Starting phenix.real_space_refine on Mon Apr 6 09:19:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dc4_46743/04_2026/9dc4_46743_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dc4_46743/04_2026/9dc4_46743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dc4_46743/04_2026/9dc4_46743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dc4_46743/04_2026/9dc4_46743.map" model { file = "/net/cci-nas-00/data/ceres_data/9dc4_46743/04_2026/9dc4_46743_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dc4_46743/04_2026/9dc4_46743_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.059 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 Fe 1 7.16 5 S 69 5.16 5 C 10661 2.51 5 N 3012 2.21 5 O 3283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17026 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 7000 Classifications: {'peptide': 891} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 24, 'TRANS': 866} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 4173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4173 Classifications: {'peptide': 532} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 507} Chain breaks: 10 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 5196 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 677, 5191 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 645} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 677, 5191 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 645} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 5303 Chain: "T" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 652 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' FE': 1, 'BCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA F 353 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA F 353 " occ=0.50 Time building chain proxies: 4.31, per 1000 atoms: 0.25 Number of scatterers: 17026 At special positions: 0 Unit cell: (117.957, 145.768, 202.349, 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) Fe 1 26.01 S 69 16.00 O 3283 8.00 N 3012 7.00 C 10661 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 446 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 562 " - pdb=" SG CYS A 572 " distance=2.04 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 38 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 350 " distance=2.03 Simple disulfide: pdb=" SG CYS F 177 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS F 180 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 190 " - pdb=" SG CYS F 196 " distance=2.04 Simple disulfide: pdb=" SG CYS F 246 " - pdb=" SG CYS F 260 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 615 " distance=2.03 Simple disulfide: pdb=" SG CYS F 364 " - pdb=" SG CYS F 396 " distance=2.03 Simple disulfide: pdb=" SG CYS F 374 " - pdb=" SG CYS F 387 " distance=2.03 Simple disulfide: pdb=" SG CYS F 421 " - pdb=" SG CYS F 693 " distance=2.03 Simple disulfide: pdb=" SG CYS F 437 " - pdb=" SG CYS F 656 " distance=2.03 Simple disulfide: pdb=" SG CYS F 469 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 493 " - pdb=" SG CYS F 684 " distance=2.02 Simple disulfide: pdb=" SG CYS F 503 " - pdb=" SG CYS F 517 " distance=2.03 Simple disulfide: pdb=" SG CYS F 514 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 582 " - pdb=" SG CYS F 596 " distance=2.03 Simple disulfide: pdb=" SG CYS F 634 " - pdb=" SG CYS F 639 " distance=2.03 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: 1.33 Conformation dependent library (CDL) restraints added in 939.9 milliseconds 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3974 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 25 sheets defined 14.6% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 75 through 79 removed outlier: 3.555A pdb=" N LEU A 79 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 177 through 182 removed outlier: 4.148A pdb=" N VAL A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.868A pdb=" N PHE A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 652 through 658 removed outlier: 3.588A pdb=" N GLY A 658 " --> pdb=" O ALA A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 881 Processing helix chain 'A' and resid 882 through 884 No H-bonds generated for 'chain 'A' and resid 882 through 884' Processing helix chain 'B' and resid 101 through 111 Processing helix chain 'F' and resid 32 through 47 removed outlier: 3.557A pdb=" N SER F 47 " --> pdb=" O ASP F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'F' and resid 84 through 89 removed outlier: 3.846A pdb=" N ASP F 88 " --> pdb=" O GLY F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 148 Processing helix chain 'F' and resid 148 through 153 removed outlier: 3.796A pdb=" N LEU F 153 " --> pdb=" O ILE F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 172 removed outlier: 3.818A pdb=" N PHE F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 removed outlier: 3.624A pdb=" N CYS F 213 " --> pdb=" O GLY F 209 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 233 Processing helix chain 'F' and resid 256 through 260 Processing helix chain 'F' and resid 279 through 294 Processing helix chain 'F' and resid 329 through 335 removed outlier: 3.646A pdb=" N LEU F 334 " --> pdb=" O ALA F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 346 Processing helix chain 'F' and resid 367 through 381 Processing helix chain 'F' and resid 392 through 402 removed outlier: 3.538A pdb=" N ALA F 398 " --> pdb=" O GLU F 394 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 420 removed outlier: 3.852A pdb=" N ILE F 417 " --> pdb=" O GLY F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 491 removed outlier: 3.911A pdb=" N LEU F 486 " --> pdb=" O PRO F 482 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN F 488 " --> pdb=" O GLY F 484 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS F 489 " --> pdb=" O LEU F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 535 through 546 removed outlier: 3.780A pdb=" N PHE F 540 " --> pdb=" O TYR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 561 removed outlier: 3.992A pdb=" N THR F 561 " --> pdb=" O PRO F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 627 removed outlier: 3.843A pdb=" N HIS F 625 " --> pdb=" O ARG F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 671 Processing helix chain 'F' and resid 671 through 679 removed outlier: 3.779A pdb=" N VAL F 675 " --> pdb=" O GLY F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 689 through 694 Processing helix chain 'T' and resid 212 through 218 Processing helix chain 'T' and resid 247 through 260 removed outlier: 3.534A pdb=" N ASN T 260 " --> pdb=" O LYS T 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 33 through 36 current: chain 'T' and resid 236 through 243 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.517A pdb=" N GLN A 174 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL A 151 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA A 172 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE A 153 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER A 170 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER A 110 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 90 removed outlier: 3.606A pdb=" N VAL A 89 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLY A 98 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 197 removed outlier: 3.635A pdb=" N LYS A 193 