed outlier: 3.506A pdb=" N LEU A 496 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 576 removed outlier: 6.019A pdb=" N GLY A 573 " --> pdb=" O VAL A 569 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ARG A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 172 Processing helix chain 'H' and resid 174 through 178 Processing helix chain 'H' and resid 200 through 213 removed outlier: 3.744A pdb=" N GLU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS H 213 " --> pdb=" O GLU H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 255 Processing helix chain 'H' and resid 257 through 259 No H-bonds generated for 'chain 'H' and resid 257 through 259' Processing helix chain 'H' and resid 270 through 281 removed outlier: 3.858A pdb=" N TRP H 277 " --> pdb=" O ALA H 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 298 Processing sheet with id=AA1, first strand: chain 'G' and resid 189 through 197 removed outlier: 6.180A pdb=" N GLN G 190 " --> pdb=" O PHE G 237 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE G 217 " --> pdb=" O CYS G 236 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASN G 238 " --> pdb=" O CYS G 215 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N CYS G 215 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 518 through 522 removed outlier: 3.947A pdb=" N LEU B 429 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 522 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N CYS B 428 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE B 542 " --> pdb=" O CYS B 428 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA B 430 " --> pdb=" O PHE B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 501 through 504 Processing sheet with id=AA4, first strand: chain 'C' and resid 453 through 455 removed outlier: 4.619A pdb=" N ASP C 478 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA C 475 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR C 521 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL C 477 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 522 " --> pdb=" O PHE C 431 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA C 430 " --> pdb=" O PHE C 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 501 through 503 removed outlier: 3.578A pdb=" N VAL C 501 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 513 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 454 through 455 removed outlier: 4.347A pdb=" N ASP D 478 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR D 521 " --> pdb=" O VAL D 477 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU D 429 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS D 428 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE D 542 " --> pdb=" O CYS D 428 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ALA D 430 " --> pdb=" O PHE D 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 501 through 503 Processing sheet with id=AA8, first strand: chain 'E' and resid 475 through 478 removed outlier: 6.075A pdb=" N LEU E 429 " --> pdb=" O VAL E 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 501 through 503 removed outlier: 3.791A pdb=" N ILE E 503 " --> pdb=" O VAL E 511 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 453 through 454 removed outlier: 7.127A pdb=" N SER F 453 " --> pdb=" O LEU F 476 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ASP F 478 " --> pdb=" O SER F 453 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU F 519 " --> pdb=" O LEU F 476 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASP F 478 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR F 521 " --> pdb=" O ASP F 478 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU F 429 " --> pdb=" O VAL F 520 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N SER F 522 " --> pdb=" O LEU F 429 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N PHE F 431 " --> pdb=" O SER F 522 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 501 through 503 Processing sheet with id=AB3, first strand: chain 'A' and resid 477 through 480 removed outlier: 6.332A pdb=" N ASP A 478 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR A 521 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU A 429 " --> pdb=" O VAL A 520 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N SER A 522 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N PHE A 431 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N CYS A 428 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N PHE A 542 " --> pdb=" O CYS A 428 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 430 " --> pdb=" O PHE