Starting phenix.real_space_refine on Sat Sep 12 16:32:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7apd_11852/09_2026/7apd_11852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7apd_11852/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7apd_11852/09_2026/7apd_11852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7apd_11852/09_2026/7apd_11852.map" model { file = "/net/cci-nas-00/data/ceres_data/7apd_11852/09_2026/7apd_11852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7apd_11852/09_2026/7apd_11852.cif" } 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17296 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1201 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 146} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2238 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 9, 'TRANS': 279} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2228 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "D" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2228 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 62 Chain: "E" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2232 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 9, 'TRANS': 277} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "F" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2229 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 276} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2213 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 5, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "H" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1184 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "P" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 805 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N GLY H 156 " occ=0.60 ... (2 atoms not shown) pdb=" O GLY H 156 " occ=0.60 residue: pdb=" N SER H 157 " occ=0.60 ... (4 atoms not shown) pdb=" OG SER H 157 " occ=0.60 residue: pdb=" N ARG H 158 " occ=0.60 ... (9 atoms not shown) pdb=" NH2 ARG H 158 " occ=0.60 Time building chain proxies: 4.24, per 1000 atoms: 0.25 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: 1.68 Conformation dependent library (CDL) restraints added in 766.0 milliseconds 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 13 sheets defined 53.3% alpha, 8.2% beta 15 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.87 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: 2.68 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5288 1.34 - 1.48: 5126 1.48 - 1.61: 7330 1.61 - 1.74: 26 1.74 - 1.87: 110 Bond restraints: 17880 Sorted by residual: bond pdb=" C1' DG T 68 " pdb=" N9 DG T 68 " ideal model delta sigma weight residual 1.468 1.373 0.095 1.40e-02 5.10e+03 4.57e+01 bond pdb=" C1' DG T 63 " pdb=" N9 DG T 63 " ideal model delta sigma weight residual 1.468 1.377 0.091 1.40e-02 5.10e+03 4.19e+01 bond pdb=" C1' DG T 49 " pdb=" N9 DG T 49 " ideal model delta sigma weight residual 1.468 1.383 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" C1' DG T 70 " pdb=" N9 DG T 70 " ideal model delta sigma weight residual 1.468 1.386 0.082 1.40e-02 5.10e+03 3.47e+01 bond pdb=" C1' DG T 58 " pdb=" N9 DG T 58 " ideal model delta sigma weight residual 1.468 1.386 0.082 1.40e-02 5.10e+03 3.42e+01 ... (remaining 17875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 24376 3.50 - 7.00: 164 7.00 - 10.50: 21 10.50 - 14.00: 5 14.00 - 17.51: 1 Bond angle restraints: 24567 Sorted by residual: angle pdb=" CA ARG G 297 " pdb=" CB ARG G 297 " pdb=" CG ARG G 297 " ideal model delta sigma weight residual 114.10 131.61 -17.51 2.00e+00 2.50e-01 7.66e+01 angle pdb=" N LYS B 506 " pdb=" CA LYS B 506 " pdb=" C LYS B 506 " ideal model delta sigma weight residual 113.19 123.13 -9.94 1.19e+00 7.06e-01 6.98e+01 angle pdb=" C LEU G 302 " pdb=" N ASN G 303 " pdb=" CA ASN G 303 " ideal model delta sigma weight residual 122.87 109.86 13.01 1.61e+00 3.86e-01 6.53e+01 angle pdb=" N LEU H 181 " pdb=" CA LEU H 181 " pdb=" C LEU H 181 " ideal model delta sigma weight residual 109.24 121.79 -12.55 1.63e+00 3.76e-01 5.93e+01 angle pdb=" O4' DT T 69 " pdb=" C1' DT T 69 " pdb=" N1 DT T 69 " ideal model delta sigma weight residual 108.00 112.35 -4.35 7.00e-01 2.04e+00 3.86e+01 ... (remaining 24562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.35: 9394 28.35 - 56.69: 768 56.69 - 85.04: 125 85.04 - 113.38: 9 113.38 - 141.73: 1 Dihedral angle restraints: 10297 sinusoidal: 4355 harmonic: 5942 Sorted by residual: dihedral pdb=" CA ARG G 180 " pdb=" C ARG G 180 " pdb=" N LEU G 181 " pdb=" CA LEU G 181 " ideal model delta harmonic sigma weight residual 180.00 -143.51 -36.49 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" CA LYS G 213 " pdb=" C LYS G 213 " pdb=" N GLN G 214 " pdb=" CA GLN G 214 " ideal model delta harmonic sigma weight