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 211 " --> pdb=" O ALA A 218 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 305 through 314 current: chain 'A' and resid 326 through 342 removed outlier: 4.540A pdb=" N VAL A 397 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY A 394 " --> pdb=" O CYS A 446 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N CYS A 446 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 406 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 465 " --> pdb=" O HIS A 445 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 464 through 486 current: chain 'A' and resid 493 through 495 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 493 through 495 current: chain 'A' and resid 555 through 560 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 555 through 560 current: chain 'A' and resid 596 through 610 removed outlier: 3.691A pdb=" N GLY A 629 " --> pdb=" O GLY A 599 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 627 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N LEU A 624 " --> pdb=" O PHE A 648 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N PHE A 648 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TRP A 626 " --> pdb=" O THR A 646 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 647 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE A 696 " --> pdb=" O GLY A 735 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 735 " --> pdb=" O PHE A 696 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER A 730 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 769 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG A 732 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 759 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 758 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 762 " --> pdb=" O ARG A 790 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 790 " --> pdb=" O ASN A 762 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 790 through 794 current: chain 'A' and resid 804 through 813 removed outlier: 3.991A pdb=" N SER A 851 " --> pdb=" O ASN A 807 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 863 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 910 " --> pdb=" O ARG A 863 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 250 Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 278 removed outlier: 7.732A pdb=" N TYR A 257 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL A 549 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A 259 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE A 551 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 380 through 382 Processing sheet with id=AA8, first strand: chain 'A' and resid 724 through 727 removed outlier: 3.715A pdb=" N THR A 776 " --> pdb=" O TYR A 708 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB1, first strand: chain 'A' and resid 778 through 779 removed outlier: 3.638A pdb=" N ILE A 778 " --> pdb=" O ALA A 826 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 45 through 46 current: chain 'B' and resid 582 through 585 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 582 through 585 current: chain 'B' and resid 606 through 612 Processing sheet with id=AB3, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AB4, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AB5, first strand: chain 'B' and resid 201 through 212 removed outlier: 4.784A pdb=" N TRP B 208 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N PHE B 262 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG B 281 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN B 295 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 308 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 337 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY B 310 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER B 335 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER B 335 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B 353 " --> pdb=" O SER B 335 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 417 through 419 removed outlier: 3.659A pdb=" N GLU B 544 " --> pdb=" O ARG B 520 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR B 515 " --> pdb=" O CYS B 506 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 428 through 431 Processing sheet with id=AB8, first strand: chain 'B' and resid 643 through 644 Processing sheet with id=AB9, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.111A pdb=" N VAL F 25 " --> pdb=" O ALA F 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 78 through 81 removed outlier: 3.748A pdb=" N VAL F 79 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL F 100 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ALA F 272 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AC3, first strand: chain 'F' and resid 136 through 137 removed outlier: 7.772A pdb=" N SER F 136 " --> pdb=" O CYS F 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 361 through 365 Processing sheet with id=AC5, first strand: chain 'F' and resid 407 through 410 removed outlier: 3.915A pdb=" N LEU F 427 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR F 608 " --> pdb=" O PRO F 425 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS F 656 " --> pdb=" O ASN F 430 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 446 through 452 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 446 through 452 current: chain 'F' and resid 501 through 503 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 501 through 503 current: chain 'F' and resid 587 through 589 No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'T' and resid 203 through 205 511 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5692 1.34 - 1.46: 4161 1.46 - 1.58: 7449 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 17394 Sorted by residual: bond pdb=" CA TYR F 204 " pdb=" CB TYR F 204 " ideal model delta sigma weight residual 1.526 1.549 -0.023 1.76e-02 3.23e+03 1.77e+00 bond pdb=" CB PRO F 159 " pdb=" CG PRO F 159 " ideal model delta sigma weight residual 1.492 1.551 -0.059 5.00e-02 4.00e+02 1.40e+00 bond pdb=" N PRO F 307 " pdb=" CA PRO F 307 " ideal model delta sigma weight residual 1.468 1.477 -0.009 7.90e-03 1.60e+04 1.40e+00 bond pdb=" CG PRO F 159 " pdb=" CD PRO F 159 " ideal model delta sigma weight residual 1.503 1.538 -0.035 3.40e-02 8.65e+02 1.05e+00 bond pdb=" CG LEU F 244 " pdb=" CD1 LEU F 244 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.04e+00 ... (remaining 17389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 22967 1.89 - 3.78: 453 3.78 - 5.68: 55 5.68 - 7.57: 10 7.57 - 9.46: 6 Bond angle restraints: 23491 Sorted by residual: angle pdb=" C ALA A 491 " pdb=" CA ALA A 491 " pdb=" CB ALA A 491 " ideal model delta sigma weight residual 117.23 110.38 6.85 1.36e+00 5.41e-01 2.54e+01 angle pdb=" C VAL B 111 " pdb=" N GLU B 112 " pdb=" CA GLU B 112 " ideal model delta sigma weight residual 121.54 131.00 -9.46 1.91e+00 2.74e-01 2.45e+01 angle pdb=" C ALA B 54 " pdb=" CA ALA B 54 " pdb=" CB ALA B 54 " ideal model delta sigma weight residual 115.89 110.28 5.61 1.32e+00 5.74e-01 1.81e+01 angle pdb=" N GLU B 112 " pdb=" CA GLU B 112 " pdb=" C GLU B 112 " ideal model delta sigma weight residual 110.80 119.72 -8.92 2.13e+00 2.20e-01 1.75e+01 angle pdb=" N GLY A 746 " pdb=" CA GLY A 746 " pdb=" C GLY A 746 " ideal model delta sigma weight residual 113.18 103.85 