A 542 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 261 through 264 removed outlier: 5.558A pdb=" N GLN H 190 " --> pdb=" O PHE H 237 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N CYS H 230 " --> pdb=" O LYS H 222 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LYS H 222 " --> pdb=" O CYS H 230 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL H 232 " --> pdb=" O MET H 220 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N MET H 220 " --> pdb=" O VAL H 232 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU H 234 " --> pdb=" O LEU H 218 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU H 218 " --> pdb=" O LEU H 234 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N CYS H 236 " --> pdb=" O SER H 216 " (cutoff:3.500A) 710 hydrogen bonds defined for protein. 1983 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5288 1.34 - 1.48: 5126 1.48 - 1.61: 7330 1.61 - 1.74: 26 1.74 - 1.87: 110 Bond restraints: 17880 Sorted by residual: bond pdb=" C1' DG T 68 " pdb=" N9 DG T 68 " ideal model delta sigma weight residual 1.468 1.373 0.095 1.40e-02 5.10e+03 4.57e+01 bond pdb=" C1' DG T 63 " pdb=" N9 DG T 63 " ideal model delta sigma weight residual 1.468 1.377 0.091 1.40e-02 5.10e+03 4.19e+01 bond pdb=" C1' DG T 49 " pdb=" N9 DG T 49 " ideal model delta sigma weight residual 1.468 1.383 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" C1' DG T 70 " pdb=" N9 DG T 70 " ideal model delta sigma weight residual 1.468 1.386 0.082 1.40e-02 5.10e+03 3.47e+01 bond pdb=" C1' DG T 58 " pdb=" N9 DG T 58 " ideal model delta sigma weight residual 1.468 1.386 0.082 1.40e-02 5.10e+03 3.42e+01 ... (remaining 17875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 24376 3.50 - 7.00: 164 7.00 - 10.50: 21 10.50 - 14.00: 5 14.00 - 17.51: 1 Bond angle restraints: 24567 Sorted by residual: angle pdb=" CA ARG G 297 " pdb=" CB ARG G 297 " pdb=" CG ARG G 297 " ideal model delta sigma weight residual 114.10 131.61 -17.51 2.00e+00 2.50e-01 7.66e+01 angle pdb=" N LYS B 506 " pdb=" CA LYS B 506 " pdb=" C LYS B 506 " ideal model delta sigma weight residual 113.19 123.13 -9.94 1.19e+00 7.06e-01 6.98e+01 angle pdb=" C LEU G 302 " pdb=" N ASN G 303 " pdb=" CA ASN G 303 " ideal model delta sigma weight residual 122.87 109.86 13.01 1.61e+00 3.86e-01 6.53e+01 angle pdb=" N LEU H 181 " pdb=" CA LEU H 181 " pdb=" C LEU H 181 " ideal model delta sigma weight residual 109.24 121.79 -12.55 1.63e+00 3.76e-01 5.93e+01 angle pdb=" O4' DT T 69 " pdb=" C1' DT T 69 " pdb=" N1 DT T 69 " ideal model delta sigma weight residual 108.00 112.35 -4.35 7.00e-01 2.04e+00 3.86e+01 ... (remaining 24562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 9394 28.35 - 56.69: 768 56.69 - 85.04: 125 85.04 - 113.38: 9 113.38 - 141.73: 1 Dihedral angle restraints: 10297 sinusoidal: 4355 harmonic: 5942 Sorted by residual: dihedral pdb=" CA ARG G 180 " pdb=" C ARG G 180 " pdb=" N LEU G 181 " pdb=" CA LEU G 181 " ideal model delta harmonic sigma weight residual 180.00 -143.51 -36.49 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA LYS G 213 " pdb=" C LYS G 213 " pdb=" N GLN G 214 " pdb=" CA GLN G 214 " ideal model delta harmonic sigma weight residual -180.00 -146.84 -33.16 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA ARG G 223 " pdb=" C ARG G 223 " pdb=" N SER G 224 " pdb=" CA SER G 224 " ideal model delta harmonic sigma weight residual 0.00 26.01 -26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 10294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2410 0.078 - 0.156: 252 0.156 - 0.234: 29 0.234 - 0.312: 8 0.312 - 0.390: 8 Chirality restraints: 2707 Sorted by residual: chirality pdb=" CA LYS B 506 " pdb=" N LYS B 506 " pdb=" C LYS B 506 " pdb=" CB LYS B 506 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA PHE H 182 " pdb=" N PHE H 182 " pdb=" C PHE H 182 " pdb=" CB PHE H 182 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB ILE D 559 " pdb=" CA ILE D 559 " pdb=" CG1 ILE D 559 " pdb=" CG2 ILE D 559 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 2704 not shown) Planarity restraints: 2855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 334 " -0.026 2.00e-02 2.50e+03 5.26e-02 2.77e+01 pdb=" CD GLU A 334 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLU A 334 " -0.033 2.00e-02 2.50e+03 pdb=" OE2 GLU A 334 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 197 " -0.056 2.00e-02 2.50e+03 3.42e-02 2.05e+01 pdb=" CG PHE H 197 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE H 197 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE H 197 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE H 197 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE H 197 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 197 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 192 " -0.060 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP H 192 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 192 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP H 192 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP H 192 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 192 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 192 " 0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 192 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 192 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 192 " -0.022 2.00e-02 2.50e+03 ... (remaining 2852 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 14 2.06 - 2.77: 3348 2.77 - 3.48: 23641 3.48 - 4.19: 38511 4.19 - 4.90: 67504 Nonbonded interactions: 133018 Sorted by model distance: nonbonded pdb=" O MET E 591 " pdb=" O6 DG T 49 " model vdw 1.349 3.040 nonbonded pdb=" N1 DA P 9 " pdb=" O6 DG T 70 " model vdw 1.357 2.496 nonbonded pdb=" OG1 THR G 187 " pdb=" C7 DT T 69 " model vdw 1.575 3.460 nonbonded pdb=" O LEU H 172 " pdb=" C5' DC T 46 " model vdw 1.679 3.440 nonbonded pdb=" O6 DG P 24 " pdb=" O6 DG T 55 " model vdw 1.783 3.040 ... (remaining 133013 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' selection = (chain 'B' and resid 308 through 591) selection = (chain 'C' and resid 308 through 591) selection = (chain 'D' and resid 308 through 591) selection = (chain 'E' and ((resid 308 through 309 and (name N or name CA or name C or name \ O or name CB )) or resid 310 through 591)) selection = (chain 'F' and ((resid 308 through 309 and (name N or name CA or name C or name \ O or name CB )) or resid 310 through 591)) } ncs_group { reference = (chain 'G' and resid 156 through 303) selection = (chain 'H' and (resid 156 through 302 or (resid 303 and (name N or name CA or na \ me C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.650 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.610 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.373 17881 Z= 0.488 Angle : 0.858 17.506 24567 Z= 0.565 Chirality : 0.056 0.390 2707 Planarity : 0.004 0.088 2855 Dihedral : 19.826 141.730 6441 Min Nonbonded Distance : 1.349 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.48 % Favored : 91.37 % Rotamer: Outliers : 2.92 % Allowed : 1.33 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.18), residues: 2004 helix: -0.55 (0.16), residues: 972 sheet: -1.67 (0.36), residues: 206 loop : -2.06 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 180 TYR 0.039 0.002 TYR H 233 PHE 0.056 0.003 PHE H 197 TRP 0.060 0.003 TRP H 192 HIS 0.004 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.40 (17880) covalent geometry : angle 0.85802 / 0.56 (24567) hydrogen bonds : bond 0.18575 / 12.08 ( 744) hydrogen bonds : angle 6.69002 / 4.67 ( 2043) Misc. bond : bond 0.37288 / 23.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: G 168 LYS cc_start: 0.5420 (OUTLIER) cc_final: 0.4953 (mptt) REVERT: B 506 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8329 (ttmt) REVERT: B 513 ILE cc_start: 0.8039 (tp) cc_final: 0.7509 (mm) REVERT: C 334 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7420 (tm-30) REVERT: E 335 TYR cc_start: 0.7948 (t80) cc_final: 0.7628 (t80) REVERT: F 378 MET cc_start: 0.8592 (tpt) cc_final: 0.8217 (tpt) REVERT: F 441 MET cc_start: 0.7277 (tmm) cc_final: 0.7014 (tmm) REVERT: F 507 HIS cc_start: 0.3935 (OUTLIER) cc_final: 0.3516 (t70) REVERT: H 253 MET cc_start: 0.0817 (ttm) cc_final: 0.0015 (ttm) outliers start: 46 outliers final: 6 residues processed: 256 average time/residue: 0.1282 time to fit residues: 48.5658 Evaluate side-chains 173 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 297 ARG Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 221 GLN ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN C 374 GLN C 405 GLN D 344 ASN D 444 ASN E 367 HIS E 460 HIS F 344 ASN A 344 ASN A 406 ASN A 444 ASN H 176 HIS ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 HIS H 248 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.166731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145196 restraints weight = 25613.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144162 restraints weight = 23849.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144239 restraints weight = 30099.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144369 restraints weight = 25988.