Starting phenix.real_space_refine on Wed Mar 4 22:46:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7apd_11852/03_2026/7apd_11852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7apd_11852/03_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_11852/03_2026/7apd_11852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7apd_11852/03_2026/7apd_11852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7apd_11852/03_2026/7apd_11852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7apd_11852/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.79, per 1000 atoms: 0.22 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: 1.47 Conformation dependent library (CDL) restraints added in 509.3 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: 1.83 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: 2.81 Time building geometry restraints manager: 1.81 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 1.460 1.373 0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C1' DG T 63 " pdb=" N9 DG T 63 " ideal model delta sigma weight residual 1.460 1.377 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C1' DG T 49 " pdb=" N9 DG T 49 " ideal model delta sigma weight residual 1.460 1.383 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C1' DG T 70 " pdb=" N9 DG T 70 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C1' DG T 58 " pdb=" N9 DG T 58 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 17875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 24377 3.50 - 7.00: 163 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=" N LEU H 234 " pdb=" CA LEU H 234 " pdb=" C LEU H 234 " ideal model delta sigma weight residual 108.52 98.56 9.96 1.63e+00 3.76e-01 3.74e+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: 2426 0.078 - 0.156: 235 0.156 - 0.234: 30 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: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.280 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 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= 0.404 Angle : 0.839 17.506 24567 Z= 0.492 Chirality : 0.054 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 covalent geometry : bond 0.00589 (17880) covalent geometry : angle 0.83889 (24567) hydrogen bonds : bond 0.18575 ( 744) hydrogen bonds : angle 6.69002 ( 2043) Misc. bond : bond 0.37288 ( 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 : 0.582 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: 0.1387 time to fit residues: 51.6607 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 : 0.584 ------------------------------------------------------------------------------- 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: 2.9990 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... Flipped N/Q/H residues before XYZ refinement: G 221 GLN B 436 ASN ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN C 374 GLN C 405 GLN D 344 ASN D 507 HIS E 367 HIS E 460 HIS F 344 ASN A 344 ASN A 406 ASN A 444 ASN H 176 HIS H 225 HIS H 248 ASN H 264 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.166985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.145774 restraints weight = 25602.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145079 restraints weight = 26543.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.144943 restraints weight = 24791.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.145013 restraints weight = 23848.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145198 restraints weight = 20530.749| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17881 Z= 0.178 Angle : 0.642 9.238 24567 Z= 0.350 Chirality : 0.042 0.188 2707 Planarity : 0.004 0.063 2855 Dihedral : 19.740 141.266 3001 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.74 % Favored : 93.21 % Rotamer: Outliers : 2.03 % Allowed : 9.21 % Favored : 88.75 % 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: -1.44 (0.18), residues: 2004 helix: -0.15 (0.16), residues: 996 sheet: -1.47 (0.36), residues: 199 loop : -1.75 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 243 TYR 0.021 0.002 TYR E 335 PHE 0.024 0.002 PHE H 204 TRP 0.016 0.002 TRP G 295 HIS 0.010 0.001 HIS D 460 Details of bonding type rmsd covalent geometry : bond 0.00389 (17880) covalent geometry : angle 0.64223 (24567) hydrogen bonds : bond 0.06114 ( 744) hydrogen bonds : angle 5.22870 ( 2043) Misc. bond : bond 0.00195 ( 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: 32 poor density : 179 time to evaluate : 0.576 Fit side-chains REVERT: B 316 MET cc_start: 0.8737 (ttt) cc_final: 0.8402 (ttt) REVERT: B 374 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: B 513 ILE cc_start: 0.7851 (tp) cc_final: 0.7435 (mm) REVERT: C 370 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7743 (mtm110) REVERT: E 364 MET cc_start: 0.8580 (mmm) cc_final: 0.8365 (mmm) REVERT: F 378 MET cc_start: 0.8634 (tpt) cc_final: 0.8247 (tpt) REVERT: F 538 ARG cc_start: 0.8307 (ptp90) cc_final: 0.7654 (ptp-170) REVERT: H 253 MET cc_start: 0.0500 (ttm) cc_final: -0.0207 (ttm) outliers start: 32 outliers final: 18 residues processed: 203 average time/residue: 0.1400 time to fit residues: 42.3469 Evaluate side-chains 177 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 164 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 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 E residue 507 HIS 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 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: 5.9990 chunk 153 optimal weight: 0.0770 chunk 36 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN E 427 ASN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.166175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.153767 restraints weight = 25861.