9.33 2.37e+00 1.78e-01 1.55e+01 ... (remaining 23486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 8731 17.85 - 35.70: 1234 35.70 - 53.54: 362 53.54 - 71.39: 71 71.39 - 89.24: 18 Dihedral angle restraints: 10416 sinusoidal: 4163 harmonic: 6253 Sorted by residual: dihedral pdb=" CB CYS F 634 " pdb=" SG CYS F 634 " pdb=" SG CYS F 639 " pdb=" CB CYS F 639 " ideal model delta sinusoidal sigma weight residual -86.00 -160.19 74.19 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CB CYS F 38 " pdb=" SG CYS F 38 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual 93.00 165.47 -72.47 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CB CYS F 177 " pdb=" SG CYS F 177 " pdb=" SG CYS F 193 " pdb=" CB CYS F 193 " ideal model delta sinusoidal sigma weight residual -86.00 -153.08 67.08 1 1.00e+01 1.00e-02 5.86e+01 ... (remaining 10413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1968 0.051 - 0.103: 415 0.103 - 0.154: 80 0.154 - 0.205: 0 0.205 - 0.256: 2 Chirality restraints: 2465 Sorted by residual: chirality pdb=" CA PRO F 159 " pdb=" N PRO F 159 " pdb=" C PRO F 159 " pdb=" CB PRO F 159 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CB ILE A 213 " pdb=" CA ILE A 213 " pdb=" CG1 ILE A 213 " pdb=" CG2 ILE A 213 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ILE B 185 " pdb=" N ILE B 185 " pdb=" C ILE B 185 " pdb=" CB ILE B 185 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2462 not shown) Planarity restraints: 3098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 158 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO F 159 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO F 159 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO F 159 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 681 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO B 682 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO B 682 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 682 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL T 273 " 0.040 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO T 274 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO T 274 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO T 274 " 0.034 5.00e-02 4.00e+02 ... (remaining 3095 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 348 2.67 - 3.23: 14809 3.23 - 3.79: 23719 3.79 - 4.34: 32544 4.34 - 4.90: 57330 Nonbonded interactions: 128750 Sorted by model distance: nonbonded pdb=" OD2 ASP F 82 " pdb="FE FE F 702 " model vdw 2.113 2.260 nonbonded pdb=" OG1 THR B 554 " pdb=" O GLY B 669 " model vdw 2.155 3.040 nonbonded pdb=" OG SER A 137 " pdb=" OE2 GLU A 401 " model vdw 2.159 3.040 nonbonded pdb=" OE2 GLU F 394 " pdb=" OG SER F 687 " model vdw 2.234 3.040 nonbonded pdb=" O THR A 635 " pdb=" OG1 THR A 635 " model vdw 2.237 3.040 ... (remaining 128745 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.730 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.670 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.003 0.059 17417 Z= 0.148 Angle : 0.667 9.458 23535 Z= 0.373 Chirality : 0.043 0.256 2465 Planarity : 0.005 0.101 3098 Dihedral : 17.891 89.239 6376 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.99 % Favored : 90.50 % Rotamer: Outliers : 4.25 % Allowed : 29.87 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.05 % Twisted Proline : 1.18 % Twisted General : 0.14 % 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: -2.32 (0.17), residues: 2161 helix: -1.06 (0.30), residues: 274 sheet: -0.62 (0.19), residues: 717 loop : -2.33 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 327 TYR 0.019 0.001 TYR B 668 PHE 0.014 0.001 PHE A 915 TRP 0.014 0.001 TRP A 312 HIS 0.007 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00310 (17394) covalent geometry : angle 0.66543 (23491) SS BOND : bond 0.00289 ( 22) SS BOND : angle 1.28307 ( 44) hydrogen bonds : bond 0.18802 ( 511) hydrogen bonds : angle 7.40742 ( 1422) Misc. bond : bond 0.00158 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 90 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8565 (mt-10) REVERT: A 114 ASP cc_start: 0.9142 (t0) cc_final: 0.8790 (m-30) REVERT: A 144 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: A 201 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8268 (mtp180) REVERT: A 231 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7337 (mtm180) REVERT: A 359 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7768 (tttt) REVERT: A 870 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8156 (mmp) REVERT: B 99 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7891 (mm-30) REVERT: B 103 ARG cc_start: 0.7651 (mtm180) cc_final: 0.7343 (mtt180) REVERT: B 112 GLU cc_start: 0.5887 (mt-10) cc_final: 0.5434 (mm-30) REVERT: B 233 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7431 (mmm160) REVERT: B 357 GLN cc_start: 0.8039 (mp10) cc_final: 0.7483 (mt0) REVERT: F 23 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8478 (pttp) REVERT: F 39 GLN cc_start: 0.8193 (tt0) cc_final: 0.7919 (pt0) REVERT: F 69 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8009 (mtt90) REVERT: F 120 VAL cc_start: 0.5401 (OUTLIER) cc_final: 0.4940 (t) REVERT: F 126 PHE cc_start: 0.3131 (OUTLIER) cc_final: 0.1548 (p90) REVERT: F 131 LEU cc_start: 0.7164 (tt) cc_final: 0.6830 (mt) REVERT: F 297 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6110 (tptm) REVERT: F 483 MET cc_start: 0.9124 (mmm) cc_final: 0.8906 (mmm) REVERT: F 610 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8648 (tptp) outliers start: 76 outliers final: 60 residues processed: 158 average time/residue: 0.1523 time to fit residues: 35.2139 Evaluate side-chains 157 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 84 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 870 MET Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 607 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 129 ASN Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 364 CYS Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 651 ARG Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 235 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 0.0270 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.0040 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.5980 chunk 212 optimal weight: 20.0000 overall best weight: 0.5050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 GLN B 283 ASN B 563 GLN B 709 GLN F 268 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.124761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.081950 restraints weight = 28203.105| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.73 r_work: 0.2955 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 17417 Z= 0.107 Angle : 0.597 10.070 23535 Z= 0.319 Chirality : 0.043 0.262 2465 Planarity : 0.004 0.101 3098 Dihedral : 9.067 77.828 2545 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.67 % Favored : 90.82 % Rotamer: Outliers : 5.70 % Allowed : 28.08 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.05 % Twisted Proline : 1.18 % 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: -2.11 (0.17), residues: 2161 helix: -0.80 (0.30), residues: 287 sheet: -0.48 (0.19), residues: 729 loop : -2.25 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 682 TYR 0.014 0.001 TYR F 155 PHE 0.013 0.001 PHE T 247 TRP 0.010 0.001 TRP A 312 HIS 0.008 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00228 (17394) covalent geometry : angle 0.59546 (23491) SS BOND : bond 0.00338 ( 22) SS BOND : angle 1.18771 ( 44) hydrogen bonds : bond 0.03734 ( 511) hydrogen bonds : angle 5.70032 ( 1422) Misc. bond : bond 0.00155 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 98 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8266 (mt-10) REVERT: A 114 ASP cc_start: 0.9102 (t0) cc_final: 0.8727 (m-30) REVERT: A 201 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7594 (mtp180) REVERT: A 510 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.7456 (tpt) REVERT: A 594 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7705 (tmt-80) REVERT: A 843 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8601 (mtt180) REVERT: B 36 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8039 (tp30) REVERT: B 46 ASP cc_start: 0.8113 (p0) cc_final: 0.7863 (p0) REVERT: B 103 ARG cc_start: 0.7495 (mtm180) cc_final: 0.7281 (mtt180) REVERT: B 112 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5562 (mm-30) REVERT: B 151 ASN cc_start: 0.8605 (m-40) cc_final: 0.8331 (m-40) REVERT: B 182 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7805 (t0) REVERT: B 233 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7279 (mmm160) REVERT: B 357 GLN cc_start: 0.7434 (mt0) cc_final: 0.6907 (mt0) REVERT: B 556 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7829 (tp30) REVERT: F 23 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8362 (pttp) REVERT: F 69 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8077 (mtt90) REVERT: F 120 VAL cc_start: 0.5374 (OUTLIER) cc_final: 0.4794 (t) REVERT: F 126 PHE cc_start: 0.3141 (OUTLIER) cc_final: 0.1417 (p90) REVERT: F 135 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6917 (tppt) REVERT: F 244 LEU cc_start: 0.5542 (mt) cc_final: 0.5316 (mt) REVERT: F 258 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6453 (mttp) REVERT: F 297 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6281 (tptm) REVERT: F 610 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8545 (tptp) REVERT: T 242 VAL cc_start: 0.3784 (OUTLIER) cc_final: 0.3504 (p) outliers start: 102 outliers final: 50 residues processed: 185 average time/residue: 0.1423 time to fit residues: 39.3660 Evaluate side-chains 161 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 94 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 135 LYS Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 364 CYS Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 651 ARG Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 ASN B 709 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.122332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.079289 restraints weight = 28626.633| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.74 r_work: 0.2906 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17417 Z= 0.169 Angle : 0.624 9.786 23535 Z= 0.333 Chirality : 0.044 0.260 2465 Planarity : 0.004 0.103 3098 Dihedral : 8.442 76.956 2493 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.94 % Favored : 90.55 % Rotamer: Outliers : 6.10 % Allowed : 27.24 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.05 % Twisted Proline : 1.18 % 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: -2.05 (0.17), residues: 2161 helix: -0.65 (0.30), residues: 289 sheet: -0.37 (0.19), residues: 719 loop : -2.28 (0.17), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 682 TYR 0.013 0.001 TYR A 583 PHE 0.012 0.001 PHE B 352 TRP 0.010 0.001 TRP A 548 HIS 0.024 0.002 HIS F 268 Details of bonding type rmsd covalent geometry : bond 0.00400 (17394) covalent geometry : angle 0.62222 (23491) SS BOND : bond 0.00287 ( 22) SS BOND : angle 1.14025 ( 44) hydrogen bonds : bond 0.04109 ( 511) hydrogen bonds : angle 5.49224 ( 1422) Misc. bond : bond 0.00166 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 90 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8303 (mt-10) REVERT: A 106 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8153 (mtpp) REVERT: A 201 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7446 (mpp-170) REVERT: A 510 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.7795 (ttt) REVERT: A 594 ARG cc_start: 0.8336 (ttp80) cc_final: 0.7659 (tmt-80) REVERT: A 843 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8620 (mtt180) REVERT: B 36 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8079 (tp30) REVERT: B 103 ARG cc_start: 0.7558 (mtm180) cc_final: 0.7341 (mtt180) REVERT: B 112 GLU cc_start: 0.6125 (mt-10) cc_final: 0.5584 (mm-30) REVERT: B 151 ASN cc_start: 0.8530 (m-40) cc_final: 0.8221 (m-40) REVERT: B 182 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7857 (t0) REVERT: B 222 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: B 233 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7301 (mmm160) REVERT: B 357 GLN cc_start: 0.7447 (mt0) cc_final: 0.6914 (mt0) REVERT: B 556 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: F 23 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8381 (pttp) REVERT: F 69 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8046 (mtt90) REVERT: F 120 VAL cc_start: 0.5360 (OUTLIER) cc_final: 0.4893 (t) REVERT: F 126 PHE cc_start: 0.3101 (OUTLIER) cc_final: 0.1269 (p90) REVERT: F 135 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6837 (tppt) REVERT: F 258 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6771 (pttp) REVERT: F 297 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6303 (tptm) REVERT: F 610 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8517 (tptp) REVERT: T 242 VAL cc_start: 0.3678 (OUTLIER) cc_final: 0.3408 (p) outliers start: 109 outliers final: 69 residues processed: 186 average time/residue: 0.1414 time to fit residues: 38.7476 Evaluate side-chains 175 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 88 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 267 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 135 LYS Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 651 ARG Chi-restraints excluded: chain F residue 656 CYS Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 0.0980 chunk 160 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.078520 restraints weight = 28423.503| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.72 r_work: 0.2887 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17417 Z= 0.175 Angle : 0.630 9.619 23535 Z= 0.335 Chirality : 0.044 0.256 2465 Planarity : 0.004 0.105 3098 Dihedral : 8.407 77.663 2489 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.99 % Favored : 90.50 % Rotamer: Outliers : 6.71 % Allowed : 26.62 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.05 % Twisted Proline : 1.18 % 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: -2.00 (0.17), residues: 2161 helix: -0.48 (0.31), residues: 285 sheet: -0.37 (0.19), residues: 714 loop : -2.25 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 682 TYR 0.013 0.001 TYR A 583 PHE 0.012 0.001 PHE B 352 TRP 0.011 0.001 TRP A 548 HIS 0.007 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00419 (17394) covalent geometry : angle 0.62823 (23491) SS BOND : bond 0.00295 ( 22) SS BOND : angle 1.15796 ( 44) hydrogen bonds : bond 0.04049 ( 511) hydrogen bonds : angle 5.42030 ( 1422) Misc. bond : bond 0.00176 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 95 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8384 (mt-10) REVERT: A 