residual -180.00 -146.84 -33.16 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CA ARG G 223 " pdb=" C ARG G 223 " pdb=" N SER G 224 " pdb=" CA SER G 224 " ideal model delta harmonic sigma weight residual 0.00 26.01 -26.01 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 10294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2410 0.078 - 0.156: 252 0.156 - 0.234: 29 0.234 - 0.312: 8 0.312 - 0.390: 8 Chirality restraints: 2707 Sorted by residual: chirality pdb=" CA LYS B 506 " pdb=" N LYS B 506 " pdb=" C LYS B 506 " pdb=" CB LYS B 506 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CA PHE H 182 " pdb=" N PHE H 182 " pdb=" C PHE H 182 " pdb=" CB PHE H 182 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CB ILE D 559 " pdb=" CA ILE D 559 " pdb=" CG1 ILE D 559 " pdb=" CG2 ILE D 559 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 2704 not shown) Planarity restraints: 2855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 334 " -0.026 2.00e-02 2.50e+03 5.26e-02 2.77e+01 pdb=" CD GLU A 334 " 0.091 2.00e-02 2.50e+03 pdb=" OE1 GLU A 334 " -0.033 2.00e-02 2.50e+03 pdb=" OE2 GLU A 334 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 197 " -0.056 2.00e-02 2.50e+03 3.42e-02 2.05e+01 pdb=" CG PHE H 197 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE H 197 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE H 197 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE H 197 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE H 197 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 197 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 192 " -0.060 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP H 192 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 192 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP H 192 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP H 192 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 192 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 192 " 0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 192 " -0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 192 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 192 " -0.022 2.00e-02 2.50e+03 ... (remaining 2852 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 14 2.06 - 2.77: 3348 2.77 - 3.48: 23641 3.48 - 4.19: 38511 4.19 - 4.90: 67504 Nonbonded interactions: 133018 Sorted by model distance: nonbonded pdb=" O MET E 591 " pdb=" O6 DG T 49 " model vdw 1.349 3.040 nonbonded pdb=" N1 DA P 9 " pdb=" O6 DG T 70 " model vdw 1.357 2.496 nonbonded pdb=" OG1 THR G 187 " pdb=" C7 DT T 69 " model vdw 1.575 3.460 nonbonded pdb=" O LEU H 172 " pdb=" C5' DC T 46 " model vdw 1.679 3.440 nonbonded pdb=" O6 DG P 24 " pdb=" O6 DG T 55 " model vdw 1.783 3.040 ... (remaining 133013 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 308 through 591) selection = (chain 'C' and resid 308 through 591) selection = (chain 'D' and resid 308 through 591) selection = (chain 'E' and ((resid 308 through 309 and (name N or name CA or name C or name \ O or name CB )) or resid 310 through 591)) selection = (chain 'F' and ((resid 308 through 309 and (name N or name CA or name C or name \ O or name CB )) or resid 310 through 591)) } ncs_group { reference = (chain 'G' and resid 156 through 303) selection = (chain 'H' and (resid 156 through 302 or (resid 303 and (name N or name CA or na \ me C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.800 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.373 17881 Z= 0.488 Angle : 0.859 17.506 24567 Z= 0.566 Chirality : 0.056 0.390 2707 Planarity : 0.004 0.088 2855 Dihedral : 19.826 141.730 6441 Min Nonbonded Distance : 1.349 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.48 % Favored : 91.37 % Rotamer: Outliers : 2.92 % Allowed : 1.33 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.18), residues: 2004 helix: -0.55 (0.16), residues: 972 sheet: -1.67 (0.36), residues: 206 loop : -2.06 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 180 TYR 0.039 0.002 TYR H 233 PHE 0.056 0.003 PHE H 197 TRP 0.060 0.003 TRP H 192 HIS 0.004 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.40 (17880) covalent geometry : angle 0.85890 / 0.57 (24567) hydrogen bonds : bond 0.18575 / 12.08 ( 744) hydrogen bonds : angle 6.69002 / 4.67 ( 2043) Misc. bond : bond 0.37288 / 23.