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.143794 restraints weight = 87203.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142382 restraints weight = 75587.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142435 restraints weight = 63283.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142938 restraints weight = 46744.162| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1901 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= 0.172 Angle : 0.590 8.891 24567 Z= 0.324 Chirality : 0.041 0.229 2707 Planarity : 0.004 0.057 2855 Dihedral : 19.536 140.853 2985 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.35 % Allowed : 12.07 % Favored : 85.58 % 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: -1.24 (0.18), residues: 2004 helix: 0.06 (0.16), residues: 981 sheet: -1.31 (0.37), residues: 199 loop : -1.72 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 297 TYR 0.020 0.001 TYR D 404 PHE 0.024 0.002 PHE G 276 TRP 0.011 0.001 TRP A 319 HIS 0.013 0.001 HIS A 460 Details of bonding type rmsd covalent geometry : bond 0.00381 (17880) covalent geometry : angle 0.59003 (24567) hydrogen bonds : bond 0.05611 ( 744) hydrogen bonds : angle 5.01862 ( 2043) Misc. bond : bond 0.00061 ( 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 200 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.615 Fit side-chains REVERT: B 316 MET cc_start: 0.8740 (ttt) cc_final: 0.8376 (ttt) REVERT: B 507 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7654 (t70) REVERT: B 513 ILE cc_start: 0.7831 (tp) cc_final: 0.7343 (mm) REVERT: C 370 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7728 (mtm110) REVERT: D 322 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8097 (t0) REVERT: F 378 MET cc_start: 0.8665 (tpt) cc_final: 0.8239 (tpt) REVERT: H 253 MET cc_start: 0.0373 (ttm) cc_final: -0.0423 (ttm) outliers start: 37 outliers final: 26 residues processed: 190 average time/residue: 0.1317 time to fit residues: 38.2418 Evaluate side-chains 183 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 410 ILE 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 C residue 352 ASN Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 322 ASP 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 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 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 492 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain H residue 225 HIS Chi-restraints excluded: chain H residue 262 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 64 optimal weight: 0.1980 chunk 194 optimal weight: 0.0000 chunk 169 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS H 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.164410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.154472 restraints weight = 25477.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142883 restraints weight = 62850.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140806 restraints weight = 58916.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.140941 restraints weight = 56259.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141489 restraints weight = 41960.603| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17881 Z= 0.122 Angle : 0.533 9.311 24567 Z= 0.293 Chirality : 0.038 0.162 2707 Planarity : 0.003 0.047 2855 Dihedral : 19.347 141.730 2985 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.22 % Allowed : 12.96 % Favored : 84.82 % 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: -0.87 (0.19), residues: 2004 helix: 0.33 (0.17), residues: 975 sheet: -1.20 (0.37), residues: 197 loop : -1.44 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 297 TYR 0.020 0.001 TYR E 325 PHE 0.016 0.001 PHE G 276 TRP 0.012 0.001 TRP A 319 HIS 0.013 0.001 HIS H 225 Details of bonding type rmsd covalent geometry : bond 0.00262 (17880) covalent geometry : angle 0.53276 (24567) hydrogen bonds : bond 0.04890 ( 744) hydrogen bonds : angle 4.62861 ( 2043) Misc. bond : bond 0.00079 ( 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 211 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: G 300 THR cc_start: 0.0812 (OUTLIER) cc_final: -0.0204 (m) REVERT: B 316 MET cc_start: 0.8732 (ttt) cc_final: 0.8451 (ttt) REVERT: B 507 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.7538 (t70) REVERT: B 513 ILE cc_start: 0.7680 (tp) cc_final: 0.7215 (mm) REVERT: C 370 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7681 (mtm110) REVERT: E 504 ASP cc_start: 0.7510 (t70) cc_final: 0.7179 (t0) REVERT: F 378 MET cc_start: 0.8643 (tpt) cc_final: 0.8282 (tpt) REVERT: F 441 MET cc_start: 0.7389 (tmm) cc_final: 0.7111 (tmm) REVERT: F 538 ARG cc_start: 0.8248 (ptp90) cc_final: 0.7770 (ptp-170) REVERT: H 253 MET cc_start: 0.0364 (ttm) cc_final: -0.0410 (ttm) outliers start: 35 outliers final: 23 residues processed: 203 average time/residue: 0.1284 time to fit residues: 39.8184 Evaluate side-chains 191 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 410 ILE 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 C residue 352 ASN 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 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 390 THR Chi-restraints excluded: chain H residue 225 HIS 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: 7.9990 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 60 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 HIS F 507 HIS H 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.163828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.143370 restraints weight = 25476.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142946 restraints weight = 25837.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142824 restraints weight = 25393.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.142955 restraints weight = 24177.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143064 restraints weight = 19335.212| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17881 Z= 0.131 Angle : 0.534 9.141 24567 Z= 0.291 Chirality : 0.038 0.149 2707 Planarity : 0.003 0.046 2855 Dihedral : 19.233 140.869 2985 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.35 % Allowed : 14.23 % Favored : 83.42 % 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: -0.68 (0.19), residues: 2004 helix: 0.46 (0.17), residues: 975 sheet: -1.03 (0.37), residues: 195 loop : -1.33 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 574 TYR 0.019 0.001 TYR C 335 PHE 0.021 0.001 PHE A 457 TRP 0.013 0.001 TRP A 319 HIS 0.009 0.001 HIS A 460 Details of bonding type rmsd covalent geometry : bond 0.00287 (17880) covalent geometry : angle 0.53355 (24567) hydrogen bonds : bond 0.04744 ( 744) hydrogen bonds : angle 4.54498 ( 2043) Misc. bond : bond 0.00058 ( 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 212 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: G 300 THR cc_start: 0.0348 (OUTLIER) cc_final: -0.0061 (m) REVERT: B 316 MET cc_start: 0.8707 (ttt) cc_final: 0.8360 (ttt) REVERT: B 334 GLU cc_start: 0.8609 (tp30) cc_final: 0.8402 (tp30) REVERT: B 507 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7564 (t70) REVERT: B 513 ILE cc_start: 0.7593 (tp) cc_final: 0.7070 (mm) REVERT: C 370 ARG cc_start: 0.7897 (ttp80) cc_final: 0.7634 (mtm110) REVERT: F 378 MET cc_start: 0.8610 (tpt) cc_final: 0.8243 (tpt) REVERT: F 441 MET cc_start: 0.7407 (tmm) cc_final: 0.7100 (tmm) REVERT: F 538 ARG cc_start: 0.8318 (ptp90) cc_final: 0.7721 (ptp-170) REVERT: H 253 MET cc_start: 0.0515 (ttm) cc_final: -0.1213 (ptt) outliers start: 37 outliers final: 26 residues processed: 201 average time/residue: 0.1330 time to fit residues: 39.8063 Evaluate side-chains 189 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 507 HIS 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 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 503 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 390 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain H residue 225 HIS 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: 6.9990 chunk 188 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 154 optimal weight: 6.9990 chunk 119 optimal weight: 0.0570 chunk 135 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 536 HIS F 507 HIS H 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.165120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145201 restraints weight = 25364.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144198 restraints weight = 27042.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144268 restraints weight = 30253.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144509 restraints weight = 23957.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144488 restraints weight = 19999.152| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17881 Z= 0.119 Angle : 0.528 11.086 24567 Z= 0.286 Chirality : 0.038 0.175 2707 Planarity : 0.003 0.044 2855 Dihedral : 19.089 140.745 2985 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.29 % Allowed : 15.06 % Favored : 82.66 % 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: 0.57 (0.17), residues: 976 sheet: -0.96 (0.37), residues: 197 loop : -1.31 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 180 TYR 0.012 0.001 TYR H 233 PHE 0.023 0.001 PHE A 457 TRP 0.012 0.001 TRP A 319 HIS 0.011 0.001 HIS F 507 Details of bonding type rmsd covalent geometry : bond 0.00259 (17880) covalent geometry : angle 0.52760 (24567) hydrogen bonds : bond 0.04508 ( 744) hydrogen bonds : angle 4.39091 ( 2043) Misc. bond : bond 0.00054 ( 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 206 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: B 316 MET cc_start: 0.8658 (ttt) cc_final: 0.8327 (ttt) REVERT: B 507 HIS cc_start: 0.7846 (OUTLIER) cc_final: 0.7636 (t70) REVERT: B 513 ILE cc_start: 0.7539 (tp) cc_final: 0.7016 (mm) REVERT: C 370 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7616 (mtm110) REVERT: F 378 MET cc_start: 0.8551 (tpt) cc_final: 0.8233 (tpt) REVERT: F 441 MET cc_start: 0.7408 (tmm) cc_final: 0.7191 (tmm) REVERT: F 538 ARG cc_start: 0.8256 (ptp90) cc_final: 0.7699 (ptp-170) REVERT: A 444 ASN cc_start: 0.8180 (t0) cc_final: 0.7917 (t0) REVERT: H 250 MET cc_start: -0.4484 (mtt) cc_final: -0.8276 (tpt) REVERT: H 253 MET cc_start: 0.0223 (ttm) cc_final: -0.0069 (ttm) outliers start: 36 outliers final: 26 residues processed: 197 average time/residue: 0.1379 time to fit residues: 41.3264 Evaluate side-chains 189 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 287 LEU 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 C residue 352 ASN Chi-restraints excluded: chain C residue 492 LEU 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 460 HIS Chi-restraints excluded: chain E residue 503 ILE 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 390 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain H residue 225 HIS 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: 2.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 507 HIS H 225 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 = 0.3949 r_free = 0.3949 target = 0.160555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.149510 restraints weight = 25604.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139590 restraints weight = 77931.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137792 restraints weight = 65218.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137794 restraints weight = 69057.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138219 restraints weight = 49335.514| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 : 0.004 0.053 17881 Z= 0.196 Angle : 0.587 9.360 24567 Z= 0.318 Chirality : 0.040 0.175 2707 Planarity : 0.003 0.037 2855 Dihedral : 19.118 138.580 2984 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.86 % Allowed : 15.57 % 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: -0.76 (0.19), residues: 2004 helix: 0.40 (0.16), residues: 977 sheet: -0.96 (0.36), residues: 203 loop : -1.43 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 366 TYR 0.014 0.001 TYR A 404 PHE 0.022 0.002 PHE C 457 TRP 0.012 0.001 TRP A 319 HIS 0.021 0.001 HIS F 507 Details of bonding type rmsd covalent geometry : bond 0.00436 (17880) covalent geometry : angle 0.58743 (24567) hydrogen bonds : bond 0.05125 ( 744) hydrogen bonds : angle 4.67590 ( 2043) Misc. bond : bond 0.00034 ( 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 208 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 316 MET cc_start: 0.8722 (ttt) cc_final: 0.8390 (ttt) REVERT: B 334 GLU cc_start: 0.8640 (tp30) cc_final: 0.8349 (tp30) REVERT: B 507 HIS cc_start: 0.8082 (OUTLIER) cc_final: 0.7760 (t70) REVERT: B 513 ILE cc_start: 0.7602 (tp) cc_final: 0.7094 (mm) REVERT: B 536 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.8344 (m170) REVERT: D 477 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8348 (p) REVERT: F 378 MET cc_start: 0.8609 (tpt) cc_final: 0.8207 (tpt) REVERT: F 538 ARG cc_start: 0.8386 (ptp90) cc_final: 0.7789 (ptp-170) REVERT: H 250 MET cc_start: -0.4890 (mtt) cc_final: -0.8361 (tpt) REVERT: H 253 MET cc_start: -0.0070 (ttm) cc_final: -0.0327 (ttm) outliers start: 45 outliers final: 35 residues processed: 198 average time/residue: 0.1241 time to fit residues: 37.6819 Evaluate side-chains 194 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 257 ARG Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain B residue 536 HIS 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 560 THR Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 460 HIS Chi-restraints excluded: chain D residue 477 VAL 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 460 HIS 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 507 HIS 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 A residue 560 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain H residue 262 MET Chi-restraints excluded: chain H residue 299 GLN 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: 0.0870 chunk 189 optimal weight: 3.9990 chunk 163 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 95 optimal weight: 0.0670 chunk 141 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 507 HIS H 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.164190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.154162 restraints weight = 25531.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.142549 restraints weight = 68831.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140649 restraints weight = 72776.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140993 restraints weight = 69593.