Starting phenix.real_space_refine on Mon Apr 6 07:16:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cmg_45747/04_2026/9cmg_45747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cmg_45747/04_2026/9cmg_45747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cmg_45747/04_2026/9cmg_45747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cmg_45747/04_2026/9cmg_45747.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cmg_45747/04_2026/9cmg_45747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cmg_45747/04_2026/9cmg_45747.map" } resolution = 3.71 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= 0.005 sd= 0.045 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 2 7.16 5 S 69 5.16 5 C 10282 2.51 5 N 2910 2.21 5 O 3197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 16460 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6735 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 859, 6713 Classifications: {'peptide': 859} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 12, 'PTRANS': 23, 'TRANS': 823} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 859, 6713 Classifications: {'peptide': 859} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 12, 'PTRANS': 23, 'TRANS': 823} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 6836 Chain: "F" Number of atoms: 5198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5198 Classifications: {'peptide': 677} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 28, 'TRANS': 643} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4517 Classifications: {'peptide': 576} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 21, 'TRANS': 551} Chain breaks: 6 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 10 Unusual residues: {' FE': 2, 'BCT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 825 " occ=0.54 ... (20 atoms not shown) pdb=" NH2BARG A 825 " occ=0.46 Time building chain proxies: 4.44, per 1000 atoms: 0.27 Number of scatterers: 16460 At special positions: 0 Unit cell: (148.5, 125.4, 146.85, 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 2 26.01 S 69 16.00 O 3197 8.00 N 2910 7.00 C 10282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, 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=2.02 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=2.03 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=2.02 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 503 " 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=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 933.7 milliseconds 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 22 sheets defined 18.7% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 50 through 55 removed outlier: 3.560A pdb=" N ASN A 53 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU A 54 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 55 " --> pdb=" O ASP A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 50 through 55' Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 75 through 80 removed outlier: 4.176A pdb=" N THR A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.817A pdb=" N CYS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 652 through 658 removed outlier: 3.546A pdb=" N GLY A 658 " --> pdb=" O ALA A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 822 removed outlier: 3.614A pdb=" N GLU A 820 " --> pdb=" O GLU A 817 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 822 " --> pdb=" O THR A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 881 removed outlier: 3.884A pdb=" N VAL A 880 " --> pdb=" O THR A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 884 No H-bonds generated for 'chain 'A' and resid 882 through 884' Processing helix chain 'A' and resid 896 through 901 removed outlier: 3.757A pdb=" N ARG A 899 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 49 Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'F' and resid 82 through 84 No H-bonds generated for 'chain 'F' and resid 82 through 84' Processing helix chain 'F' and resid 85 through 91 Processing helix chain 'F' and resid 121 through 125 removed outlier: 3.732A pdb=" N GLY F 125 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'F' and resid 149 through 158 removed outlier: 3.779A pdb=" N LEU F 153 " --> pdb=" O ILE F 149 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N CYS F 156 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 172 Processing helix chain 'F' and resid 186 through 191 removed outlier: 3.899A pdb=" N GLN F 191 " --> pdb=" O GLN F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 227 through 233 removed outlier: 4.162A pdb=" N GLU F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 240 Processing helix chain 'F' and resid 278 through 294 removed outlier: 3.501A pdb=" N ILE F 282 " --> pdb=" O LYS F 278 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 335 removed outlier: 3.956A pdb=" N LEU F 334 " --> pdb=" O ALA F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 367 through 381 removed outlier: 3.602A pdb=" N LYS F 373 " --> pdb=" O HIS F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 402 Processing helix chain 'F' and resid 411 through 422 Processing helix chain 'F' and resid 436 through 440 Processing helix chain 'F' and resid 480 through 491 removed outlier: 3.854A pdb=" N LYS F 489 " --> pdb=" O LEU F 485 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 520 through 524 Processing helix chain 'F' and resid 534 through 546 Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 567 through 571 removed outlier: 3.971A pdb=" N LYS F 571 " --> pdb=" O PRO F 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 591 through 596 removed outlier: 4.980A pdb=" N ALA F 594 " --> pdb=" O GLU F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 627 removed outlier: 3.577A pdb=" N LYS F 618 " --> pdb=" O ALA F 614 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG F 621 " --> pdb=" O HIS F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 647 removed outlier: 4.148A pdb=" N LYS F 646 " --> pdb=" O SER F 643 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP F 647 " --> pdb=" O GLU F 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 643 through 647' Processing helix chain 'F' and resid 665 through 671 Processing helix chain 'F' and resid 671 through 680 removed outlier: 3.744A pdb=" N VAL F 675 " --> pdb=" O GLY F 671 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN F 680 " --> pdb=" O LYS F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 681 through 685 Processing helix chain 'F' and resid 687 through 694 removed outlier: 3.804A pdb=" N GLU F 691 " --> pdb=" O SER F 687 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR F 694 " --> pdb=" O LEU F 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.691A pdb=" N LYS B 73 " --> pdb=" O PRO B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 665 through 668 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 64 removed outlier: 6.881A pdb=" N GLN A 174 