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144425 restraints weight = 20585.069| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17881 Z= 0.181 Angle : 0.678 9.499 24567 Z= 0.371 Chirality : 0.045 0.276 2707 Planarity : 0.004 0.060 2855 Dihedral : 19.985 141.385 3001 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.94 % Favored : 93.01 % Rotamer: Outliers : 2.10 % Allowed : 8.96 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.18), residues: 2004 helix: -0.19 (0.16), residues: 990 sheet: -1.51 (0.38), residues: 186 loop : -1.76 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 505 TYR 0.020 0.002 TYR E 335 PHE 0.018 0.002 PHE H 204 TRP 0.018 0.002 TRP A 319 HIS 0.011 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (17880) covalent geometry : angle 0.67804 / 0.37 (24567) hydrogen bonds : bond 0.06681 / 4.62 ( 744) hydrogen bonds : angle 5.40817 / 3.79 ( 2043) Misc. bond : bond 0.00974 / 0.61 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.510 Fit side-chains REVERT: B 316 MET cc_start: 0.8740 (ttt) cc_final: 0.8391 (ttt) REVERT: B 374 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: B 410 ILE cc_start: 0.9029 (tt) cc_final: 0.8803 (mt) REVERT: B 513 ILE cc_start: 0.7887 (tp) cc_final: 0.7479 (mm) REVERT: E 325 TYR cc_start: 0.8518 (m-80) cc_final: 0.8293 (m-10) REVERT: F 378 MET cc_start: 0.8621 (tpt) cc_final: 0.8271 (tpt) REVERT: H 253 MET cc_start: 0.0578 (ttm) cc_final: -0.0152 (ttm) REVERT: H 262 MET cc_start: -0.2268 (mtp) cc_final: -0.2570 (mtp) outliers start: 33 outliers final: 21 residues processed: 204 average time/residue: 0.1235 time to fit residues: 37.9397 Evaluate side-chains 184 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 253 MET Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 558 ASN Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 569 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 225 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 436 ASN ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 ASN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.160789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.149837 restraints weight = 25865.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138783 restraints weight = 76174.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136989 restraints weight = 61901.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137161 restraints weight = 65720.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.137562 restraints weight = 49820.392| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3603 r_free = 0.3603 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17881 Z= 0.207 Angle : 0.647 9.587 24567 Z= 0.356 Chirality : 0.044 0.266 2707 Planarity : 0.004 0.056 2855 Dihedral : 19.715 140.449 2988 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.54 % Allowed : 12.33 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 2004 helix: -0.15 (0.16), residues: 987 sheet: -1.44 (0.37), residues: 187 loop : -1.73 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 505 TYR 0.024 0.002 TYR H 233 PHE 0.034 0.002 PHE H 182 TRP 0.015 0.002 TRP G 295 HIS 0.015 0.001 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 (17880) covalent geometry : angle 0.64743 / 0.36 (24567) hydrogen bonds : bond 0.06296 / 4.38 ( 744) hydrogen bonds : angle 5.28371 / 3.71 ( 2043) Misc. bond : bond 0.00586 / 0.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.489 Fit side-chains REVERT: G 253 MET cc_start: 0.4919 (OUTLIER) cc_final: 0.4569 (ttt) REVERT: B 316 MET cc_start: 0.8747 (ttt) cc_final: 0.8378 (ttt) REVERT: B 513 ILE cc_start: 0.7843 (tp) cc_final: 0.7383 (mm) REVERT: E 325 TYR cc_start: 0.8511 (m-10) cc_final: 0.8301 (m-10) REVERT: F 378 MET cc_start: 0.8658 (tpt) cc_final: 0.8204 (tpt) REVERT: H 222 LYS cc_start: 0.0864 (mmtm) cc_final: 0.0504 (mmtt) REVERT: H 253 MET cc_start: 0.0209 (ttm) cc_final: -0.0749 (ttm) outliers start: 40 outliers final: 28 residues processed: 208 average time/residue: 0.1197 time to fit residues: 38.1529 Evaluate side-chains 188 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 253 MET Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 558 ASN Chi-restraints excluded: chain B residue 569 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 569 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain H residue 225 HIS Chi-restraints excluded: chain H residue 233 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 2.9990 chunk 86 optimal weight: 0.1980 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 194 optimal weight: 0.0770 chunk 169 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 ASN H 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.169010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158215 restraints weight = 25633.