Starting phenix.real_space_refine on Fri Jul 3 23:33:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cmg_45747/07_2026/9cmg_45747.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cmg_45747/07_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_45747/07_2026/9cmg_45747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cmg_45747/07_2026/9cmg_45747.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cmg_45747/07_2026/9cmg_45747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cmg_45747/07_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-dev-6108/lib/python3.11/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, 8 Ad-hoc single atom residues: {' FE': 2} Unusual residues: {'BCT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 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: 4.41, 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: 1.38 Conformation dependent library (CDL) restraints added in 731.2 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: 0.55 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: 2.90 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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 3.000 nonbonded pdb=" O1 BCT F 701 " pdb="FE FE F 704 " model vdw 1.969 3.000 nonbonded pdb=" O1 BCT F 702 " pdb="FE FE F 703 " model vdw 2.093 3.000 nonbonded pdb=" NE2 HIS F 268 " pdb="FE FE F 704 " model vdw 2.099 3.080 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.360 Find NCS groups from input model: 0.090 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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/Z covalent geometry : bond 0.00320 / 0.15 (16815) covalent geometry : angle 0.61583 / 0.33 (22714) SS BOND : bond 0.00349 / 0.23 ( 23) SS BOND : angle 0.98029 / 0.81 ( 46) hydrogen bonds : bond 0.21088 / 14.12 ( 595) hydrogen bonds : angle 8.12343 / 5.76 ( 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 : 0.625 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: 0.1300 time to fit residues: 45.3410 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 : 0.662 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3949 r_free = 0.3949 target = 0.130656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093861 restraints weight = 63561.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.098740 restraints weight = 24857.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100238 restraints weight = 11810.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100481 restraints weight = 9210.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101479 restraints weight = 8339.339| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 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 = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16838 Z= 0.212 Angle : 0.639 10.426 22760 Z= 0.339 Chirality : 0.044 0.194 2378 Planarity : 0.004 0.051 3002 Dihedral : 8.198 65.739 2452 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.65 % Favored : 93.30 % Rotamer: Outliers : 6.66 % Allowed : 23.78 % 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: -1.10 (0.18), residues: 2096 helix: -0.53 (0.33), residues: 247 sheet: -0.32 (0.20), residues: 666 loop : -0.98 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 93 TYR 0.017 0.002 TYR A 791 PHE 0.030 0.002 PHE B 216 TRP 0.011 0.002 TRP B 579 HIS 0.007 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (16815) covalent geometry : angle 0.63804 / 0.34 (22714) SS BOND : bond 0.00431 / 0.28 ( 23) SS BOND : angle 0.99101 / 0.66 ( 46) hydrogen bonds : bond 0.04241 / 2.87 ( 595) hydrogen bonds : angle 6.57313 / 4.64 ( 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 272 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 158 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7461 (mtt90) REVERT: A 114 ASP cc_start: 0.8307 (t0) cc_final: 0.7946 (t0) REVERT: A 154 SER cc_start: 0.9304 (m) cc_final: 0.8884 (t) REVERT: A 817 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8229 (mm-30) REVERT: A 832 SER cc_start: 0.9044 (p) cc_final: 0.8423 (m) REVERT: A 833 ARG cc_start: 0.8165 (mmm160) cc_final: 0.7397 (mtm110) REVERT: F 60 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6372 (tppt) REVERT: F 69 ARG cc_start: 0.8381 (ptm160) cc_final: 0.7989 (ptm-80) REVERT: F 223 PHE cc_start: 0.1941 (OUTLIER) cc_final: 0.1309 (m-80) REVERT: F 264 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7550 (pm20) REVERT: F 553 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8013 (ptmm) REVERT: F 556 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8149 (p) REVERT: B 69 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7376 (t80) REVERT: B 267 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8251 (t70) REVERT: B 319 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6101 (mp0) REVERT: B 513 MET cc_start: 0.6614 (ppp) cc_final: 0.6025 (pmm) REVERT: B 563 TYR cc_start: 0.7558 (m-80) cc_final: 0.6878 (m-80) REVERT: B 594 PHE cc_start: 0.8202 (m-80) cc_final: 0.7819 (m-80) outliers start: 114 outliers final: 71 residues processed: 254 average time/residue: 0.1225 time to fit residues: 47.7117 Evaluate side-chains 226 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 148 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 300 PHE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 353 VAL 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 663 VAL 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 793 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 468 SER Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 553 LYS Chi-restraints excluded: chain F residue 556 THR 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 656 CYS 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 300 THR Chi-restraints excluded: chain B residue 309 THR 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 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: 3.9990 chunk 51 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3961 r_free = 0.3961 target = 0.132839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097477 restraints weight = 66647.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.101349 restraints weight = 25062.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.104096 restraints weight = 11991.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103923 restraints weight = 8459.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.104083 restraints weight = 8064.788| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16838 Z= 0.207 Angle : 0.635 10.093 22760 Z= 0.335 Chirality : 0.044 0.193 2378 Planarity : 0.004 0.051 3002 Dihedral : 6.979 60.256 2381 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.32 % Favored : 93.64 % Rotamer: Outliers : 7.35 % Allowed : 23.38 % 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: -1.24 (0.18), residues: 2096 helix: -0.80 (0.31), residues: 261 sheet: -0.39 (0.20), residues: 669 loop : -1.05 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 239 TYR 0.024 0.002 TYR A 582 PHE 0.018 0.002 PHE B 348 TRP 0.012 0.002 TRP B 579 HIS 0.006 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (16815) covalent geometry : angle 0.63443 / 0.34 (22714) SS BOND : bond 0.00411 / 0.27 ( 23) SS BOND : angle 0.82175 / 0.53 ( 46) hydrogen bonds : bond 0.03833 / 2.60 ( 595) hydrogen bonds : angle 6.33554 / 4.47 ( 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 290 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 164 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8325 (t0) cc_final: 0.7984 (t0) REVERT: A 154 SER cc_start: 0.9285 (m) cc_final: 0.8864 (t) REVERT: A 550 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 832 SER cc_start: 0.9044 (p) cc_final: 0.8544 (m) REVERT: A 833 ARG cc_start: 0.8183 (mmm160) cc_final: 0.7349 (mtm110) REVERT: F 60 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6769 (tptp) REVERT: F 223 PHE cc_start: 0.2101 (OUTLIER) cc_final: 0.1442 (m-80) REVERT: F 264 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7513 (pm20) REVERT: F 315 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7732 (ptpp) REVERT: F 408 MET cc_start: 0.7580 (ptm) cc_final: 0.7376 (ptm) REVERT: F 556 THR cc_start: 0.8527 (m) cc_final: 0.8254 (p) REVERT: B 106 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9072 (mmtm) REVERT: B 209 ASP cc_start: 0.8792 (p0) cc_final: 0.8498 (p0) REVERT: B 319 GLU cc_start: 0.7619 (tm-30) cc_final: 0.6320 (mp0) REVERT: B 459 LYS cc_start: 0.8816 (tptt) cc_final: 0.8324 (tppt) REVERT: B 509 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8034 (tp) REVERT: B 564 ARG cc_start: 0.7154 (mpp80) cc_final: 0.6191 (mpp-170) REVERT: B 594 PHE cc_start: 0.8087 (m-80) cc_final: 0.7835 (m-80) outliers start: 126 outliers final: 85 residues processed: 271 average time/residue: 0.1275 time to fit residues: 53.3766 Evaluate side-chains 244 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 152 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 56 THR 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 143 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 300 PHE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 353 VAL 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 616 VAL 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 787 GLN Chi-restraints excluded: chain A residue 792 VAL 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 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 252 LYS 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 315 LYS 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 451 VAL Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 507 SER Chi-restraints excluded: chain F residue 511 SER 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 629 SER Chi-restraints excluded: chain F residue 638 PHE Chi-restraints excluded: chain F residue 640 LEU Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 656 CYS 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 82 SER 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 203 VAL Chi-restraints excluded: chain B residue 210 THR 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 309 THR Chi-restraints excluded: chain B residue 358 VAL 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: 9.9990 chunk 170 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** B 267 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.136821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.102358 restraints weight = 68792.