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A 151 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA A 172 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE A 153 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER A 170 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 197 removed outlier: 4.407A pdb=" N VAL A 397 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY A 394 " --> pdb=" O CYS A 446 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N CYS A 446 " --> pdb=" O GLY A 394 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 465 through 485 current: chain 'A' and resid 494 through 510 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 494 through 510 current: chain 'A' and resid 556 through 560 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 556 through 560 current: chain 'A' and resid 596 through 610 removed outlier: 9.262A pdb=" N LEU A 624 " --> pdb=" O PHE A 648 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE A 648 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TRP A 626 " --> pdb=" O THR A 646 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLN A 729 " --> pdb=" O ASP A 702 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE A 704 " --> pdb=" O ASN A 727 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASN A 727 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG A 706 " --> pdb=" O TYR A 725 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR A 725 " --> pdb=" O ARG A 706 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR A 708 " --> pdb=" O PRO A 723 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N ALA A 710 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N GLY A 721 " --> pdb=" O ALA A 710 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 756 through 766 current: chain 'A' and resid 804 through 813 Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 250 Processing sheet with id=AA4, first strand: chain 'A' and resid 277 through 278 removed outlier: 7.487A pdb=" N TYR A 257 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL A 549 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE A 259 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE A 551 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 382 Processing sheet with id=AA6, first strand: chain 'A' and resid 823 through 826 Processing sheet with id=AA7, first strand: chain 'F' and resid 24 through 29 removed outlier: 5.719A pdb=" N VAL F 25 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL F 59 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TRP F 27 " --> pdb=" O VAL F 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 79 through 81 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 79 through 81 current: chain 'F' and resid 110 through 111 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 113 through 120 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 113 through 120 current: chain 'F' and resid 173 through 176 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 361 through 366 Processing sheet with id=AB2, first strand: chain 'F' and resid 408 through 410 removed outlier: 4.264A pdb=" N LEU F 427 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR F 608 " --> pdb=" O PRO F 425 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA F 428 " --> pdb=" O ALA F 658 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS F 656 " --> pdb=" O ASN F 430 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 445 through 452 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 445 through 452 current: chain 'F' and resid 501 through 502 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 501 through 502 current: chain 'F' and resid 588 through 589 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AB5, first strand: chain 'B' and resid 76 through 77 removed outlier: 3.625A pdb=" N THR B 210 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 141 through 142 Processing sheet with id=AB7, first strand: chain 'B' and resid 163 through 165 Processing sheet with id=AB8, first strand: chain 'B' and resid 191 through 193 Processing sheet with id=AB9, first strand: chain 'B' and resid 197 through 208 removed outlier: 3.969A pdb=" N ALA B 297 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG B 277 " --> pdb=" O GLN B 291 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLN B 291 " --> pdb=" O ARG B 277 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N PHE B 304 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER B 333 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY B 306 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER B 331 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER B 331 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 349 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 413 through 415 removed outlier: 3.540A pdb=" N GLY B 512 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 424 through 427 Processing sheet with id=AC3, first strand: chain 'B' and resid 579 through 581 removed outlier: 4.375A pdb=" N ALA B 676 " --> pdb=" O LYS B 658 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYS B 658 " --> pdb=" O ALA B 676 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 639 through 640 removed outlier: 3.761A pdb=" N PHE B 639 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 652 " --> pdb=" O PHE B 639 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 595 hydrogen bonds defined for protein. 1584 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: 3.01 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5523 1.34 - 1.46: 4026 1.46 - 1.58: 7174 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 16815 Sorted by residual: bond pdb=" CB LYS F 167 " pdb=" CG LYS F 167 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" CA VAL A 345 " pdb=" CB VAL A 345 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.29e-02 6.01e+03 1.56e+00 bond pdb=" CA VAL B 413 " pdb=" CB VAL B 413 " ideal model delta sigma weight residual 1.530 1.543 -0.012 1.05e-02 9.07e+03 1.37e+00 bond pdb=" N GLY B 154 " pdb=" CA GLY B 154 " ideal model delta sigma weight residual 1.453 1.443 0.010 8.60e-03 1.35e+04 1.30e+00 bond pdb=" C SER A 97 " pdb=" N GLY A 98 " ideal model delta sigma weight residual 1.331 1.314 0.016 1.46e-02 4.69e+03 1.25e+00 ... (remaining 16810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 22305 1.92 - 3.83: 358 3.83 - 5.75: 35 5.75 - 7.67: 13 7.67 - 9.59: 3 Bond angle restraints: 22714 Sorted by residual: angle pdb=" C CYS F 634 " pdb=" CA CYS F 634 " pdb=" CB CYS F 634 " ideal model delta sigma weight residual 117.23 111.42 5.81 1.36e+00 5.41e-01 1.82e+01 angle pdb=" N ARG A 594 " pdb=" CA ARG A 594 " pdb=" C ARG A 594 " ideal model delta sigma weight residual 113.02 108.20 4.82 1.20e+00 6.94e-01 1.61e+01 angle pdb=" CA CYS F 634 " pdb=" C CYS F 634 " pdb=" N SER F 635 " ideal model delta sigma weight residual 119.98 116.81 3.17 8.50e-01 1.38e+00 1.39e+01 angle pdb=" CB LYS B 167 " pdb=" CG LYS B 167 " pdb=" CD