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147404 restraints weight = 75284.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145903 restraints weight = 61673.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.145849 restraints weight = 66604.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.146472 restraints weight = 47298.009| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17881 Z= 0.128 Angle : 0.568 9.405 24567 Z= 0.313 Chirality : 0.041 0.271 2707 Planarity : 0.003 0.048 2855 Dihedral : 19.544 141.849 2985 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.16 % Allowed : 13.91 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.19), residues: 2004 helix: 0.19 (0.16), residues: 967 sheet: -1.27 (0.36), residues: 195 loop : -1.50 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 243 TYR 0.016 0.001 TYR H 233 PHE 0.035 0.002 PHE H 182 TRP 0.014 0.001 TRP A 319 HIS 0.014 0.001 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (17880) covalent geometry : angle 0.56798 / 0.31 (24567) hydrogen bonds : bond 0.05361 / 3.78 ( 744) hydrogen bonds : angle 4.82586 / 3.36 ( 2043) Misc. bond : bond 0.00203 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: G 300 THR cc_start: 0.0432 (OUTLIER) cc_final: -0.0561 (m) REVERT: B 316 MET cc_start: 0.8720 (ttt) cc_final: 0.8388 (ttt) REVERT: B 513 ILE cc_start: 0.7675 (tp) cc_final: 0.7218 (mm) REVERT: D 534 TYR cc_start: 0.6580 (m-80) cc_final: 0.5997 (m-80) REVERT: F 378 MET cc_start: 0.8629 (tpt) cc_final: 0.8237 (tpt) REVERT: F 441 MET cc_start: 0.7479 (tmm) cc_final: 0.7217 (tmm) REVERT: F 538 ARG cc_start: 0.8338 (ptp90) cc_final: 0.7684 (ptp-170) REVERT: H 253 MET cc_start: 0.0384 (ttm) cc_final: -0.0410 (ttm) outliers start: 34 outliers final: 21 residues processed: 206 average time/residue: 0.1219 time to fit residues: 38.2237 Evaluate side-chains 180 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 460 HIS Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 262 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.166960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147469 restraints weight = 25679.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147192 restraints weight = 36886.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147165 restraints weight = 36563.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147219 restraints weight = 29050.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147234 restraints weight = 25341.221| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17881 Z= 0.160 Angle : 0.576 8.905 24567 Z= 0.317 Chirality : 0.041 0.171 2707 Planarity : 0.003 0.047 2855 Dihedral : 19.474 140.985 2985 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.60 % Allowed : 15.06 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.19), residues: 2004 helix: 0.23 (0.16), residues: 966 sheet: -1.26 (0.36), residues: 199 loop : -1.51 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 370 TYR 0.026 0.001 TYR E 325 PHE 0.032 0.002 PHE H 182 TRP 0.014 0.001 TRP A 319 HIS 0.005 0.001 HIS H 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (17880) covalent geometry : angle 0.57618 / 0.32 (24567) hydrogen bonds : bond 0.05427 / 3.83 ( 744) hydrogen bonds : angle 4.85297 / 3.38 ( 2043) Misc. bond : bond 0.00146 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.393 Fit side-chains REVERT: G 300 THR cc_start: 0.0348 (OUTLIER) cc_final: -0.0669 (m) REVERT: B 316 MET cc_start: 0.8732 (ttt) cc_final: 0.8352 (ttt) REVERT: B 513 ILE cc_start: 0.7646 (tp) cc_final: 0.7197 (mm) REVERT: F 378 MET cc_start: 0.8638 (tpt) cc_final: 0.8237 (tpt) REVERT: F 441 MET cc_start: 0.7501 (tmm) cc_final: 0.7209 (tmm) REVERT: F 538 ARG cc_start: 0.8437 (ptp90) cc_final: 0.7718 (ptp-170) REVERT: H 253 MET cc_start: 0.0718 (ttm) cc_final: -0.0144 (ttm) outliers start: 41 outliers final: 28 residues processed: 193 average time/residue: 0.1186 time to fit residues: 35.7462 Evaluate side-chains 182 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 460 HIS Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 262 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 94 optimal weight: 0.0030 chunk 188 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 chunk 72 optimal weight: 0.6980 overall best weight: 0.6950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 436 ASN B 536 HIS F 482 HIS A 444 ASN H 264 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.168987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.157901 restraints weight = 25540.