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 0.622 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: 0.8323 (ttmt) REVERT: B 513 ILE cc_start: 0.8039 (tp) cc_final: 0.7507 (mm) REVERT: C 334 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7419 (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: 0.7015 (tmm) REVERT: F 507 HIS cc_start: 0.3935 (OUTLIER) cc_final: 0.3509 (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: 0.1504 time to fit residues: 56.9736 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 : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 297 ARG Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain A residue 508 LYS Chi-restraints excluded: chain A residue 511 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 221 GLN ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN C 374 GLN C 405 GLN ** C 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 ASN D 444 ASN E 367 HIS E 460 HIS F 344 ASN A 344 ASN A 406 ASN A 444 ASN H 176 HIS ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 225 HIS H 248 ASN H 264 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.166870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.155698 restraints weight = 25595.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.144179 restraints weight = 69301.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142379 restraints weight = 56808.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.142572 restraints weight = 52282.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142689 restraints weight = 42554.537| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 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 = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17881 Z= 0.180 Angle : 0.685 9.792 24567 Z= 0.373 Chirality : 0.045 0.247 2707 Planarity : 0.004 0.059 2855 Dihedral : 19.917 140.544 3001 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.79 % Favored : 93.16 % Rotamer: Outliers : 2.16 % Allowed : 8.83 % Favored : 89.01 % 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: -1.47 (0.18), residues: 2004 helix: -0.19 (0.16), residues: 991 sheet: -1.51 (0.37), residues: 186 loop : -1.75 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 505 TYR 0.019 0.002 TYR E 335 PHE 0.018 0.002 PHE G 208 TRP 0.018 0.002 TRP A 319 HIS 0.010 0.001 HIS D 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (17880) covalent geometry : angle 0.68513 / 0.37 (24567) hydrogen bonds : bond 0.06565 / 4.53 ( 744) hydrogen bonds : angle 5.36613 / 3.76 ( 2043) Misc. bond : bond 0.00451 / 0.28 ( 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 210 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.603 Fit side-chains REVERT: G 221 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7248 (pt0) REVERT: B 316 MET cc_start: 0.8724 (ttt) cc_final: 0.8380 (ttt) REVERT: B 374 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: B 410 ILE cc_start: 0.9022 (tt) cc_final: 0.8794 (mt) REVERT: B 513 ILE cc_start: 0.7900 (tp) cc_final: 0.7491 (mm) REVERT: F 378 MET cc_start: 0.8622 (tpt) cc_final: 0.8272 (tpt) REVERT: H 253 MET cc_start: 0.0421 (ttm) cc_final: -0.0297 (ttm) REVERT: H 262 MET cc_start: -0.2341 (mtp) cc_final: -0.2703 (mtp) outliers start: 34 outliers final: 21 residues processed: 203 average time/residue: 0.1448 time to fit residues: 44.2802 Evaluate side-chains 178 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 CYS Chi-restraints excluded: chain G residue 221 GLN Chi-restraints excluded: chain G residue 253 MET Chi-restraints excluded: chain G residue 294 GLU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain B residue 546 GLN Chi-restraints excluded: chain B residue 558 ASN Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 569 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 225 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 139 optimal weight: 0.0570 chunk 197 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 289 HIS ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN D 436 ASN A 406 ASN H 225 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.164513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.152987 restraints weight = 25978.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.141693 restraints weight = 81410.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139877 restraints weight = 76289.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139839 restraints weight = 80763.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140576 restraints weight = 51165.937| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17881 Z= 0.135 Angle : 0.585 9.207 24567 Z= 0.324 Chirality : 0.041 0.274 2707 Planarity : 0.003 0.050 2855 Dihedral : 19.613 141.939 2988 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.16 % Allowed : 11.44 % Favored : 86.40 % 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: -1.13 (0.19), residues: 2004 helix: 0.11 (0.16), residues: 973 sheet: -1.36 (0.37), residues: 197 loop : -1.57 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 505 TYR 0.021 0.001 TYR H 233 PHE 0.019 0.002 PHE A 457 TRP 0.016 0.001 TRP G 295 HIS 0.017 0.001 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (17880) covalent geometry : angle 0.58512 / 0.32 (24567) hydrogen bonds : bond 0.05694 / 