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.141782 restraints weight = 45176.252| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2798 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= 0.116 Angle : 0.537 12.864 24567 Z= 0.288 Chirality : 0.038 0.204 2707 Planarity : 0.003 0.048 2855 Dihedral : 19.025 140.297 2984 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.35 % Allowed : 16.90 % Favored : 80.75 % 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: -0.54 (0.19), residues: 2004 helix: 0.61 (0.17), residues: 970 sheet: -0.83 (0.36), residues: 202 loop : -1.36 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 366 TYR 0.013 0.001 TYR E 335 PHE 0.022 0.001 PHE D 557 TRP 0.013 0.001 TRP A 319 HIS 0.006 0.001 HIS A 460 Details of bonding type rmsd covalent geometry : bond 0.00253 (17880) covalent geometry : angle 0.53700 (24567) hydrogen bonds : bond 0.04615 ( 744) hydrogen bonds : angle 4.37950 ( 2043) Misc. bond : bond 0.00052 ( 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 209 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 220 MET cc_start: 0.6799 (mtt) cc_final: 0.6444 (mtp) REVERT: G 253 MET cc_start: 0.4402 (ttt) cc_final: 0.4110 (ttt) REVERT: B 316 MET cc_start: 0.8664 (ttt) cc_final: 0.8330 (ttt) REVERT: B 507 HIS cc_start: 0.7961 (OUTLIER) cc_final: 0.7636 (t70) REVERT: B 513 ILE cc_start: 0.7527 (tp) cc_final: 0.7030 (mm) REVERT: F 378 MET cc_start: 0.8537 (tpt) cc_final: 0.8225 (tpt) REVERT: F 538 ARG cc_start: 0.8278 (ptp90) cc_final: 0.7804 (ptp-170) REVERT: H 250 MET cc_start: -0.5134 (mtt) cc_final: -0.8418 (tpt) outliers start: 37 outliers final: 31 residues processed: 197 average time/residue: 0.1279 time to fit residues: 38.6462 Evaluate side-chains 194 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 PHE Chi-restraints excluded: chain G residue 235 ILE 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 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 C residue 352 ASN 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 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 460 HIS 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 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 390 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain H residue 262 MET Chi-restraints excluded: chain H residue 299 GLN 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: 0.3980 chunk 104 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 507 HIS H 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.162011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.141918 restraints weight = 25567.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140989 restraints weight = 22675.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141047 restraints weight = 29494.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141157 restraints weight = 24195.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.141158 restraints weight = 20914.859| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17881 Z= 0.159 Angle : 0.566 11.954 24567 Z= 0.303 Chirality : 0.039 0.211 2707 Planarity : 0.003 0.042 2855 Dihedral : 19.035 139.352 2984 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.48 % Allowed : 17.53 % Favored : 79.99 % 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: -0.61 (0.19), residues: 2004 helix: 0.54 (0.16), residues: 970 sheet: -0.78 (0.36), residues: 203 loop : -1.38 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 366 TYR 0.012 0.001 TYR E 335 PHE 0.029 0.002 PHE C 457 TRP 0.013 0.001 TRP A 319 HIS 0.006 0.001 HIS F 507 Details of bonding type rmsd covalent geometry : bond 0.00354 (17880) covalent geometry : angle 0.56621 (24567) hydrogen bonds : bond 0.04943 ( 744) hydrogen bonds : angle 4.51024 ( 2043) Misc. bond : bond 0.00041 ( 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 198 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 220 MET cc_start: 0.6926 (mtt) cc_final: 0.6600 (mtp) REVERT: B 316 MET cc_start: 0.8728 (ttt) cc_final: 0.8372 (ttt) REVERT: B 507 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7757 (t70) REVERT: B 513 ILE cc_start: 0.7560 (tp) cc_final: 0.7027 (mm) REVERT: C 370 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7583 (ttp80) REVERT: F 378 MET cc_start: 0.8582 (tpt) cc_final: 0.8239 (tpt) REVERT: F 538 ARG cc_start: 0.8333 (ptp90) cc_final: 0.7791 (ptp-170) REVERT: H 250 MET cc_start: -0.4803 (mtt) cc_final: -0.8331 (tpt) outliers start: 39 outliers final: 36 residues processed: 189 average time/residue: 0.1331 time to fit residues: 38.3193 Evaluate side-chains 190 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 PHE 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 507 HIS 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 560 THR Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 460 HIS 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 460 HIS 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 399 LEU 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 390 THR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain H residue 262 MET Chi-restraints excluded: chain H residue 299 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 9 optimal weight: 2.9990 chunk 95 optimal weight: 0.0040 chunk 18 optimal weight: 3.9990 chunk 179 optimal weight: 0.1980 chunk 188 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 150 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 0.0270 chunk 167 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 overall best weight: 0.2250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 507 HIS H 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.166066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.156304 restraints weight = 25231.