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146910 restraints weight = 71430.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145223 restraints weight = 58954.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145338 restraints weight = 63232.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146009 restraints weight = 45286.768| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3724 r_free = 0.3724 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17881 Z= 0.128 Angle : 0.552 8.970 24567 Z= 0.303 Chirality : 0.040 0.217 2707 Planarity : 0.003 0.045 2855 Dihedral : 19.380 141.430 2985 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.22 % Allowed : 16.20 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 2004 helix: 0.32 (0.16), residues: 968 sheet: -1.18 (0.37), residues: 193 loop : -1.45 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 493 TYR 0.013 0.001 TYR E 335 PHE 0.036 0.001 PHE H 182 TRP 0.014 0.001 TRP A 319 HIS 0.012 0.001 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (17880) covalent geometry : angle 0.55209 / 0.30 (24567) hydrogen bonds : bond 0.05092 / 3.60 ( 744) hydrogen bonds : angle 4.66622 / 3.23 ( 2043) Misc. bond : bond 0.00079 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.384 Fit side-chains REVERT: G 300 THR cc_start: 0.0253 (OUTLIER) cc_final: -0.0143 (m) REVERT: B 316 MET cc_start: 0.8724 (ttt) cc_final: 0.8354 (ttt) REVERT: B 513 ILE cc_start: 0.7611 (tp) cc_final: 0.7119 (mm) REVERT: D 534 TYR cc_start: 0.6651 (m-80) cc_final: 0.6053 (m-80) REVERT: F 378 MET cc_start: 0.8646 (tpt) cc_final: 0.8278 (tpt) REVERT: F 441 MET cc_start: 0.7430 (tmm) cc_final: 0.7157 (tmm) REVERT: F 538 ARG cc_start: 0.8392 (ptp90) cc_final: 0.7739 (ptp-170) REVERT: H 253 MET cc_start: 0.0429 (ttm) cc_final: -0.0406 (ttm) outliers start: 35 outliers final: 23 residues processed: 190 average time/residue: 0.1151 time to fit residues: 33.9577 Evaluate side-chains 176 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 460 HIS Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 262 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 83 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 99 optimal weight: 0.1980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS F 507 HIS H 299 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.165449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144844 restraints weight = 25603.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144168 restraints weight = 33486.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144238 restraints weight = 37785.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144268 restraints weight = 31700.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144265 restraints weight = 27900.401| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17881 Z= 0.193 Angle : 0.617 12.507 24567 Z= 0.333 Chirality : 0.042 0.193 2707 Planarity : 0.004 0.048 2855 Dihedral : 19.357 140.428 2983 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.54 % Allowed : 16.58 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.18), residues: 2004 helix: 0.20 (0.16), residues: 971 sheet: -1.16 (0.37), residues: 191 loop : -1.46 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 370 TYR 0.031 0.002 TYR E 325 PHE 0.036 0.002 PHE H 182 TRP 0.014 0.001 TRP A 319 HIS 0.007 0.001 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (17880) covalent geometry : angle 0.61691 / 0.33 (24567) hydrogen bonds : bond 0.05557 / 3.90 ( 744) hydrogen bonds : angle 4.89643 / 3.40 ( 2043) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.404 Fit side-chains REVERT: G 211 LEU cc_start: 0.4756 (OUTLIER) cc_final: 0.4475 (mp) REVERT: G 300 THR cc_start: 0.0375 (OUTLIER) cc_final: 0.0150 (m) REVERT: B 316 MET cc_start: 0.8803 (ttt) cc_final: 0.8414 (ttt) REVERT: B 513 ILE cc_start: 0.7689 (tp) cc_final: 0.7188 (mm) REVERT: F 378 MET cc_start: 0.8641 (tpt) cc_final: 0.8230 (tpt) REVERT: F 538 ARG cc_start: 0.8461 (ptp90) cc_final: 0.7784 (ptp-170) REVERT: H 253 MET cc_start: 0.0507 (ttm) cc_final: -0.0270 (ttm) outliers start: 40 outliers final: 33 residues processed: 194 average time/residue: 0.1111 time to fit residues: 33.5197 Evaluate side-chains 188 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 558 ASN Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 460 HIS Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 233 TYR Chi-restraints excluded: chain H residue 262 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 24 optimal weight: 0.9990 chunk 127 optimal weight: 0.4980 chunk 189 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 141 optimal weight: 0.0770 chunk 198 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.168475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148395 restraints weight = 25651.