LYS B 167 " ideal model delta sigma weight residual 111.30 118.82 -7.52 2.30e+00 1.89e-01 1.07e+01 angle pdb=" CB LYS F 167 " pdb=" CG LYS F 167 " pdb=" CD LYS F 167 " ideal model delta sigma weight residual 111.30 118.58 -7.28 2.30e+00 1.89e-01 1.00e+01 ... (remaining 22709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 8611 17.79 - 35.58: 1091 35.58 - 53.36: 295 53.36 - 71.15: 44 71.15 - 88.94: 20 Dihedral angle restraints: 10061 sinusoidal: 4012 harmonic: 6049 Sorted by residual: dihedral pdb=" CB CYS F 374 " pdb=" SG CYS F 374 " pdb=" SG CYS F 387 " pdb=" CB CYS F 387 " ideal model delta sinusoidal sigma weight residual 93.00 175.44 -82.44 1 1.00e+01 1.00e-02 8.34e+01 dihedral pdb=" CB CYS A 562 " pdb=" SG CYS A 562 " pdb=" SG CYS A 572 " pdb=" CB CYS A 572 " ideal model delta sinusoidal sigma weight residual 93.00 21.48 71.52 1 1.00e+01 1.00e-02 6.56e+01 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 -154.81 68.81 1 1.00e+01 1.00e-02 6.13e+01 ... (remaining 10058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1698 0.041 - 0.082: 512 0.082 - 0.122: 149 0.122 - 0.163: 17 0.163 - 0.204: 2 Chirality restraints: 2378 Sorted by residual: chirality pdb=" CB ILE A 778 " pdb=" CA ILE A 778 " pdb=" CG1 ILE A 778 " pdb=" CG2 ILE A 778 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE A 230 " pdb=" CA ILE A 230 " pdb=" CG1 ILE A 230 " pdb=" CG2 ILE A 230 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.63e-01 chirality pdb=" CA ASP F 647 " pdb=" N ASP F 647 " pdb=" C ASP F 647 " pdb=" CB ASP F 647 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 2375 not shown) Planarity restraints: 3002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 49 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO F 50 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 50 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 50 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 27 " -0.011 2.00e-02 2.50e+03 1.05e-02 2.76e+00 pdb=" CG TRP F 27 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP F 27 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP F 27 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 27 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 27 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 27 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 27 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 27 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 27 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 555 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO B 556 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 556 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 556 " 0.022 5.00e-02 4.00e+02 ... (remaining 2999 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 209 2.55 - 3.14: 13012 3.14 - 3.73: 25872 3.73 - 4.31: 34244 4.31 - 4.90: 57882 Nonbonded interactions: 131219 Sorted by model distance: nonbonded pdb=" OH TYR F 536 " pdb="FE FE F 703 " model vdw 1.964 2.260 nonbonded pdb=" O1 BCT F 701 " pdb="FE FE F 704 " model vdw 1.969 2.260 nonbonded pdb=" O1 BCT F 702 " pdb="FE FE F 703 " model vdw 2.093 2.260 nonbonded pdb=" NE2 HIS F 268 " pdb="FE FE F 704 " model vdw 2.099 2.340 nonbonded pdb=" OH TYR F 536 " pdb=" O1 BCT F 702 " model vdw 2.107 3.040 ... (remaining 131214 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.080 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 0.040 16838 Z= 0.147 Angle : 0.617 9.587 22760 Z= 0.331 Chirality : 0.042 0.204 2378 Planarity : 0.004 0.050 3002 Dihedral : 16.785 88.939 6152 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.86 % Allowed : 25.58 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.18), residues: 2096 helix: -0.32 (0.36), residues: 222 sheet: -0.24 (0.20), residues: 679 loop : -0.86 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 217 TYR 0.018 0.001 TYR A 582 PHE 0.024 0.001 PHE F 41 TRP 0.028 0.002 TRP F 27 HIS 0.006 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00320 (16815) covalent geometry : angle 0.61583 (22714) SS BOND : bond 0.00349 ( 23) SS BOND : angle 0.98029 ( 46) hydrogen bonds : bond 0.21088 ( 595) hydrogen bonds : angle 8.12343 ( 1584) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 159 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 SER cc_start: 0.9325 (m) cc_final: 0.8908 (t) REVERT: A 718 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8059 (pp20) REVERT: A 755 TRP cc_start: 0.5636 (OUTLIER) cc_final: 0.5171 (p90) REVERT: A 817 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8212 (mm-30) REVERT: A 832 SER cc_start: 0.9073 (p) cc_final: 0.8398 (m) REVERT: A 833 ARG cc_start: 0.8065 (mmm160) cc_final: 0.7409 (mtm110) REVERT: F 23 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7602 (tmtt) REVERT: F 60 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6111 (tppt) REVERT: F 223 PHE cc_start: 0.1876 (OUTLIER) cc_final: 0.1178 (m-80) REVERT: F 553 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7985 (ptmm) REVERT: F 662 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8066 (t70) REVERT: B 69 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7650 (t80) REVERT: B 319 GLU cc_start: 0.6944 (tm-30) cc_final: 0.5847 (mp0) REVERT: B 564 ARG cc_start: 0.7017 (mpp80) cc_final: 0.6270 (mpp-170) REVERT: B 594 PHE cc_start: 0.7673 (m-80) cc_final: 0.7193 (m-80) outliers start: 83 outliers final: 68 residues processed: 226 average time/residue: 0.1232 time to fit residues: 42.8660 Evaluate side-chains 232 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 156 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 675 SER Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 718 GLU Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 912 GLU Chi-restraints excluded: chain F residue 23 LYS Chi-restraints excluded: chain F residue 45 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 148 ASN Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 462 ASN Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 553 LYS Chi-restraints excluded: chain F residue 556 THR Chi-restraints excluded: chain F residue 625 HIS Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 629 SER Chi-restraints excluded: chain F residue 638 PHE Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 653 ASP Chi-restraints excluded: chain F residue 656 CYS Chi-restraints excluded: chain F residue 662 ASP Chi-restraints excluded: chain F residue 684 CYS Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 507 ASN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.3980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 531 GLN ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 HIS ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 623 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.130930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094461 restraints weight = 64251.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.099215 restraints weight = 24825.