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146051 restraints weight = 58106.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143793 restraints weight = 63720.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143817 restraints weight = 70420.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.144521 restraints weight = 49043.882| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17881 Z= 0.110 Angle : 0.537 11.567 24567 Z= 0.286 Chirality : 0.037 0.206 2707 Planarity : 0.003 0.048 2855 Dihedral : 18.931 140.880 2984 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.91 % Allowed : 18.23 % Favored : 79.86 % 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: -0.41 (0.19), residues: 2004 helix: 0.65 (0.17), residues: 975 sheet: -0.65 (0.36), residues: 200 loop : -1.23 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 366 TYR 0.013 0.001 TYR E 335 PHE 0.037 0.001 PHE H 182 TRP 0.016 0.001 TRP A 572 HIS 0.009 0.001 HIS F 507 Details of bonding type rmsd covalent geometry : bond 0.00239 (17880) covalent geometry : angle 0.53733 (24567) hydrogen bonds : bond 0.04517 ( 744) hydrogen bonds : angle 4.28884 ( 2043) Misc. bond : bond 0.00060 ( 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 201 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 220 MET cc_start: 0.6901 (mtt) cc_final: 0.6540 (mtp) REVERT: B 316 MET cc_start: 0.8646 (ttt) cc_final: 0.8371 (ttt) REVERT: B 507 HIS cc_start: 0.7921 (OUTLIER) cc_final: 0.7637 (t70) REVERT: B 513 ILE cc_start: 0.7503 (tp) cc_final: 0.6975 (mm) REVERT: C 370 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7505 (ttp80) REVERT: D 316 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.6932 (ttm) REVERT: E 441 MET cc_start: 0.7384 (tmm) cc_final: 0.7182 (tmm) REVERT: E 499 TYR cc_start: 0.8116 (m-80) cc_final: 0.7916 (m-80) REVERT: F 378 MET cc_start: 0.8468 (tpt) cc_final: 0.8213 (tpt) REVERT: F 538 ARG cc_start: 0.8246 (ptp90) cc_final: 0.7799 (ptp-170) REVERT: H 250 MET cc_start: -0.4927 (mtt) cc_final: -0.8326 (tpt) outliers start: 30 outliers final: 25 residues processed: 193 average time/residue: 0.1338 time to fit residues: 39.2150 Evaluate side-chains 187 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 182 PHE 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 507 HIS 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 560 THR Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 460 HIS 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 460 HIS Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 507 HIS 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 575 LEU Chi-restraints excluded: chain H residue 262 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 39 optimal weight: 0.9980 chunk 118 optimal weight: 0.0970 chunk 48 optimal weight: 3.9990 chunk 190 optimal weight: 8.9990 chunk 188 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 507 HIS H 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.164588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.154466 restraints weight = 25272.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143852 restraints weight = 62828.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.141588 restraints weight = 60471.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141829 restraints weight = 62019.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142029 restraints weight = 45101.612| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3125 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= 0.126 Angle : 0.539 10.956 24567 Z= 0.288 Chirality : 0.038 0.198 2707 Planarity : 0.003 0.042 2855 Dihedral : 18.892 140.074 2984 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.91 % Allowed : 18.30 % Favored : 79.80 % 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: -0.36 (0.19), residues: 2004 helix: 0.69 (0.17), residues: 967 sheet: -0.67 (0.36), residues: 200 loop : -1.20 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 366 TYR 0.014 0.001 TYR E 335 PHE 0.027 0.001 PHE C 457 TRP 0.018 0.001 TRP B 572 HIS 0.007 0.001 HIS F 507 Details of bonding type rmsd covalent geometry : bond 0.00279 (17880) covalent geometry : angle 0.53931 (24567) hydrogen bonds : bond 0.04717 ( 744) hydrogen bonds : angle 4.34317 ( 2043) Misc. bond : bond 0.00053 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.33 seconds wall clock time: 41 minutes 3.72 seconds (2463.72 seconds total)