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.106308 restraints weight = 25868.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.107914 restraints weight = 12952.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.108870 restraints weight = 8812.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.108867 restraints weight = 7813.263| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 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 = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1404 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= 0.109 Angle : 0.580 10.019 22760 Z= 0.303 Chirality : 0.043 0.174 2378 Planarity : 0.004 0.050 3002 Dihedral : 6.461 59.280 2370 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.55 % Favored : 94.40 % Rotamer: Outliers : 4.80 % Allowed : 25.69 % Favored : 69.50 % 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: -1.02 (0.18), residues: 2096 helix: -0.54 (0.32), residues: 254 sheet: -0.30 (0.19), residues: 686 loop : -0.89 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 427 TYR 0.018 0.001 TYR A 582 PHE 0.017 0.001 PHE B 59 TRP 0.012 0.001 TRP F 27 HIS 0.003 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (16815) covalent geometry : angle 0.58016 / 0.30 (22714) SS BOND : bond 0.00300 / 0.19 ( 23) SS BOND : angle 0.70223 / 0.48 ( 46) hydrogen bonds : bond 0.03192 / 2.16 ( 595) hydrogen bonds : angle 6.05659 / 4.28 ( 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 268 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 186 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 ASP cc_start: 0.8233 (t0) cc_final: 0.7901 (t0) REVERT: A 154 SER cc_start: 0.9285 (m) cc_final: 0.8838 (t) REVERT: A 550 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8559 (p) REVERT: A 817 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8074 (mm-30) REVERT: A 832 SER cc_start: 0.8995 (p) cc_final: 0.8528 (m) REVERT: A 833 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7163 (mtm110) REVERT: F 60 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6597 (tptp) REVERT: F 69 ARG cc_start: 0.8494 (ptm160) cc_final: 0.8138 (ptm-80) REVERT: F 223 PHE cc_start: 0.1773 (OUTLIER) cc_final: 0.1169 (m-80) REVERT: F 264 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: F 315 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7802 (ptpp) REVERT: F 395 ASP cc_start: 0.8635 (t70) cc_final: 0.8159 (t0) REVERT: B 106 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9081 (mmtm) REVERT: B 209 ASP cc_start: 0.8785 (p0) cc_final: 0.8526 (p0) REVERT: B 319 GLU cc_start: 0.7548 (tm-30) cc_final: 0.6281 (mp0) REVERT: B 342 GLU cc_start: 0.8153 (pm20) cc_final: 0.7626 (mp0) REVERT: B 416 LEU cc_start: 0.8401 (mt) cc_final: 0.8134 (mt) REVERT: B 459 LYS cc_start: 0.8845 (tptt) cc_final: 0.8284 (tppt) REVERT: B 495 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7225 (mtmm) REVERT: B 564 ARG cc_start: 0.7158 (mpp80) cc_final: 0.6280 (mpp-170) REVERT: B 594 PHE cc_start: 0.8005 (m-80) cc_final: 0.7781 (m-80) outliers start: 82 outliers final: 52 residues processed: 252 average time/residue: 0.1362 time to fit residues: 51.8742 Evaluate side-chains 220 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 299 ARG 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 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 838 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 888 VAL 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 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 315 LYS 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 642 ARG 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 106 LYS Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 292 TYR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 100 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 22 optimal weight: 0.0010 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3958 r_free = 0.3958 target = 0.131346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.094984 restraints weight = 68309.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.099540 restraints weight = 25811.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101981 restraints weight = 11966.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.102225 restraints weight = 8146.