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101741 restraints weight = 11612.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.101911 restraints weight = 8574.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101961 restraints weight = 7275.902| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16838 Z= 0.193 Angle : 0.629 10.325 22760 Z= 0.333 Chirality : 0.044 0.193 2378 Planarity : 0.004 0.051 3002 Dihedral : 8.167 66.173 2452 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.51 % Favored : 93.44 % Rotamer: Outliers : 6.25 % Allowed : 24.07 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.18), residues: 2096 helix: -0.64 (0.33), residues: 254 sheet: -0.31 (0.20), residues: 670 loop : -0.96 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 456 TYR 0.016 0.002 TYR A 791 PHE 0.029 0.002 PHE B 216 TRP 0.013 0.002 TRP B 579 HIS 0.006 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00441 (16815) covalent geometry : angle 0.62783 (22714) SS BOND : bond 0.00407 ( 23) SS BOND : angle 0.96083 ( 46) hydrogen bonds : bond 0.04073 ( 595) hydrogen bonds : angle 6.49557 ( 1584) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 159 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7988 (mtt180) cc_final: 0.7488 (mtt90) REVERT: A 114 ASP cc_start: 0.8318 (t0) cc_final: 0.7951 (t0) REVERT: A 154 SER cc_start: 0.9304 (m) cc_final: 0.8873 (t) REVERT: A 437 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8854 (mt) REVERT: A 817 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8220 (mm-30) REVERT: A 832 SER cc_start: 0.9041 (p) cc_final: 0.8406 (m) REVERT: A 833 ARG cc_start: 0.8173 (mmm160) cc_final: 0.7425 (mtm110) REVERT: F 60 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6307 (tppt) REVERT: F 69 ARG cc_start: 0.8395 (ptm160) cc_final: 0.8010 (ptm-80) REVERT: F 223 PHE cc_start: 0.1871 (OUTLIER) cc_final: 0.1258 (m-80) REVERT: F 264 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: F 395 ASP cc_start: 0.8657 (t70) cc_final: 0.8237 (t0) REVERT: F 553 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8034 (ptmm) REVERT: F 556 THR cc_start: 0.8464 (m) cc_final: 0.8208 (p) REVERT: B 69 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7385 (t80) REVERT: B 267 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.8164 (t70) REVERT: B 319 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6035 (mp0) REVERT: B 513 MET cc_start: 0.6606 (ppp) cc_final: 0.6023 (pmm) REVERT: B 563 TYR cc_start: 0.7553 (m-80) cc_final: 0.6856 (m-80) REVERT: B 594 PHE cc_start: 0.8142 (m-80) cc_final: 0.7731 (m-80) outliers start: 107 outliers final: 65 residues processed: 250 average time/residue: 0.1197 time to fit residues: 45.8602 Evaluate side-chains 223 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 151 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 264 GLN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 415 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 553 LYS Chi-restraints excluded: chain F residue 629 SER Chi-restraints excluded: chain F residue 638 PHE Chi-restraints excluded: chain F residue 642 ARG Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 65 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 44 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 623 GLN ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN B 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.133099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.098236 restraints weight = 67103.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.101854 restraints weight = 25482.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.103798 restraints weight = 12627.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.104575 restraints weight = 8643.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104596 restraints weight = 8104.559| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16838 Z= 0.179 Angle : 0.617 9.942 22760 Z= 0.325 Chirality : 0.043 0.182 2378 Planarity : 0.004 0.054 3002 Dihedral : 6.933 61.035 2380 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 6.89 % Allowed : 24.02 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.18), residues: 2096 helix: -0.76 (0.31), residues: 261 sheet: -0.34 (0.20), residues: 673 loop : -0.99 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 239 TYR 0.023 0.001 TYR A 582 PHE 0.017 0.002 PHE B 348 TRP 0.013 0.001 TRP B 579 HIS 0.006 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00408 (16815) covalent geometry : angle 0.61638 (22714) SS BOND : bond 0.00372 ( 23) SS BOND : angle 0.82518 ( 46) hydrogen bonds : bond 0.03727 ( 595) hydrogen bonds : angle 6.28556 ( 1584) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 163 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8322 (t0) cc_final: 0.7986 (t0) REVERT: A 154 SER cc_start: 0.9284 (m) cc_final: 0.8858 (t) REVERT: A 437 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8828 (mt) REVERT: A 550 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8601 (p) REVERT: A 832 SER cc_start: 0.9026 (p) cc_final: 0.8526 (m) REVERT: A 833 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7292 (mtm110) REVERT: F 60 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6657 (tptp) REVERT: F 69 ARG cc_start: 0.8419 (ptm160) cc_final: 0.8057 (ptm-80) REVERT: F 223 PHE cc_start: 0.2050 (OUTLIER) cc_final: 0.1442 (m-80) REVERT: F 264 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: F 395 ASP cc_start: 0.8682 (t70) cc_final: 0.8240 (t0) REVERT: F 556 THR cc_start: 0.8437 (m) cc_final: 0.8189 (p) REVERT: B 106 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9069 (mmtm) REVERT: B 209 ASP cc_start: 0.8790 (p0) cc_final: 0.8490 (p0) REVERT: B 229 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7585 (mtp85) REVERT: B 267 HIS cc_start: 0.8417 (OUTLIER) cc_final: 0.8207 (t70) REVERT: B 319 GLU cc_start: 0.7594 (tm-30) cc_final: 0.6310 (mp0) REVERT: B 509 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7984 (tp) REVERT: B 513 MET cc_start: 0.6648 (ppp) cc_final: 0.6176 (pmm) REVERT: B 564 ARG cc_start: 0.7202 (mpp80) cc_final: 0.6260 (mpp-170) REVERT: B 594 PHE cc_start: 0.8173 (m-80) cc_final: 0.7905 (m-80) outliers start: 118 outliers final: 80 residues processed: 263 average time/residue: 0.1212 time to fit residues: 49.5050 Evaluate side-chains 239 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 150 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 264 GLN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 400 ILE Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 415 VAL Chi-restraints excluded: chain F residue 448 VAL Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 629 SER Chi-restraints excluded: chain F residue 638 PHE Chi-restraints excluded: chain F residue 640 LEU Chi-restraints excluded: chain F residue 642 ARG Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain F residue 695 PHE Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 188 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 169 optimal weight: 0.0050 chunk 128 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 185 optimal weight: 0.0980 chunk 43 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN F 623 GLN ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.136049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.101646 restraints weight = 69167.