3.99 ( 744) hydrogen bonds : angle 4.92089 / 3.42 ( 2043) Misc. bond : bond 0.00226 / 0.14 ( 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 212 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: G 253 MET cc_start: 0.4778 (OUTLIER) cc_final: 0.4443 (ttt) REVERT: B 316 MET cc_start: 0.8700 (ttt) cc_final: 0.8374 (ttt) REVERT: B 374 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: B 513 ILE cc_start: 0.7916 (tp) cc_final: 0.7405 (mm) REVERT: E 364 MET cc_start: 0.8387 (mmm) cc_final: 0.8180 (mmm) REVERT: F 378 MET cc_start: 0.8612 (tpt) cc_final: 0.8264 (tpt) REVERT: F 441 MET cc_start: 0.7479 (tmm) cc_final: 0.7217 (tmm) REVERT: F 538 ARG cc_start: 0.8284 (ptp90) cc_final: 0.7675 (ptp-170) REVERT: H 253 MET cc_start: 0.0270 (ttm) cc_final: -0.0547 (ttm) outliers start: 34 outliers final: 24 residues processed: 204 average time/residue: 0.1375 time to fit residues: 42.7519 Evaluate side-chains 185 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 253 MET Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 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 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 505 ARG Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 406 ASN Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain H residue 225 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 112 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 174 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 194 optimal weight: 0.0170 chunk 169 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN A 406 ASN H 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.169901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.158715 restraints weight = 25722.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147628 restraints weight = 80574.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.145906 restraints weight = 64372.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146016 restraints weight = 67726.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146698 restraints weight = 47420.536| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17881 Z= 0.130 Angle : 0.560 9.352 24567 Z= 0.308 Chirality : 0.041 0.252 2707 Planarity : 0.003 0.048 2855 Dihedral : 19.494 141.305 2987 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.54 % Allowed : 12.45 % Favored : 85.01 % 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: -0.95 (0.19), residues: 2004 helix: 0.25 (0.16), residues: 975 sheet: -1.21 (0.37), residues: 197 loop : -1.48 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 505 TYR 0.024 0.001 TYR E 325 PHE 0.027 0.001 PHE H 182 TRP 0.014 0.001 TRP A 319 HIS 0.006 0.001 HIS G 289 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (17880) covalent geometry : angle 0.56041 / 0.31 (24567) hydrogen bonds : bond 0.05269 / 3.72 ( 744) hydrogen bonds : angle 4.74358 / 3.29 ( 2043) Misc. bond : bond 0.00212 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4008 Ramachandran restraints generated. 2004 Oldfield, 0 Emsley, 2004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.574 Fit side-chains REVERT: B 316 MET cc_start: 0.8686 (ttt) cc_final: 0.8363 (ttt) REVERT: B 513 ILE cc_start: 0.7847 (tp) cc_final: 0.7326 (mm) REVERT: C 364 MET cc_start: 0.8497 (tpp) cc_final: 0.8279 (mmm) REVERT: D 322 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7809 (t0) REVERT: D 534 TYR cc_start: 0.6567 (m-10) cc_final: 0.5997 (m-80) REVERT: F 378 MET cc_start: 0.8625 (tpt) cc_final: 0.8276 (tpt) REVERT: F 441 MET cc_start: 0.7441 (tmm) cc_final: 0.7166 (tmm) REVERT: F 538 ARG cc_start: 0.8306 (ptp90) cc_final: 0.7718 (ptp-170) REVERT: H 253 MET cc_start: 0.0208 (ttm) cc_final: -0.0637 (ttm) outliers start: 40 outliers final: 25 residues processed: 198 average time/residue: 0.1303 time to fit residues: 40.3056 Evaluate side-chains 186 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain B residue 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 C residue 352 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 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 A residue 317 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 0.0870 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 111 optimal weight: 0.0670 chunk 86 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 ASN H 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.170669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.159109 restraints weight = 25581.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148497 restraints weight = 80099.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146742 restraints weight = 60426.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147033 restraints weight = 55811.