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102503 restraints weight = 8073.113| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16838 Z= 0.152 Angle : 0.591 10.011 22760 Z= 0.310 Chirality : 0.043 0.157 2378 Planarity : 0.004 0.051 3002 Dihedral : 6.223 58.295 2360 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 5.56 % Allowed : 25.12 % Favored : 69.33 % 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: -1.05 (0.18), residues: 2096 helix: -0.42 (0.33), residues: 247 sheet: -0.32 (0.19), residues: 692 loop : -0.95 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 881 TYR 0.020 0.001 TYR A 582 PHE 0.023 0.002 PHE B 216 TRP 0.017 0.001 TRP B 579 HIS 0.006 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (16815) covalent geometry : angle 0.59023 / 0.31 (22714) SS BOND : bond 0.00337 / 0.22 ( 23) SS BOND : angle 0.79714 / 0.57 ( 46) hydrogen bonds : bond 0.03334 / 2.29 ( 595) hydrogen bonds : angle 6.01190 / 4.24 ( 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 257 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 162 time to evaluate : 0.568 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: 0.8279 (t0) cc_final: 0.7887 (t0) REVERT: A 154 SER cc_start: 0.9264 (m) cc_final: 0.8785 (t) REVERT: A 550 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8576 (p) REVERT: A 817 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8165 (mm-30) REVERT: A 832 SER cc_start: 0.9007 (p) cc_final: 0.8526 (m) REVERT: A 833 ARG cc_start: 0.8153 (mmm160) cc_final: 0.7312 (mtm110) REVERT: F 60 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6687 (tptp) REVERT: F 69 ARG cc_start: 0.8456 (ptm160) cc_final: 0.8117 (ptm-80) REVERT: F 223 PHE cc_start: 0.1995 (OUTLIER) cc_final: 0.1353 (m-80) REVERT: F 264 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7449 (pm20) REVERT: F 315 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7822 (ptpp) REVERT: F 370 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8380 (mm-30) REVERT: F 395 ASP cc_start: 0.8681 (t70) cc_final: 0.8213 (t0) REVERT: B 106 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9098 (mmtm) REVERT: B 209 ASP cc_start: 0.8735 (p0) cc_final: 0.8407 (p0) REVERT: B 319 GLU cc_start: 0.7572 (tm-30) cc_final: 0.6207 (mp0) REVERT: B 342 GLU cc_start: 0.8165 (pm20) cc_final: 0.7467 (mp0) REVERT: B 343 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: B 459 LYS cc_start: 0.8859 (tptt) cc_final: 0.8257 (tppt) REVERT: B 495 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7272 (mtmm) REVERT: B 564 ARG cc_start: 0.7166 (mpp80) cc_final: 0.6142 (mpp-170) outliers start: 95 outliers final: 74 residues processed: 242 average time/residue: 0.1352 time to fit residues: 50.0848 Evaluate side-chains 239 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 157 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 69 SER 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 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 468 SER 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 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 798 ASP Chi-restraints excluded: chain A residue 811 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 315 LYS 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 376 GLU 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 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 642 ARG 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 272 THR 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 309 THR Chi-restraints excluded: chain B residue 343 GLU 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 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: 2.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 118 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.131020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093805 restraints weight = 88923.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.098878 restraints weight = 28985.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.100775 restraints weight = 13670.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101498 restraints weight = 8955.