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.105476 restraints weight = 25792.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.107787 restraints weight = 12521.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.108041 restraints weight = 8776.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.108333 restraints weight = 7414.159| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16838 Z= 0.106 Angle : 0.577 9.945 22760 Z= 0.301 Chirality : 0.042 0.167 2378 Planarity : 0.004 0.050 3002 Dihedral : 6.515 60.142 2373 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.60 % Favored : 94.35 % Rotamer: Outliers : 4.69 % Allowed : 25.58 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.18), residues: 2096 helix: -0.65 (0.31), residues: 261 sheet: -0.27 (0.19), residues: 690 loop : -0.90 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 703 TYR 0.017 0.001 TYR A 582 PHE 0.018 0.001 PHE B 216 TRP 0.011 0.001 TRP F 27 HIS 0.003 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00235 (16815) covalent geometry : angle 0.57692 (22714) SS BOND : bond 0.00305 ( 23) SS BOND : angle 0.65655 ( 46) hydrogen bonds : bond 0.03185 ( 595) hydrogen bonds : angle 6.04704 ( 1584) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 177 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8251 (t0) cc_final: 0.7897 (t0) REVERT: A 154 SER cc_start: 0.9295 (m) cc_final: 0.8863 (t) REVERT: A 550 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8553 (p) REVERT: A 755 TRP cc_start: 0.5606 (OUTLIER) cc_final: 0.5186 (p90) REVERT: A 817 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8054 (mm-30) REVERT: A 832 SER cc_start: 0.8982 (p) cc_final: 0.8504 (m) REVERT: A 833 ARG cc_start: 0.8128 (mmm160) cc_final: 0.7143 (mtm110) REVERT: F 37 LYS cc_start: 0.7949 (mmtm) cc_final: 0.7716 (mmtt) REVERT: F 60 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6372 (tptp) REVERT: F 69 ARG cc_start: 0.8428 (ptm160) cc_final: 0.8097 (ptm-80) REVERT: F 223 PHE cc_start: 0.1874 (OUTLIER) cc_final: 0.1262 (m-80) REVERT: F 264 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: F 395 ASP cc_start: 0.8608 (t70) cc_final: 0.8117 (t0) REVERT: B 106 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.9076 (mmtm) REVERT: B 229 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7506 (mtp85) REVERT: B 267 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.8118 (t70) REVERT: B 319 GLU cc_start: 0.7520 (tm-30) cc_final: 0.6268 (mp0) REVERT: B 342 GLU cc_start: 0.8168 (pm20) cc_final: 0.7650 (mp0) REVERT: B 459 LYS cc_start: 0.8760 (tptt) cc_final: 0.8286 (tppt) REVERT: B 495 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7242 (mtmm) REVERT: B 564 ARG cc_start: 0.7209 (mpp80) cc_final: 0.6330 (mpp-170) REVERT: B 594 PHE cc_start: 0.8032 (m-80) cc_final: 0.7801 (m-80) outliers start: 80 outliers final: 48 residues processed: 244 average time/residue: 0.1271 time to fit residues: 47.0757 Evaluate side-chains 217 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 264 GLN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 690 LEU Chi-restraints excluded: chain F residue 695 PHE Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 587 THR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 100 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 180 optimal weight: 0.0370 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 235 ASN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 623 GLN ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.101910 restraints weight = 69529.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105487 restraints weight = 25533.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.108109 restraints weight = 12324.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.108380 restraints weight = 8100.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.108555 restraints weight = 7584.252| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16838 Z= 0.114 Angle : 0.570 10.016 22760 Z= 0.297 Chirality : 0.042 0.156 2378 Planarity : 0.004 0.050 3002 Dihedral : 6.105 59.961 2361 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 4.98 % Allowed : 25.35 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.18), residues: 2096 helix: -0.43 (0.32), residues: 253 sheet: -0.24 (0.19), residues: 684 loop : -0.90 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 881 TYR 0.017 0.001 TYR A 582 PHE 0.018 0.001 PHE B 216 TRP 0.010 0.001 TRP F 27 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00256 (16815) covalent geometry : angle 0.56963 (22714) SS BOND : bond 0.00268 ( 23) SS BOND : angle 0.63348 ( 46) hydrogen bonds : bond 0.03139 ( 595) hydrogen bonds : angle 5.93132 ( 1584) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 165 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8290 (t0) cc_final: 0.7929 (t0) REVERT: A 154 SER cc_start: 0.9300 (m) cc_final: 0.8854 (t) REVERT: A 550 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8544 (p) REVERT: A 755 TRP cc_start: 0.5445 (OUTLIER) cc_final: 0.5159 (p90) REVERT: A 817 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8100 (mm-30) REVERT: A 832 SER cc_start: 0.8973 (p) cc_final: 0.8525 (m) REVERT: A 833 ARG cc_start: 0.8107 (mmm160) cc_final: 0.7112 (mtm110) REVERT: F 60 LYS cc_start: 0.6892 (OUTLIER) cc_final: 0.6409 (tptp) REVERT: F 69 ARG cc_start: 0.8429 (ptm160) cc_final: 0.8112 (ptm-80) REVERT: F 223 PHE cc_start: 0.1767 (OUTLIER) cc_final: 0.1146 (m-80) REVERT: F 264 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: F 370 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8377 (mm-30) REVERT: F 395 ASP cc_start: 0.8612 (t70) cc_final: 0.8122 (t0) REVERT: B 106 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9071 (mmtm) REVERT: B 229 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7531 (mtp85) REVERT: B 267 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.8072 (t70) REVERT: B 342 GLU cc_start: 0.8141 (pm20) cc_final: 0.7410 (mp0) REVERT: B 343 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7457 (mt-10) REVERT: B 459 LYS cc_start: 0.8868 (tptt) cc_final: 0.8294 (tppt) REVERT: B 495 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7225 (mtmm) REVERT: B 564 ARG cc_start: 0.7152 (mpp80) cc_final: 0.6174 (mpp-170) REVERT: B 579 TRP cc_start: 0.7551 (t-100) cc_final: 0.7318 (t-100) outliers start: 85 outliers final: 58 residues processed: 238 average time/residue: 0.1300 time to fit residues: 46.9192 Evaluate side-chains 224 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 156 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain F residue 38 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 264 GLN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 638 PHE Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 695 PHE Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 140 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 202 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 193 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 623 GLN ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.135874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.100282 restraints weight = 90319.