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147370 restraints weight = 41063.333| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17881 Z= 0.119 Angle : 0.537 8.818 24567 Z= 0.296 Chirality : 0.039 0.177 2707 Planarity : 0.003 0.044 2855 Dihedral : 19.385 141.374 2987 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.48 % Allowed : 13.60 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.19), residues: 2004 helix: 0.40 (0.17), residues: 974 sheet: -1.13 (0.37), residues: 197 loop : -1.38 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 505 TYR 0.011 0.001 TYR H 233 PHE 0.034 0.001 PHE H 182 TRP 0.013 0.001 TRP A 319 HIS 0.006 0.001 HIS H 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (17880) covalent geometry : angle 0.53722 / 0.30 (24567) hydrogen bonds : bond 0.04949 / 3.51 ( 744) hydrogen bonds : angle 4.58685 / 3.17 ( 2043) Misc. bond : bond 0.00310 / 0.19 ( 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 200 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.653 Fit side-chains REVERT: G 220 MET cc_start: 0.7027 (mtt) cc_final: 0.6757 (mtp) REVERT: B 316 MET cc_start: 0.8718 (ttt) cc_final: 0.8397 (ttt) REVERT: B 513 ILE cc_start: 0.7731 (tp) cc_final: 0.7240 (mm) REVERT: C 364 MET cc_start: 0.8500 (tpp) cc_final: 0.8285 (mmm) REVERT: D 322 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7743 (t0) REVERT: F 378 MET cc_start: 0.8595 (tpt) cc_final: 0.8262 (tpt) REVERT: F 441 MET cc_start: 0.7448 (tmm) cc_final: 0.7169 (tmm) REVERT: F 538 ARG cc_start: 0.8269 (ptp90) cc_final: 0.7701 (ptp-170) REVERT: H 253 MET cc_start: 0.0138 (ttm) cc_final: -0.0641 (ttm) outliers start: 39 outliers final: 28 residues processed: 191 average time/residue: 0.1274 time to fit residues: 38.2129 Evaluate side-chains 183 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 182 PHE 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 C residue 352 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 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 D residue 560 THR Chi-restraints excluded: chain E residue 328 GLU Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 505 ARG Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain 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: 0.2980 chunk 48 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 ASN E 427 ASN H 264 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.168782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.157632 restraints weight = 25529.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146970 restraints weight = 78950.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145511 restraints weight = 64283.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.145565 restraints weight = 63423.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.145969 restraints weight = 47444.548| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 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 = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17881 Z= 0.142 Angle : 0.551 8.840 24567 Z= 0.302 Chirality : 0.040 0.178 2707 Planarity : 0.003 0.047 2855 Dihedral : 19.338 140.353 2987 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.60 % Allowed : 14.61 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.19), residues: 2004 helix: 0.44 (0.17), residues: 973 sheet: -1.08 (0.37), residues: 197 loop : -1.35 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 505 TYR 0.025 0.001 TYR E 325 PHE 0.031 0.002 PHE H 182 TRP 0.013 0.001 TRP A 319 HIS 0.005 0.001 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (17880) covalent geometry : angle 0.55119 / 0.30 (24567) hydrogen bonds : bond 0.05029 / 3.56 ( 744) hydrogen bonds : angle 4.63120 / 3.20 ( 2043) Misc. bond : bond 0.00223 / 0.14 ( 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 201 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.633 Fit side-chains REVERT: B 316 MET cc_start: 0.8749 (ttt) cc_final: 0.8367 (ttt) REVERT: B 334 GLU cc_start: 0.8630 (tp30) cc_final: 0.8352 (tp30) REVERT: B 507 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7544 (t70) REVERT: B 513 ILE cc_start: 0.7651 (tp) cc_final: 0.7182 (mm) REVERT: C 364 MET cc_start: 0.8568 (tpp) cc_final: 0.8348 (mmm) REVERT: D 322 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7820 (t0) REVERT: F 378 MET cc_start: 0.8601 (tpt) cc_final: 0.8250 (tpt) REVERT: F 441 MET cc_start: 0.7464 (tmm) cc_final: 0.7160 (tmm) REVERT: F 538 ARG cc_start: 0.8330 (ptp90) cc_final: 0.7717 (ptp-170) REVERT: H 253 MET cc_start: 0.0375 (ttm) cc_final: -0.0451 (ttm) outliers start: 41 outliers final: 29 residues processed: 192 average time/residue: 0.1309 time to fit residues: 39.1806 Evaluate side-chains 186 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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 511 VAL 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 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 481 THR Chi-restraints excluded: chain E residue 503 ILE Chi-restraints excluded: chain E residue 505 ARG Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain 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: 3.