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.101894 restraints weight = 8352.457| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16838 Z= 0.163 Angle : 0.606 9.975 22760 Z= 0.314 Chirality : 0.043 0.176 2378 Planarity : 0.004 0.051 3002 Dihedral : 6.108 57.128 2356 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.17 % Favored : 93.78 % Rotamer: Outliers : 6.19 % Allowed : 24.88 % Favored : 68.92 % 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: -0.44 (0.33), residues: 252 sheet: -0.39 (0.20), residues: 686 loop : -0.93 (0.18), residues: 1158 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 0.019 0.002 PHE B 59 TRP 0.012 0.001 TRP F 147 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (16815) covalent geometry : angle 0.60566 / 0.31 (22714) SS BOND : bond 0.00355 / 0.23 ( 23) SS BOND : angle 0.73284 / 0.49 ( 46) hydrogen bonds : bond 0.03388 / 2.33 ( 595) hydrogen bonds : angle 5.99940 / 4.23 ( 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 267 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 161 time to evaluate : 0.535 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: 0.8276 (t0) cc_final: 0.7943 (t0) REVERT: A 154 SER cc_start: 0.9267 (m) cc_final: 0.8829 (t) REVERT: A 510 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7101 (tmm) REVERT: A 550 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8559 (p) REVERT: A 817 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8172 (mm-30) REVERT: A 832 SER cc_start: 0.9001 (p) cc_final: 0.8531 (m) REVERT: A 833 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7325 (mtm110) REVERT: F 60 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6784 (tptp) REVERT: F 69 ARG cc_start: 0.8437 (ptm160) cc_final: 0.8103 (ptm-80) REVERT: F 223 PHE cc_start: 0.2041 (OUTLIER) cc_final: 0.1384 (m-80) REVERT: F 264 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: F 315 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7826 (ptpp) REVERT: F 380 ASN cc_start: 0.8987 (OUTLIER) cc_final: 0.8769 (t0) REVERT: F 395 ASP cc_start: 0.8650 (t70) cc_final: 0.8123 (t0) REVERT: B 209 ASP cc_start: 0.8686 (p0) cc_final: 0.8465 (p0) REVERT: B 319 GLU cc_start: 0.7587 (tm-30) cc_final: 0.6185 (mp0) REVERT: B 342 GLU cc_start: 0.8176 (pm20) cc_final: 0.7498 (mp0) REVERT: B 343 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: B 459 LYS cc_start: 0.8854 (tptt) cc_final: 0.8182 (tppt) REVERT: B 495 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7316 (mtmm) REVERT: B 594 PHE cc_start: 0.7819 (m-80) cc_final: 0.7600 (m-80) outliers start: 106 outliers final: 79 residues processed: 250 average time/residue: 0.1184 time to fit residues: 45.1211 Evaluate side-chains 245 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 157 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 112 THR 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 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 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 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 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 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 315 LYS 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 380 ASN 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 548 ASP Chi-restraints excluded: chain F residue 549 VAL 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 642 ARG 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 272 THR 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 309 THR Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 349 LEU 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 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: 0.9980 chunk 92 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 91 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 382 ASN ** A 433 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.134036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.097699 restraints weight = 91644.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102500 restraints weight = 29684.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.105579 restraints weight = 12710.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105123 restraints weight = 9337.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105440 restraints weight = 8745.296| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16838 Z= 0.146 Angle : 0.612 9.942 22760 Z= 0.316 Chirality : 0.043 0.163 2378 Planarity : 0.004 0.051 3002 Dihedral : 6.075 56.552 2356 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 5.50 % Allowed : 25.41 % 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: -1.06 (0.18), residues: 2096 helix: -0.44 (0.33), residues: 252 sheet: -0.39 (0.20), residues: 686 loop : -0.90 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 239 TYR 0.035 0.001 TYR B 563 PHE 0.019 0.002 PHE B 59 TRP 0.011 0.001 TRP F 283 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16815) covalent geometry : angle 0.61172 / 0.32 (22714) SS BOND : bond 0.00339 / 0.22 ( 23) SS BOND : angle 0.68914 / 0.45 ( 46) hydrogen bonds : bond 0.03360 / 2.32 ( 595) hydrogen bonds : angle 5.99769 / 4.22 ( 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 256 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 162 time to evaluate : 0.439 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 50 ARG cc_start: 0.7987 (mtt180) cc_final: 0.7464 (mtt90) REVERT: A 114 ASP cc_start: 0.8252 (t0) cc_final: 0.7931 (t0) REVERT: A 154 SER cc_start: 0.9325 (m) cc_final: 0.8876 (t) REVERT: A 510 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7140 (tmm) REVERT: A 550 