106 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8110 (mtpp) REVERT: A 201 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7360 (mpp-170) REVERT: A 510 MET cc_start: 0.9280 (OUTLIER) cc_final: 0.7863 (ttt) REVERT: A 594 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7961 (tmt-80) REVERT: A 843 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8608 (mtt180) REVERT: B 46 ASP cc_start: 0.8391 (p0) cc_final: 0.8066 (p0) REVERT: B 103 ARG cc_start: 0.7619 (mtm180) cc_final: 0.7393 (mtt180) REVERT: B 112 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5528 (mm-30) REVERT: B 151 ASN cc_start: 0.8541 (m-40) cc_final: 0.8237 (m-40) REVERT: B 182 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7831 (t0) REVERT: B 222 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: B 233 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7321 (mmm160) REVERT: B 357 GLN cc_start: 0.7582 (mt0) cc_final: 0.7033 (mt0) REVERT: B 517 MET cc_start: 0.8795 (mmt) cc_final: 0.8474 (mmt) REVERT: F 23 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8361 (pttp) REVERT: F 69 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8116 (mtt90) REVERT: F 120 VAL cc_start: 0.5275 (OUTLIER) cc_final: 0.4892 (t) REVERT: F 126 PHE cc_start: 0.3261 (OUTLIER) cc_final: 0.1192 (p90) REVERT: F 135 LYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6834 (tppt) REVERT: F 258 LYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6757 (pttp) REVERT: F 279 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8058 (pp20) REVERT: F 462 ASN cc_start: 0.7729 (OUTLIER) cc_final: 0.6968 (p0) REVERT: F 610 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8533 (tptp) REVERT: T 242 VAL cc_start: 0.3633 (OUTLIER) cc_final: 0.3384 (p) outliers start: 120 outliers final: 78 residues processed: 201 average time/residue: 0.1301 time to fit residues: 39.5327 Evaluate side-chains 181 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 85 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 542 GLN Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 135 LYS Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 462 ASN Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 651 ARG Chi-restraints excluded: chain F residue 656 CYS Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 132 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.078160 restraints weight = 28379.575| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.75 r_work: 0.2886 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 17417 Z= 0.189 Angle : 0.649 10.270 23535 Z= 0.344 Chirality : 0.045 0.257 2465 Planarity : 0.004 0.106 3098 Dihedral : 8.208 77.424 2481 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.51 % Allowed : 9.50 % Favored : 89.99 % Rotamer: Outliers : 7.21 % Allowed : 26.45 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.05 % Twisted Proline : 1.18 % 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: -2.01 (0.17), residues: 2161 helix: -0.45 (0.31), residues: 285 sheet: -0.41 (0.19), residues: 714 loop : -2.25 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 456 TYR 0.014 0.001 TYR A 393 PHE 0.012 0.001 PHE B 352 TRP 0.020 0.001 TRP F 147 HIS 0.007 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00455 (17394) covalent geometry : angle 0.64091 (23491) SS BOND : bond 0.00313 ( 22) SS BOND : angle 2.44301 ( 44) hydrogen bonds : bond 0.04072 ( 511) hydrogen bonds : angle 5.40483 ( 1422) Misc. bond : bond 0.00182 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 87 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8390 (mt-10) REVERT: A 106 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8082 (mtpp) REVERT: A 201 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7317 (mpp-170) REVERT: A 245 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.5787 (ttt90) REVERT: A 446 CYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6595 (t) REVERT: A 510 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.7872 (ttt) REVERT: A 594 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7973 (tmt-80) REVERT: A 691 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8065 (mp) REVERT: A 843 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8615 (mtt180) REVERT: A 859 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7141 (p90) REVERT: B 103 ARG cc_start: 0.7637 (mtm180) cc_final: 0.7374 (mtt180) REVERT: B 112 GLU cc_start: 0.6304 (OUTLIER) cc_final: 0.5803 (mm-30) REVERT: B 151 ASN cc_start: 0.8537 (m-40) cc_final: 0.8220 (m-40) REVERT: B 182 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7859 (t0) REVERT: B 222 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7645 (tp30) REVERT: B 233 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6495 (ttt-90) REVERT: B 357 GLN cc_start: 0.7589 (mt0) cc_final: 0.7021 (mt0) REVERT: F 23 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8370 (pttp) REVERT: F 69 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8112 (mtt90) REVERT: F 120 VAL cc_start: 0.5016 (OUTLIER) cc_final: 0.4738 (t) REVERT: F 126 PHE cc_start: 0.3300 (OUTLIER) cc_final: 0.1227 (p90) REVERT: F 135 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6832 (tppt) REVERT: F 147 TRP cc_start: 0.7118 (m-90) cc_final: 0.6333 (m100) REVERT: F 258 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6734 (pttp) REVERT: F 279 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8074 (pp20) REVERT: F 380 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8447 (m-40) REVERT: F 462 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.6967 (p0) REVERT: F 610 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8531 (tptp) REVERT: F 682 ARG cc_start: 0.8614 (ttp80) cc_final: 0.8341 (ttp80) REVERT: T 242 VAL cc_start: 0.3594 (OUTLIER) cc_final: 0.3360 (p) outliers start: 129 outliers final: 90 residues processed: 202 average time/residue: 0.1386 time to fit residues: 41.8122 Evaluate side-chains 197 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 84 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 873 ARG Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 126 PHE Chi-restraints excluded: chain F residue 135 LYS Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 380 ASN Chi-restraints excluded: chain F residue 462 ASN Chi-restraints excluded: chain F residue 476 THR Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 620 LEU Chi-restraints excluded: chain F residue 651 ARG Chi-restraints excluded: chain F residue 656 CYS Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 235 HIS Chi-restraints excluded: chain T residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 48 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 115 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 166 optimal weight: 0.0470 chunk 172 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 overall best weight: 0.8684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN F 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.123000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.080093 restraints weight = 28282.980| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.74 r_work: 0.2919 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17417 Z= 0.120 Angle : 0.593 10.353 23535 Z= 0.315 Chirality : 0.043 0.258 2465 Planarity : 0.004 0.107 3098 Dihedral : 8.023 78.973 2481 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.29 % Favored : 