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.105038 restraints weight = 29387.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.106951 restraints weight = 13321.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.107607 restraints weight = 8761.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.107951 restraints weight = 8512.212| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16838 Z= 0.122 Angle : 0.579 9.991 22760 Z= 0.300 Chirality : 0.042 0.160 2378 Planarity : 0.004 0.050 3002 Dihedral : 5.934 58.904 2357 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.69 % Favored : 94.26 % Rotamer: Outliers : 5.50 % Allowed : 25.06 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.18), residues: 2096 helix: -0.41 (0.33), residues: 253 sheet: -0.24 (0.19), residues: 691 loop : -0.88 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 642 TYR 0.017 0.001 TYR A 582 PHE 0.020 0.001 PHE B 59 TRP 0.012 0.001 TRP F 147 HIS 0.004 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00277 (16815) covalent geometry : angle 0.57898 (22714) SS BOND : bond 0.00320 ( 23) SS BOND : angle 0.62974 ( 46) hydrogen bonds : bond 0.03098 ( 595) hydrogen bonds : angle 5.86314 ( 1584) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 161 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8257 (t0) cc_final: 0.7907 (t0) REVERT: A 154 SER cc_start: 0.9264 (m) cc_final: 0.8811 (t) REVERT: A 510 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7128 (tmm) REVERT: A 550 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8543 (p) REVERT: A 755 TRP cc_start: 0.5475 (OUTLIER) cc_final: 0.5156 (p90) REVERT: A 817 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8102 (mm-30) REVERT: A 832 SER cc_start: 0.8961 (p) cc_final: 0.8555 (m) REVERT: A 833 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7139 (mtm110) REVERT: F 60 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6443 (tptt) REVERT: F 69 ARG cc_start: 0.8451 (ptm160) cc_final: 0.8134 (ptm-80) REVERT: F 155 TYR cc_start: 0.7726 (t80) cc_final: 0.7512 (t80) REVERT: F 223 PHE cc_start: 0.1866 (OUTLIER) cc_final: 0.1226 (m-80) REVERT: F 264 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7374 (pm20) REVERT: F 395 ASP cc_start: 0.8597 (t70) cc_final: 0.8088 (t0) REVERT: F 587 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7737 (mtm-85) REVERT: B 106 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9070 (mmtm) REVERT: B 229 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7519 (mtp85) REVERT: B 267 HIS cc_start: 0.8264 (OUTLIER) cc_final: 0.8060 (t70) REVERT: B 342 GLU cc_start: 0.8126 (pm20) cc_final: 0.7446 (mp0) REVERT: B 343 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: B 459 LYS cc_start: 0.8867 (tptt) cc_final: 0.8303 (tppt) REVERT: B 495 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7255 (mtmm) REVERT: B 594 PHE cc_start: 0.7608 (m-80) cc_final: 0.7246 (m-80) outliers start: 94 outliers final: 70 residues processed: 240 average time/residue: 0.1245 time to fit residues: 45.4281 Evaluate side-chains 238 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 156 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain F residue 38 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 264 GLN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 548 ASP Chi-restraints excluded: chain F residue 587 ARG Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 621 ARG Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 638 PHE Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 695 PHE Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 267 HIS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 4 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 199 optimal weight: 20.0000 chunk 91 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 623 GLN F 625 HIS ** B 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.135120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099394 restraints weight = 92301.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.104214 restraints weight = 29831.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.106049 restraints weight = 13666.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.106743 restraints weight = 9013.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107060 restraints weight = 8149.404| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16838 Z= 0.142 Angle : 0.592 9.974 22760 Z= 0.307 Chirality : 0.043 0.158 2378 Planarity : 0.004 0.050 3002 Dihedral : 5.954 57.957 2357 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.12 % Favored : 93.83 % Rotamer: Outliers : 5.73 % Allowed : 24.59 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 2096 helix: -0.37 (0.33), residues: 252 sheet: -0.34 (0.19), residues: 695 loop : -0.88 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 703 TYR 0.030 0.001 TYR B 563 PHE 0.019 0.001 PHE B 59 TRP 0.021 0.001 TRP B 579 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00324 (16815) covalent geometry : angle 0.59041 (22714) SS BOND : bond 0.00349 ( 23) SS BOND : angle 1.06175 ( 46) hydrogen bonds : bond 0.03251 ( 595) hydrogen bonds : angle 5.88954 ( 1584) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 161 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8259 (t0) cc_final: 0.7917 (t0) REVERT: A 154 SER cc_start: 0.9280 (m) cc_final: 0.8829 (t) REVERT: A 510 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7139 (tmm) REVERT: A 550 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8537 (p) REVERT: A 755 TRP cc_start: 0.5588 (OUTLIER) cc_final: 0.5234 (p90) REVERT: A 817 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 832 SER cc_start: 0.8969 (p) cc_final: 0.8725 (m) REVERT: A 833 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7052 (mtm110) REVERT: F 60 LYS cc_start: 0.6938 (OUTLIER) cc_final: 0.6386 (tptp) REVERT: F 69 ARG cc_start: 0.8436 (ptm160) cc_final: 0.8114 (ptm-80) REVERT: F 223 PHE cc_start: 0.1886 (OUTLIER) cc_final: 0.1214 (m-80) REVERT: F 264 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: F 395 ASP cc_start: 0.8611 (t70) cc_final: 0.8073 (t0) REVERT: B 106 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9096 (mmtm) REVERT: B 229 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7532 (mtp85) REVERT: B 319 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6148 (mp0) REVERT: B 342 GLU cc_start: 0.8120 (pm20) cc_final: 0.7460 (mp0) REVERT: B 343 