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 HIS F 482 HIS A 444 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.158116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146558 restraints weight = 25768.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136585 restraints weight = 84335.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134655 restraints weight = 74098.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134710 restraints weight = 74554.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.135123 restraints weight = 52406.388| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17881 Z= 0.265 Angle : 0.690 9.701 24567 Z= 0.376 Chirality : 0.046 0.193 2707 Planarity : 0.004 0.050 2855 Dihedral : 19.456 137.989 2987 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.05 % Allowed : 15.12 % Favored : 81.83 % 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: -1.20 (0.18), residues: 2004 helix: 0.02 (0.16), residues: 977 sheet: -1.27 (0.37), residues: 191 loop : -1.59 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 366 TYR 0.024 0.002 TYR A 404 PHE 0.028 0.003 PHE F 313 TRP 0.015 0.002 TRP A 319 HIS 0.007 0.001 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.27 (17880) covalent geometry : angle 0.69029 / 0.38 (24567) hydrogen bonds : bond 0.06127 / 4.27 ( 744) hydrogen bonds : angle 5.25724 / 3.66 ( 2043) Misc. bond : bond 0.00114 / 0.07 ( 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 212 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: G 220 MET cc_start: 0.7018 (mtt) cc_final: 0.6653 (mtp) REVERT: B 316 MET cc_start: 0.8822 (ttt) cc_final: 0.8407 (ttt) REVERT: B 507 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7891 (t70) REVERT: B 513 ILE cc_start: 0.7844 (tp) cc_final: 0.7360 (mm) REVERT: C 364 MET cc_start: 0.8654 (tpp) cc_final: 0.8338 (mmm) REVERT: C 378 MET cc_start: 0.7773 (tpt) cc_final: 0.7543 (tpp) REVERT: C 482 HIS cc_start: 0.8697 (OUTLIER) cc_final: 0.8146 (t70) REVERT: D 322 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.7942 (t0) REVERT: D 534 TYR cc_start: 0.6674 (m-80) cc_final: 0.6097 (m-80) REVERT: E 424 PRO cc_start: 0.8507 (Cg_exo) cc_final: 0.8297 (Cg_endo) REVERT: F 378 MET cc_start: 0.8657 (tpt) cc_final: 0.8203 (tpt) REVERT: H 253 MET cc_start: 0.0223 (ttm) cc_final: -0.0577 (ttm) outliers start: 48 outliers final: 34 residues processed: 201 average time/residue: 0.1281 time to fit residues: 40.1404 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 : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 487 TYR 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 392 GLU Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 511 VAL 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 D residue 559 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain E residue 386 CYS Chi-restraints excluded: chain E residue 398 ILE 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 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 A residue 560 THR Chi-restraints excluded: chain H residue 262 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 24 optimal weight: 0.3980 chunk 127 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 0.0270 chunk 141 optimal weight: 0.0970 chunk 198 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 536 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.169195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.149892 restraints weight = 25643.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149737 restraints weight = 28609.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149681 restraints weight = 25581.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.149700 restraints weight = 24804.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.149686 restraints weight = 24403.161| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3790 r_free = 0.3790 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 17881 Z= 0.121 Angle : 0.568 14.585 24567 Z= 0.306 Chirality : 0.040 0.218 2707 Planarity : 0.003 0.044 2855 Dihedral : 19.310 141.166 2987 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.10 % Allowed : 17.03 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.19), residues: 2004 helix: 0.43 (0.16), residues: 971 sheet: -1.06 (0.36), residues: 201 loop : -1.37 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 366 TYR 0.017 0.001 TYR E 325 PHE 0.021 0.002 PHE D 557 TRP 0.038 0.001 TRP H 277 HIS 0.005 0.001 HIS B 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (17880) covalent geometry : angle 0.56819 / 0.31 (24567) hydrogen bonds : bond 0.04977 / 3.52 ( 744) hydrogen bonds : angle 4.62347 / 3.18 ( 2043) Misc. bond : bond 0.00034 / 0.02 ( 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 193 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: G 300 THR cc_start: -0.0223 (OUTLIER) cc_final: -0.0465 (m) REVERT: B 316 MET cc_start: 0.8630 (ttt) cc_final: 0.8249 (ttt) REVERT: B 334 GLU cc_start: 0.8630 (tp30) cc_final: 0.8364 (tp30) REVERT: B 507 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7690 (t70) REVERT: B 513 ILE cc_start: 0.7541 (tp) cc_final: 0.7026 (mm) REVERT: C 364 MET cc_start: 0.8509 (tpp) cc_final: 0.8269 (mmm) REVERT: D 322 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7873 (t0) REVERT: D 534 TYR cc_start: 0.6620 (m-80) cc_final: 0.6007 (m-80) REVERT: F 378 MET cc_start: 0.8600 (tpt) cc_final: 0.8246 (tpt) REVERT: F 441 MET cc_start: 0.7470 (tmm) cc_final: 0.7163 (tmm) REVERT: H 253 MET cc_start: 0.0397 (ttm) cc_final: -0.0361 (ttm) outliers start: 33 outliers final: 22 residues processed: 188 average time/residue: 0.1391 time to fit residues: 40.0104 Evaluate side-chains 179 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 C residue 352 ASN Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 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 D residue 559 ILE Chi-restraints excluded: chain E residue 398 ILE Chi-restraints excluded: chain E residue 460 HIS Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain H residue 262 MET 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: 0.0370 chunk 104 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 28 optimal weight: 0.0370 chunk 65 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 436 ASN D 436 ASN ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.169870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149306 restraints weight = 25462.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.149013 restraints weight = 25924.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148642 restraints weight = 41771.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148933 restraints weight = 37360.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.148905 restraints weight = 26244.638| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17881 Z= 0.115 Angle : 0.540 11.898 24567 Z= 0.293 Chirality : 0.039 0.196 2707 Planarity : 0.004 0.094 2855 Dihedral : 19.146 142.272 2985 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.10 % Allowed : 17.92 % 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: -0.54 (0.19), residues: 2004 helix: 0.58 (0.17), residues: 973 sheet: -0.93 (0.37), residues: 192 loop : -1.29 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 538 TYR 0.015 0.001 TYR F 499 PHE 0.033 0.001 PHE C 457 TRP 0.016 0.001 TRP H 277 HIS 0.004 0.001 HIS D 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (17880) covalent geometry : angle 0.54037 / 0.29 (24567) hydrogen bonds : bond 0.04814 / 3.41 ( 744) hydrogen bonds : angle 4.44483 / 3.06 ( 2043) Misc. bond : bond 0.00033 / 0.02 ( 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 199 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 220 MET cc_start: 0.6984 (mtt) cc_final: 0.6593 (mtp) REVERT: G 300 THR cc_start: -0.0141 (OUTLIER) cc_final: -0.0378 (m) REVERT: B 316 MET cc_start: 0.8650 (ttt) cc_final: 0.8312 (ttt) REVERT: B 334 GLU cc_start: 0.8614 (tp30) cc_final: 0.8315 (tp30) REVERT: B 507 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7577 (t70) REVERT: B 513 ILE cc_start: 0.7429 (tp) cc_final: 0.6871 (mm) REVERT: C 364 MET cc_start: 0.8529 (tpp) cc_final: 0.8312 (mmm) REVERT: D 316 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.6632 (ttm) REVERT: F 378 MET cc_start: 0.8552 (tpt) cc_final: 0.8252 (tpt) REVERT: A 364 MET cc_start: 0.8532 (mmm) cc_final: 0.8256 (mmm) REVERT: H 253 MET cc_start: 0.0439 (ttm) cc_final: -0.0296 (ttm) outliers start: 33 outliers final: 23 residues processed: 191 average time/residue: 0.1346 time to fit residues: 39.6796 Evaluate side-chains 181 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 C residue 352 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 436 ASN 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 398 ILE Chi-restraints excluded: chain E residue 460 HIS Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 471 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 575 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 9 optimal weight: 8.9990 chunk 95 optimal weight: 0.0370 chunk 18 optimal weight: 0.0770 chunk 179 optimal weight: 0.2980 chunk 188 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 289 HIS ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS H 299 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.170283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150088 restraints weight = 25495.