91.24 % Rotamer: Outliers : 6.32 % Allowed : 27.74 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.05 % Twisted Proline : 1.18 % 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: -1.91 (0.17), residues: 2161 helix: -0.38 (0.31), residues: 285 sheet: -0.36 (0.19), residues: 728 loop : -2.18 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 682 TYR 0.017 0.001 TYR A 393 PHE 0.011 0.001 PHE F 113 TRP 0.017 0.001 TRP F 147 HIS 0.008 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00279 (17394) covalent geometry : angle 0.58792 (23491) SS BOND : bond 0.00340 ( 22) SS BOND : angle 1.90850 ( 44) hydrogen bonds : bond 0.03285 ( 511) hydrogen bonds : angle 5.30707 ( 1422) Misc. bond : bond 0.00158 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 96 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7261 (mpp-170) REVERT: A 209 LEU cc_start: 0.8228 (tt) cc_final: 0.8023 (mt) REVERT: A 245 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.5821 (ttt90) REVERT: A 510 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.7625 (tpt) REVERT: A 594 ARG cc_start: 0.8363 (ttp80) cc_final: 0.7736 (tmt-80) REVERT: A 817 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8268 (mm-30) REVERT: A 859 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.7106 (p90) REVERT: B 46 ASP cc_start: 0.8417 (p0) cc_final: 0.8082 (p0) REVERT: B 99 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: B 103 ARG cc_start: 0.7572 (mtm180) cc_final: 0.7321 (mtt180) REVERT: B 112 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5842 (mm-30) REVERT: B 151 ASN cc_start: 0.8420 (m-40) cc_final: 0.8081 (m-40) REVERT: B 182 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7703 (t0) REVERT: B 205 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7677 (mmmt) REVERT: B 222 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7618 (tp30) REVERT: B 233 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6490 (ttt-90) REVERT: B 357 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6912 (mt0) REVERT: B 509 ASN cc_start: 0.8017 (t0) cc_final: 0.7805 (t0) REVERT: B 556 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7871 (tp30) REVERT: F 23 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8427 (pttp) REVERT: F 69 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.8093 (mtt90) REVERT: F 131 LEU cc_start: 0.7256 (tt) cc_final: 0.6954 (mt) REVERT: F 135 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6980 (tppt) REVERT: F 147 TRP cc_start: 0.7196 (m-90) cc_final: 0.6365 (m100) REVERT: F 258 LYS cc_start: 0.6980 (OUTLIER) cc_final: 0.6723 (pttp) REVERT: F 279 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8073 (pp20) REVERT: F 462 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7003 (p0) REVERT: F 610 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8522 (tptp) REVERT: F 682 ARG cc_start: 0.8554 (ttp80) cc_final: 0.8283 (ttp80) REVERT: T 242 VAL cc_start: 0.3567 (OUTLIER) cc_final: 0.3336 (p) outliers start: 113 outliers final: 71 residues processed: 195 average time/residue: 0.1396 time to fit residues: 40.1251 Evaluate side-chains 180 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 88 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 873 ARG Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 542 GLN Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain F residue 135 LYS Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 462 ASN Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 651 ARG Chi-restraints excluded: chain F residue 656 CYS Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 235 HIS Chi-restraints excluded: chain T residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 177 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.121126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.078217 restraints weight = 28329.631| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.71 r_work: 0.2881 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17417 Z= 0.191 Angle : 0.629 10.092 23535 Z= 0.335 Chirality : 0.044 0.255 2465 Planarity : 0.005 0.109 3098 Dihedral : 8.048 78.431 2476 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.18 % Favored : 90.36 % Rotamer: Outliers : 6.43 % Allowed : 27.74 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.05 % Twisted Proline : 1.18 % 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: -1.94 (0.17), residues: 2161 helix: -0.42 (0.31), residues: 288 sheet: -0.35 (0.19), residues: 705 loop : -2.19 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 456 TYR 0.014 0.001 TYR A 583 PHE 0.012 0.001 PHE B 352 TRP 0.013 0.001 TRP F 147 HIS 0.007 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00461 (17394) covalent geometry : angle 0.62817 (23491) SS BOND : bond 0.00279 ( 22) SS BOND : angle 1.06744 ( 44) hydrogen bonds : bond 0.04002 ( 511) hydrogen bonds : angle 5.32792 ( 1422) Misc. bond : bond 0.00163 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 85 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8070 (mtpp) REVERT: A 201 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7306 (mpp-170) REVERT: A 209 LEU cc_start: 0.8288 (tt) cc_final: 0.8071 (mt) REVERT: A 245 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.5880 (ttt90) REVERT: A 510 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.7888 (ttt) REVERT: A 594 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8003 (tmt-80) REVERT: A 691 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8024 (mp) REVERT: A 859 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7065 (p90) REVERT: B 46 ASP cc_start: 0.8434 (p0) cc_final: 0.8109 (p0) REVERT: B 99 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: B 103 ARG cc_start: 0.7613 (mtm180) cc_final: 0.7379 (mtt180) REVERT: B 112 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.5793 (mm-30) REVERT: B 151 ASN cc_start: 0.8496 (m-40) cc_final: 0.8177 (m-40) REVERT: B 182 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7817 (t0) REVERT: B 205 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7667 (mmmt) REVERT: B 222 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7637 (tp30) REVERT: B 233 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6494 (ttt-90) REVERT: B 300 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 357 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6920 (mt0) REVERT: B 509 ASN cc_start: 0.8088 (t0) cc_final: 0.7857 (t0) REVERT: F 23 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8450 (pttp) REVERT: F 69 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8115 (mtt90) REVERT: F 147 TRP cc_start: 0.7177 (m-90) cc_final: 0.6346 (m100) REVERT: F 258 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6759 (pttp) REVERT: F 279 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8082 (pp20) REVERT: F 462 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.6999 (p0) REVERT: F 610 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8563 (tptp) REVERT: F 682 ARG cc_start: 0.8605 (ttp80) cc_final: 0.8322 (ttp80) outliers start: 115 outliers final: 84 residues processed: 189 average time/residue: 0.1422 time to fit residues: 39.9170 Evaluate side-chains 188 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 85 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 630 ILE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 873 ARG Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 