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: B 459 LYS cc_start: 0.8878 (tptt) cc_final: 0.8301 (tppt) REVERT: B 495 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7337 (mtmm) REVERT: B 594 PHE cc_start: 0.7745 (m-80) cc_final: 0.7358 (m-80) outliers start: 98 outliers final: 72 residues processed: 245 average time/residue: 0.1193 time to fit residues: 45.0076 Evaluate side-chains 235 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 153 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain F residue 38 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 264 GLN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 548 ASP Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 621 ARG Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 638 PHE Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 695 PHE Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 563 TYR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 104 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 623 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.131033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.095508 restraints weight = 58061.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099776 restraints weight = 22737.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101843 restraints weight = 10856.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.102031 restraints weight = 7998.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.102150 restraints weight = 7519.916| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16838 Z= 0.163 Angle : 0.611 9.942 22760 Z= 0.317 Chirality : 0.043 0.177 2378 Planarity : 0.004 0.050 3002 Dihedral : 6.015 57.473 2357 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.12 % Favored : 93.83 % Rotamer: Outliers : 5.38 % Allowed : 25.35 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.18), residues: 2096 helix: -0.47 (0.32), residues: 260 sheet: -0.41 (0.19), residues: 704 loop : -0.92 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 456 TYR 0.020 0.001 TYR A 582 PHE 0.023 0.002 PHE B 59 TRP 0.014 0.002 TRP B 579 HIS 0.005 0.001 HIS F 604 Details of bonding type rmsd covalent geometry : bond 0.00373 (16815) covalent geometry : angle 0.61034 (22714) SS BOND : bond 0.00376 ( 23) SS BOND : angle 0.96713 ( 46) hydrogen bonds : bond 0.03271 ( 595) hydrogen bonds : angle 5.87929 ( 1584) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 159 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8298 (t0) cc_final: 0.7928 (t0) REVERT: A 154 SER cc_start: 0.9264 (m) cc_final: 0.8797 (t) REVERT: A 510 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7106 (tmm) REVERT: A 550 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8553 (p) REVERT: A 817 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8143 (mm-30) REVERT: A 832 SER cc_start: 0.9105 (p) cc_final: 0.8681 (m) REVERT: A 833 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7285 (mtm110) REVERT: F 69 ARG cc_start: 0.8404 (ptm160) cc_final: 0.8081 (ptm-80) REVERT: F 223 PHE cc_start: 0.2089 (OUTLIER) cc_final: 0.1429 (m-80) REVERT: F 264 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: F 395 ASP cc_start: 0.8619 (t70) cc_final: 0.8072 (t0) REVERT: B 229 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7526 (mtp85) REVERT: B 319 GLU cc_start: 0.7509 (tm-30) cc_final: 0.6093 (mp0) REVERT: B 342 GLU cc_start: 0.8142 (pm20) cc_final: 0.7496 (mp0) REVERT: B 343 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: B 458 ARG cc_start: 0.6811 (tpt-90) cc_final: 0.6544 (tpt-90) REVERT: B 459 LYS cc_start: 0.8842 (tptt) cc_final: 0.8337 (tppt) REVERT: B 495 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7365 (mtmm) REVERT: B 594 PHE cc_start: 0.7616 (m-80) cc_final: 0.7263 (m-80) outliers start: 92 outliers final: 76 residues processed: 238 average time/residue: 0.1213 time to fit residues: 44.2735 Evaluate side-chains 238 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 155 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 38 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 264 GLN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 548 ASP Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 621 ARG Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 638 PHE Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 695 PHE Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 141 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 623 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.131020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093998 restraints weight = 84164.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.098936 restraints weight = 28055.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.101034 restraints weight = 12931.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.101606 restraints weight = 8610.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.102071 restraints weight = 7816.829| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16838 Z= 0.163 Angle : 0.616 10.182 22760 Z= 0.319 Chirality : 0.043 0.182 2378 Planarity : 0.004 0.051 3002 Dihedral : 5.976 58.276 2353 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 5.67 % Allowed : 25.46 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.18), residues: 2096 helix: -0.54 (0.32), residues: 261 sheet: -0.42 (0.19), residues: 691 loop : -0.93 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 456 TYR 0.031 0.001 TYR B 563 PHE 0.022 0.002 PHE B 59 TRP 0.052 0.002 TRP F 479 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00374 (16815) covalent geometry : angle 0.61470 (22714) SS BOND : bond 0.00521 ( 23) SS BOND : angle 0.98012 ( 46) hydrogen bonds : bond 0.03370 ( 595) hydrogen bonds : angle 5.92879 ( 1584) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 157 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7438 (mtt90) REVERT: A 114 ASP cc_start: 0.8251 (t0) cc_final: 0.7934 (t0) REVERT: A 154 SER cc_start: 0.9265 (m) cc_final: 0.8823 (t) REVERT: A 510 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7107 (tmm) REVERT: A 550 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8542 (p) REVERT: A 817 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8148 (mm-30) REVERT: A 832 SER cc_start: 0.9150 (p) cc_final: 0.8704 (m) REVERT: A 833 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7321 (mtm110) REVERT: F 69 ARG cc_start: 0.8387 (ptm160) cc_final: 0.8057 (ptm-80) REVERT: F 223 PHE cc_start: 0.2109 (OUTLIER) cc_final: 0.1439 (m-80) REVERT: F 264 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7355 (pm20) REVERT: F 395 ASP cc_start: 0.8620 (t70) cc_final: 0.8033 (t0) REVERT: B 229 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7540 (mtp85) REVERT: B 319 GLU cc_start: 0.7510 (tm-30) cc_final: 0.6089 (mp0) REVERT: B 342 GLU cc_start: 0.8141 (pm20) cc_final: 0.7519 (mp0) REVERT: B 343 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: B 459 LYS cc_start: 0.8839 (tptt) cc_final: 0.8245 (tppt) REVERT: B 495 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7382 (mtmm) REVERT: B 594 PHE cc_start: 0.7824 (m-80) cc_final: 0.7489 (m-80) outliers start: 97 outliers final: 82 residues processed: 239 average time/residue: 0.1244 time to fit residues: 45.9488 Evaluate side-chains 240 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 151 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 38 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 264 GLN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 548 ASP Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 621 ARG Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 638 PHE Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 695 PHE Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 118 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 623 GLN B 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.129472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.093045 restraints weight = 80494.