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148396 restraints weight = 29081.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148396 restraints weight = 24485.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148396 restraints weight = 24485.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148396 restraints weight = 24485.836| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17881 Z= 0.124 Angle : 0.566 11.356 24567 Z= 0.306 Chirality : 0.040 0.245 2707 Planarity : 0.003 0.046 2855 Dihedral : 19.275 141.379 2983 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.35 % Allowed : 17.47 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 2004 helix: 0.39 (0.17), residues: 968 sheet: -1.07 (0.36), residues: 193 loop : -1.39 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 370 TYR 0.013 0.001 TYR D 404 PHE 0.023 0.001 PHE D 557 TRP 0.030 0.001 TRP H 277 HIS 0.024 0.001 HIS F 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (17880) covalent geometry : angle 0.56616 / 0.31 (24567) hydrogen bonds : bond 0.05052 / 3.57 ( 744) hydrogen bonds : angle 4.65011 / 3.21 ( 2043) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.506 Fit side-chains REVERT: G 300 THR cc_start: 0.0054 (OUTLIER) cc_final: -0.0178 (m) REVERT: B 316 MET cc_start: 0.8690 (ttt) cc_final: 0.8302 (ttt) REVERT: B 513 ILE cc_start: 0.7609 (tp) cc_final: 0.7103 (mm) REVERT: D 534 TYR cc_start: 0.6674 (m-80) cc_final: 0.6058 (m-80) REVERT: F 378 MET cc_start: 0.8619 (tpt) cc_final: 0.8253 (tpt) REVERT: F 441 MET cc_start: 0.7433 (tmm) cc_final: 0.7129 (tmm) REVERT: F 538 ARG cc_start: 0.8412 (ptp90) cc_final: 0.7807 (ptp-170) REVERT: H 253 MET cc_start: 0.0565 (ttm) cc_final: -0.0150 (ttm) outliers start: 37 outliers final: 29 residues processed: 194 average time/residue: 0.1112 time to fit residues: 33.7752 Evaluate side-chains 186 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 460 HIS Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 233 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 79 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.168022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148355 restraints weight = 25547.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147633 restraints weight = 27762.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147486 restraints weight = 32296.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147539 restraints weight = 29822.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.147579 restraints weight = 24159.760| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3749 r_free = 0.3749 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17881 Z= 0.138 Angle : 0.570 11.122 24567 Z= 0.307 Chirality : 0.040 0.179 2707 Planarity : 0.003 0.047 2855 Dihedral : 19.239 141.672 2983 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.67 % Allowed : 17.79 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.19), residues: 2004 helix: 0.42 (0.16), residues: 973 sheet: -1.03 (0.37), residues: 193 loop : -1.33 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 370 TYR 0.029 0.001 TYR E 325 PHE 0.030 0.001 PHE C 457 TRP 0.019 0.001 TRP H 277 HIS 0.004 0.001 HIS B 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (17880) covalent geometry : angle 0.56984 / 0.31 (24567) hydrogen bonds : bond 0.05035 / 3.57 ( 744) hydrogen bonds : angle 4.61471 / 3.19 ( 2043) Misc. bond : bond 0.00046 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: G 211 LEU cc_start: 0.4651 (OUTLIER) cc_final: 0.4375 (mp) REVERT: G 300 THR cc_start: -0.0156 (OUTLIER) cc_final: -0.0418 (m) REVERT: B 316 MET cc_start: 0.8698 (ttt) cc_final: 0.8296 (ttt) REVERT: B 513 ILE cc_start: 0.7531 (tp) cc_final: 0.6984 (mm) REVERT: C 312 ASP cc_start: 0.6763 (m-30) cc_final: 0.6557 (m-30) REVERT: D 316 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7708 (ttp) REVERT: D 534 TYR cc_start: 0.6656 (m-80) cc_final: 0.6042 (m-80) REVERT: F 378 MET cc_start: 0.8603 (tpt) cc_final: 0.8245 (tpt) REVERT: F 441 MET cc_start: 0.7445 (tmm) cc_final: 0.7132 (tmm) REVERT: F 538 ARG cc_start: 0.8432 (ptp90) cc_final: 0.7809 (ptp-170) REVERT: H 253 MET cc_start: 0.0564 (ttm) cc_final: -0.0215 (ttm) outliers start: 42 outliers final: 