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149213 restraints weight = 43842.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149234 restraints weight = 46899.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149390 restraints weight = 40861.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149236 restraints weight = 39145.582| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3751 r_free = 0.3751 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2933 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= 0.116 Angle : 0.563 11.950 24567 Z= 0.301 Chirality : 0.039 0.191 2707 Planarity : 0.004 0.104 2855 Dihedral : 19.111 142.114 2985 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.72 % Allowed : 18.42 % 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: -0.52 (0.19), residues: 2004 helix: 0.61 (0.17), residues: 975 sheet: -0.84 (0.37), residues: 192 loop : -1.31 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 538 TYR 0.025 0.001 TYR F 534 PHE 0.026 0.001 PHE D 557 TRP 0.015 0.001 TRP H 277 HIS 0.015 0.001 HIS F 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (17880) covalent geometry : angle 0.56307 / 0.30 (24567) hydrogen bonds : bond 0.04784 / 3.40 ( 744) hydrogen bonds : angle 4.39475 / 3.01 ( 2043) Misc. bond : bond 0.00049 / 0.03 ( 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 183 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 220 MET cc_start: 0.6980 (mtt) cc_final: 0.6600 (mtp) REVERT: G 264 GLN cc_start: 0.6684 (mm-40) cc_final: 0.6451 (mm110) REVERT: G 300 THR cc_start: -0.0109 (OUTLIER) cc_final: -0.0316 (m) REVERT: B 316 MET cc_start: 0.8663 (ttt) cc_final: 0.8324 (ttt) REVERT: B 334 GLU cc_start: 0.8591 (tp30) cc_final: 0.8282 (tp30) REVERT: B 507 HIS cc_start: 0.7888 (OUTLIER) cc_final: 0.7560 (t70) REVERT: B 513 ILE cc_start: 0.7450 (tp) cc_final: 0.6891 (mm) REVERT: C 364 MET cc_start: 0.8514 (tpp) cc_final: 0.8294 (mmm) REVERT: D 316 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.6819 (ttm) REVERT: E 441 MET cc_start: 0.7515 (tmm) cc_final: 0.7314 (tmm) REVERT: F 378 MET cc_start: 0.8482 (tpt) cc_final: 0.8201 (tpt) REVERT: F 538 ARG cc_start: 0.8279 (ptp-170) cc_final: 0.8024 (ptp-170) REVERT: A 364 MET cc_start: 0.8536 (mmm) cc_final: 0.8227 (mmm) REVERT: A 441 MET cc_start: 0.8281 (tmm) cc_final: 0.7991 (tmm) REVERT: A 444 ASN cc_start: 0.8260 (t0) cc_final: 0.8016 (t0) REVERT: H 253 MET cc_start: 0.0326 (ttm) cc_final: -0.0360 (ttm) outliers start: 27 outliers final: 23 residues processed: 178 average time/residue: 0.1403 time to fit residues: 38.0478 Evaluate side-chains 178 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 C residue 352 ASN Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 560 THR Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 460 HIS Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 523 ASN Chi-restraints excluded: chain D residue 559 ILE Chi-restraints excluded: chain E residue 460 HIS Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 560 THR Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain H residue 225 HIS 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 39 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 190 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 289 HIS ** E 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.170357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150997 restraints weight = 25425.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150822 restraints weight = 38841.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.150937 restraints weight = 29633.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150989 restraints weight = 23063.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.150987 restraints weight = 22668.084| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.228 17881 Z= 0.205 Angle : 0.804 59.119 24567 Z= 0.476 Chirality : 0.048 1.144 2707 Planarity : 0.005 0.197 2855 Dihedral : 19.113 142.116 2985 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.91 % Allowed : 18.30 % Favored : 79.80 % Cbeta Deviations : 0.10 % 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: -0.51 (0.19), residues: 2004 helix: 0.61 (0.17), residues: 975 sheet: -0.84 (0.37), residues: 192 loop : -1.31 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 538 TYR 0.022 0.001 TYR F 534 PHE 0.021 0.001 PHE D 557 TRP 0.014 0.001 TRP B 572 HIS 0.264 0.003 HIS F 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.20 (17880) covalent geometry : angle 0.80442 / 0.48 (24567) hydrogen bonds : bond 0.04794 / 3.41 ( 744) hydrogen bonds : angle 4.39483 / 3.01 ( 2043) Misc. bond : bond 0.00047 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2473.56 seconds wall clock time: 43 minutes 48.84 seconds (2628.84 seconds total)