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097578 restraints weight = 28584.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099310 restraints weight = 13730.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.099964 restraints weight = 9706.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.100342 restraints weight = 8591.431| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16838 Z= 0.219 Angle : 0.655 10.556 22760 Z= 0.341 Chirality : 0.045 0.209 2378 Planarity : 0.004 0.051 3002 Dihedral : 6.119 59.115 2353 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.46 % Favored : 93.44 % Rotamer: Outliers : 5.50 % Allowed : 25.69 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.18), residues: 2096 helix: -0.59 (0.32), residues: 260 sheet: -0.49 (0.19), residues: 684 loop : -1.01 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 456 TYR 0.024 0.002 TYR B 563 PHE 0.016 0.002 PHE A 441 TRP 0.041 0.002 TRP F 479 HIS 0.006 0.001 HIS F 604 Details of bonding type rmsd covalent geometry : bond 0.00504 (16815) covalent geometry : angle 0.65449 (22714) SS BOND : bond 0.00434 ( 23) SS BOND : angle 1.02184 ( 46) hydrogen bonds : bond 0.03512 ( 595) hydrogen bonds : angle 6.00788 ( 1584) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 153 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8316 (t0) cc_final: 0.7974 (t0) REVERT: A 154 SER cc_start: 0.9290 (m) cc_final: 0.8880 (t) REVERT: A 510 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7031 (tmm) REVERT: A 550 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8571 (p) REVERT: A 817 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8184 (mm-30) REVERT: A 832 SER cc_start: 0.9160 (p) cc_final: 0.8721 (m) REVERT: A 833 ARG cc_start: 0.8080 (mmm160) cc_final: 0.7387 (mtm110) REVERT: F 69 ARG cc_start: 0.8416 (ptm160) cc_final: 0.8074 (ptm-80) REVERT: F 223 PHE cc_start: 0.2238 (OUTLIER) cc_final: 0.1537 (m-80) REVERT: F 264 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: F 324 VAL cc_start: 0.9503 (p) cc_final: 0.9229 (m) REVERT: F 395 ASP cc_start: 0.8696 (t70) cc_final: 0.8134 (t0) REVERT: B 229 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7537 (mtp85) REVERT: B 319 GLU cc_start: 0.7581 (tm-30) cc_final: 0.6113 (mp0) REVERT: B 342 GLU cc_start: 0.8159 (pm20) cc_final: 0.7578 (mp0) REVERT: B 343 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: B 459 LYS cc_start: 0.8759 (tptt) cc_final: 0.8334 (tppt) REVERT: B 495 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7438 (mtmm) REVERT: B 594 PHE cc_start: 0.7857 (m-80) cc_final: 0.7501 (m-80) outliers start: 94 outliers final: 83 residues processed: 233 average time/residue: 0.1266 time to fit residues: 45.3070 Evaluate side-chains 242 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 152 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 510 MET Chi-restraints excluded: chain A residue 537 ILE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 582 TYR Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 713 LYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 755 TRP Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 819 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 888 VAL Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain F residue 28 CYS Chi-restraints excluded: chain F residue 38 CYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 223 PHE Chi-restraints excluded: chain F residue 264 GLN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 374 CYS Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 396 CYS Chi-restraints excluded: chain F residue 404 GLU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain F residue 548 ASP Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 619 ILE Chi-restraints excluded: chain F residue 621 ARG Chi-restraints excluded: chain F residue 626 LEU Chi-restraints excluded: chain F residue 638 PHE Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 678 VAL Chi-restraints excluded: chain F residue 687 SER Chi-restraints excluded: chain F residue 695 PHE Chi-restraints excluded: chain B residue 69 TYR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain B residue 495 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 9 optimal weight: 0.6980 chunk 208 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 13 optimal weight: 0.0570 chunk 195 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 HIS ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 623 GLN B 267 HIS ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.131439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095372 restraints weight = 73716.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099775 restraints weight = 26327.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.101634 restraints weight = 12714.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.102394 restraints weight = 8498.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.102833 restraints weight = 7784.748| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16838 Z= 0.137 Angle : 0.614 10.962 22760 Z= 0.316 Chirality : 0.043 0.162 2378 Planarity : 0.004 0.051 3002 Dihedral : 5.967 59.988 2353 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.31 % Rotamer: Outliers : 5.27 % Allowed : 25.98 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.74 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.18), residues: 2096 helix: -0.56 (0.32), residues: 260 sheet: -0.46 (0.19), residues: 689 loop : -0.94 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 881 TYR 0.021 0.001 TYR F 578 PHE 0.016 0.001 PHE F 627 TRP 0.035 0.002 TRP F 479 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd covalent geometry : bond 0.00313 (16815) covalent geometry : angle 0.61367 (22714) SS BOND : bond 0.00331 ( 23) SS BOND : angle 0.88769 ( 46) hydrogen bonds : bond 0.03194 ( 595) hydrogen bonds : angle 5.88403 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2977.06 seconds wall clock time: 52 minutes 11.67 seconds (3131.67 seconds total)