542 GLN Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 697 SER Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 462 ASN Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 651 ARG Chi-restraints excluded: chain F residue 656 CYS Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 223 THR Chi-restraints excluded: chain T residue 235 HIS Chi-restraints excluded: chain T residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 153 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 86 optimal weight: 0.0170 chunk 143 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.080713 restraints weight = 28457.277| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.77 r_work: 0.2930 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2806 r_free = 0.2806 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 17417 Z= 0.099 Angle : 0.581 8.785 23535 Z= 0.308 Chirality : 0.042 0.254 2465 Planarity : 0.004 0.109 3098 Dihedral : 7.843 80.571 2476 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.74 % Favored : 91.80 % Rotamer: Outliers : 5.31 % Allowed : 28.80 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.05 % Twisted Proline : 1.18 % 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: -1.85 (0.17), residues: 2161 helix: -0.34 (0.31), residues: 287 sheet: -0.32 (0.19), residues: 722 loop : -2.12 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 456 TYR 0.011 0.001 TYR B 668 PHE 0.011 0.001 PHE F 113 TRP 0.016 0.001 TRP F 147 HIS 0.015 0.001 HIS F 268 Details of bonding type rmsd covalent geometry : bond 0.00214 (17394) covalent geometry : angle 0.57936 (23491) SS BOND : bond 0.00298 ( 22) SS BOND : angle 1.17863 ( 44) hydrogen bonds : bond 0.03043 ( 511) hydrogen bonds : angle 5.24104 ( 1422) Misc. bond : bond 0.00148 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 94 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7337 (mpp-170) REVERT: A 245 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.5945 (ttt90) REVERT: A 323 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8926 (mppt) REVERT: A 510 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.7552 (tpt) REVERT: A 594 ARG cc_start: 0.8366 (ttp80) cc_final: 0.7781 (tmt-80) REVERT: A 691 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8023 (mp) REVERT: A 859 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.7038 (p90) REVERT: B 46 ASP cc_start: 0.8444 (p0) cc_final: 0.8128 (p0) REVERT: B 99 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7980 (mm-30) REVERT: B 103 ARG cc_start: 0.7637 (mtm180) cc_final: 0.7400 (mtt180) REVERT: B 112 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6224 (mm-30) REVERT: B 151 ASN cc_start: 0.8414 (m-40) cc_final: 0.8108 (m-40) REVERT: B 182 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7752 (t0) REVERT: B 205 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7820 (mmmt) REVERT: B 222 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: B 233 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6527 (ttt-90) REVERT: B 357 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.6937 (mt0) REVERT: B 509 ASN cc_start: 0.7985 (t0) cc_final: 0.7743 (t0) REVERT: B 556 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7811 (tp30) REVERT: F 23 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8416 (pttp) REVERT: F 69 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8138 (mtt90) REVERT: F 131 LEU cc_start: 0.7251 (tt) cc_final: 0.6943 (mt) REVERT: F 135 LYS cc_start: 0.6869 (tppt) cc_final: 0.6194 (tppt) REVERT: F 147 TRP cc_start: 0.7240 (m-90) cc_final: 0.6372 (m100) REVERT: F 258 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6724 (pttp) REVERT: F 279 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8117 (pp20) REVERT: F 280 ASP cc_start: 0.9117 (m-30) cc_final: 0.8502 (m-30) REVERT: F 610 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8566 (tptp) REVERT: T 235 HIS cc_start: 0.3949 (OUTLIER) cc_final: 0.3209 (p-80) outliers start: 95 outliers final: 66 residues processed: 175 average time/residue: 0.1434 time to fit residues: 37.0408 Evaluate side-chains 174 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 88 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 873 ARG Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 542 GLN Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 651 ARG Chi-restraints excluded: chain F residue 656 CYS Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 235 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 145 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 83 optimal weight: 0.0070 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 241 GLN F 268 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.122604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.079630 restraints weight = 28397.933| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.73 r_work: 0.2906 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17417 Z= 0.135 Angle : 0.598 9.631 23535 Z= 0.318 Chirality : 0.043 0.253 2465 Planarity : 0.004 0.110 3098 Dihedral : 7.842 78.138 2476 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.80 % Favored : 90.73 % Rotamer: Outliers : 5.09 % Allowed : 28.41 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.05 % Twisted Proline : 1.18 % 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: -1.83 (0.17), residues: 2161 helix: -0.31 (0.31), residues: 288 sheet: -0.30 (0.19), residues: 718 loop : -2.12 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 682 TYR 0.010 0.001 TYR A 583 PHE 0.010 0.001 PHE B 352 TRP 0.013 0.001 TRP F 147 HIS 0.008 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00320 (17394) covalent geometry : angle 0.59364 (23491) SS BOND : bond 0.00224 ( 22) SS BOND : angle 1.84983 ( 44) hydrogen bonds : bond 0.03439 ( 511) hydrogen bonds : angle 5.24550 ( 1422) Misc. bond : bond 0.00148 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 88 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7275 (mpp-170) REVERT: A 245 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.5864 (ttt90) REVERT: A 323 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8918 (mppt) REVERT: A 510 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.7825 (ttt) REVERT: A 594 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7764 (tmt-80) REVERT: A 691 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7942 (mp) REVERT: A 859 HIS cc_start: 0.7578 (OUTLIER) cc_final: 0.6834 (p90) REVERT: B 46 ASP cc_start: 0.8435 (p0) cc_final: 0.8207 (p0) REVERT: B 99 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7987 (mm-30) REVERT: B 103 ARG cc_start: 0.7616 (mtm180) cc_final: 0.7364 (mtt180) REVERT: B 112 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6302 (mm-30) REVERT: B 151 ASN cc_start: 0.8466 (m-40) cc_final: 0.8174 (m-40) REVERT: B 182 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7735 (t0) REVERT: B 205 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7721 (mmmt) REVERT: B 222 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7607 (tp30) REVERT: B 233 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6495 (ttt-90) REVERT: B 357 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6847 (mt0) REVERT: B 556 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: F 23 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8483 (pttp) REVERT: F 69 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7969 (mtt90) REVERT: F 135 LYS cc_start: 0.6967 (tppt) cc_final: 0.6234 (tppt) REVERT: F 147 TRP cc_start: 0.7263 (m-90) cc_final: 0.6527 (m100) REVERT: F 258 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6709 (pttp) REVERT: F 279 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8103 (pp20) REVERT: F 280 ASP cc_start: 0.9119 (m-30) cc_final: 0.8516 (m-30) REVERT: F 610 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8555 (tptp) outliers start: 91 outliers final: 64 residues processed: 166 average time/residue: 0.1388 time to fit residues: 34.2777 Evaluate side-chains 167 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 84 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 873 ARG Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 187 TYR Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 357 GLN Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 552 VAL Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 651 ARG Chi-restraints excluded: chain F residue 656 CYS Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 235 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 122 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 209 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 213 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 309 ASN F 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.119845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.076799 restraints weight = 28196.067| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.72 r_work: 0.2860 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17417 Z= 0.249 Angle : 0.692 11.370 23535 Z= 0.367 Chirality : 0.046 0.253 2465 Planarity : 0.005 0.112 3098 Dihedral : 7.940 71.624 2469 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.82 % Favored : 89.71 % Rotamer: Outliers : 4.98 % Allowed : 28.47 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.05 % Twisted Proline : 1.18 % 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: -1.94 (0.17), residues: 2161 helix: -0.33 (0.32), residues: 285 sheet: -0.40 (0.19), residues: 715 loop : -2.19 (0.17), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 682 TYR 0.017 0.002 TYR A 583 PHE 0.014 0.002 PHE B 632 TRP 0.009 0.001 TRP A 548 HIS 0.011 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00607 (17394) covalent geometry : angle 0.68535 (23491) SS BOND : bond 0.00344 ( 22) SS BOND : angle 2.36068 ( 44) hydrogen bonds : bond 0.04462 ( 511) hydrogen bonds : angle 5.40324 ( 1422) Misc. bond : bond 0.00170 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4322 Ramachandran restraints generated. 2161 Oldfield, 0 Emsley, 2161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 84 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8089 (mtpp) REVERT: A 201 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7351 (mpp-170) REVERT: A 245 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.5945 (ttt180) REVERT: A 510 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.8065 (ttt) REVERT: A 594 ARG cc_start: 0.8419 (ttp80) cc_final: 0.7803 (tmt-80) REVERT: A 691 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8051 (mp) REVERT: A 859 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.6982 (p90) REVERT: B 46 ASP cc_start: 0.8636 (p0) cc_final: 0.8387 (p0) REVERT: B 99 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8022 (mm-30) REVERT: B 103 ARG cc_start: 0.7729 (mtm180) cc_final: 0.7473 (mtt180) REVERT: B 112 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6373 (mm-30) REVERT: B 151 ASN cc_start: 0.8543 (m-40) cc_final: 0.8239 (m-40) REVERT: B 182 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7930 (t0) REVERT: B 205 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7887 (mmmt) REVERT: B 222 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7698 (tp30) REVERT: B 233 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6466 (ttt-90) REVERT: B 357 GLN cc_start: 0.7583 (mt0) cc_final: 0.7036 (mt0) REVERT: F 23 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8547 (pttp) REVERT: F 69 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7968 (mtt90) REVERT: F 135 LYS cc_start: 0.6997 (tppt) cc_final: 0.6255 (tppt) REVERT: F 147 TRP cc_start: 0.7283 (m-90) cc_final: 0.6494 (m100) REVERT: F 258 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6834 (pttp) REVERT: F 279 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8120 (pp20) REVERT: F 280 ASP cc_start: 0.9123 (m-30) cc_final: 0.8509 (m-30) REVERT: F 610 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8608 (tptp) outliers start: 89 outliers final: 67 residues processed: 163 average time/residue: 0.1404 time to fit residues: 34.0993 Evaluate side-chains 165 residues out of total 1813 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 82 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 106 LYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 201 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 323 LYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 533 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 851 SER Chi-restraints excluded: chain A residue 859 HIS Chi-restraints excluded: chain A residue 873 ARG Chi-restraints excluded: chain B residue 68 LYS Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 502 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 32 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 213 CYS Chi-restraints excluded: chain F residue 239 ARG Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 258 LYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 278 LYS Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 518 MET Chi-restraints excluded: chain F residue 525 CYS Chi-restraints excluded: chain F residue 610 LYS Chi-restraints excluded: chain F residue 651 ARG Chi-restraints excluded: chain F residue 656 CYS Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain T residue 200 LEU Chi-restraints excluded: chain T residue 235 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 79 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 163 optimal weight: 20.0000 chunk 73 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079731 restraints weight = 28338.107| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.71 r_work: 0.2908 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17417 Z= 0.116 Angle : 0.600 11.028 23535 Z= 0.317 Chirality : 0.043 0.252 2465 Planarity : 0.004 0.111 3098 Dihedral : 7.638 72.553 2469 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.25 % Favored : 91.29 % Rotamer: Outliers : 4.75 % Allowed : 28.75 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.05 % Twisted Proline : 1.18 % 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: -1.81 (0.17), residues: 2161 helix: -0.23 (0.32), residues: 285 sheet: -0.30 (0.19), residues: 719 loop : -2.11 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 682 TYR 0.015 0.001 TYR B 668 PHE 0.015 0.001 PHE A 684 TRP 0.014 0.001 TRP F 147 HIS 0.008 0.001 HIS F 617 Details of bonding type rmsd covalent geometry : bond 0.00267 (17394) covalent geometry : angle 0.59541 (23491) SS BOND : bond 0.00217 ( 22) SS BOND : angle 1.75745 ( 44) hydrogen bonds : bond 0.03237 ( 511) hydrogen bonds : angle 5.27116 ( 1422) Misc. bond : bond 0.00159 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6628.22 seconds wall clock time: 113 minutes 11.21 seconds (6791.21 seconds total)