34 residues processed: 192 average time/residue: 0.1115 time to fit residues: 33.2552 Evaluate side-chains 192 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 257 ARG Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 460 HIS Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 233 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 9 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 18 optimal weight: 0.0770 chunk 179 optimal weight: 0.0570 chunk 188 optimal weight: 0.0470 chunk 5 optimal weight: 20.0000 chunk 150 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 167 optimal weight: 0.0050 chunk 45 optimal weight: 0.9980 overall best weight: 0.1968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.171000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.151719 restraints weight = 25330.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.150227 restraints weight = 30690.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150047 restraints weight = 42544.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.150208 restraints weight = 38053.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.150221 restraints weight = 29282.543| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17881 Z= 0.111 Angle : 0.557 10.973 24567 Z= 0.300 Chirality : 0.039 0.168 2707 Planarity : 0.003 0.048 2855 Dihedral : 19.120 142.525 2983 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.72 % Allowed : 18.93 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.19), residues: 2004 helix: 0.54 (0.17), residues: 973 sheet: -0.86 (0.36), residues: 200 loop : -1.28 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 366 TYR 0.028 0.001 TYR E 325 PHE 0.025 0.001 PHE D 557 TRP 0.019 0.001 TRP H 277 HIS 0.043 0.001 HIS F 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (17880) covalent geometry : angle 0.55727 / 0.30 (24567) hydrogen bonds : bond 0.04741 / 3.37 ( 744) hydrogen bonds : angle 4.40243 / 3.03 ( 2043) Misc. bond : bond 0.00058 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 211 LEU cc_start: 0.4670 (OUTLIER) cc_final: 0.4366 (mp) REVERT: G 300 THR cc_start: -0.0055 (OUTLIER) cc_final: -0.0280 (m) REVERT: B 316 MET cc_start: 0.8668 (ttt) cc_final: 0.8327 (ttt) REVERT: B 513 ILE cc_start: 0.7475 (tp) cc_final: 0.6911 (mm) REVERT: C 370 ARG cc_start: 0.7561 (mtm110) cc_final: 0.7275 (ttp80) REVERT: D 316 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.6954 (ttm) REVERT: F 378 MET cc_start: 0.8518 (tpt) cc_final: 0.8227 (tpt) REVERT: F 538 ARG cc_start: 0.8348 (ptp90) cc_final: 0.7735 (ptp-170) REVERT: H 244 GLU cc_start: 0.5306 (mm-30) cc_final: 0.5101 (mm-30) REVERT: H 253 MET cc_start: 0.0452 (ttm) cc_final: -0.0305 (ttm) outliers start: 27 outliers final: 22 residues processed: 184 average time/residue: 0.1199 time to fit residues: 33.6703 Evaluate side-chains 181 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 257 ARG Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain C residue 352 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 460 HIS Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 233 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 188 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.168833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148595 restraints weight = 25385.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148498 restraints weight = 39433.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148462 restraints weight = 33402.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148537 restraints weight = 27362.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148530 restraints weight = 26121.511| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17881 Z= 0.130 Angle : 0.563 10.540 24567 Z= 0.301 Chirality : 0.040 0.166 2707 Planarity : 0.003 0.044 2855 Dihedral : 19.109 141.656 2983 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.78 % Allowed : 19.12 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.19), residues: 2004 helix: 0.56 (0.17), residues: 975 sheet: -0.86 (0.36), residues: 200 loop : -1.25 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 366 TYR 0.026 0.001 TYR E 325 PHE 0.031 0.001 PHE C 457 TRP 0.016 0.001 TRP H 277 HIS 0.006 0.001 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (17880) covalent geometry : angle 0.56327 / 0.30 (24567) hydrogen bonds : bond 0.04930 / 3.50 ( 744) hydrogen bonds : angle 4.43522 / 3.06 ( 2043) Misc. bond : bond 0.00048 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2178.23 seconds wall clock time: 38 minutes 44.58 seconds (2324.58 seconds total)