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8547 (p) REVERT: A 817 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8179 (mm-30) REVERT: A 832 SER cc_start: 0.8978 (p) cc_final: 0.8650 (m) REVERT: A 833 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7179 (mtm110) REVERT: F 69 ARG cc_start: 0.8420 (ptm160) cc_final: 0.8098 (ptm-80) REVERT: F 223 PHE cc_start: 0.2150 (OUTLIER) cc_final: 0.1496 (m-80) REVERT: F 264 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7108 (pm20) REVERT: F 315 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7805 (ptpp) REVERT: F 395 ASP cc_start: 0.8619 (t70) cc_final: 0.8092 (t0) REVERT: B 209 ASP cc_start: 0.8706 (p0) cc_final: 0.8481 (p0) REVERT: B 319 GLU cc_start: 0.7626 (tm-30) cc_final: 0.6126 (mp0) REVERT: B 342 GLU cc_start: 0.8156 (pm20) cc_final: 0.7548 (mp0) REVERT: B 343 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7540 (mt-10) REVERT: B 459 LYS cc_start: 0.8756 (tptt) cc_final: 0.8260 (tppt) REVERT: B 495 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7352 (mtmm) REVERT: B 594 PHE cc_start: 0.7832 (m-80) cc_final: 0.7482 (m-80) REVERT: B 667 LYS cc_start: 0.8915 (tppt) cc_final: 0.8671 (tptp) outliers start: 94 outliers final: 78 residues processed: 242 average time/residue: 0.1194 time to fit residues: 44.3273 Evaluate side-chains 244 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 159 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 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 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 798 ASP Chi-restraints excluded: chain A residue 811 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 28 CYS Chi-restraints excluded: chain F residue 38 CYS Chi-restraints excluded: chain F residue 59 VAL 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 315 LYS 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 549 VAL 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 642 ARG 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 250 THR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 295 LEU 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 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 696 THR 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: 0.0050 chunk 20 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 96 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN F 623 GLN ** B 704 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 = 0.4003 r_free = 0.4003 target = 0.135703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101918 restraints weight = 57792.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.106222 restraints weight = 22264.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.107822 restraints weight = 10763.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.107913 restraints weight = 8259.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.108248 restraints weight = 8064.696| |-----------------------------------------------------------------------------| 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 = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16838 Z= 0.111 Angle : 0.592 10.705 22760 Z= 0.302 Chirality : 0.042 0.155 2378 Planarity : 0.004 0.051 3002 Dihedral : 5.822 57.019 2352 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 4.75 % Allowed : 25.98 % 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: -0.99 (0.18), residues: 2096 helix: -0.38 (0.33), residues: 254 sheet: -0.33 (0.19), residues: 696 loop : -0.87 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 239 TYR 0.036 0.001 TYR B 563 PHE 0.021 0.001 PHE B 59 TRP 0.015 0.001 TRP B 674 HIS 0.004 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (16815) covalent geometry : angle 0.59181 / 0.30 (22714) SS BOND : bond 0.00279 / 0.17 ( 23) SS BOND : angle 0.62699 / 0.40 ( 46) hydrogen bonds : bond 0.03123 / 2.15 ( 595) hydrogen bonds : angle 5.84804 / 4.13 ( 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 249 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 168 time to evaluate : 0.595 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 50 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7435 (mtt90) REVERT: A 114 ASP cc_start: 0.8303 (t0) cc_final: 0.7958 (t0) REVERT: A 154 SER cc_start: 0.9248 (m) cc_final: 0.8772 (t) REVERT: A 510 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7168 (tmm) REVERT: A 809 MET cc_start: 0.7399 (ptp) cc_final: 0.6984 (mtm) REVERT: A 817 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 832 SER cc_start: 0.9111 (p) cc_final: 0.8816 (m) REVERT: A 833 ARG cc_start: 0.7966 (mmm160) cc_final: 0.7213 (mtm110) REVERT: F 69 ARG cc_start: 0.8435 (ptm160) cc_final: 0.8113 (ptm-80) REVERT: F 223 PHE cc_start: 0.2073 (OUTLIER) cc_final: 0.1416 (m-80) REVERT: F 264 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: F 315 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7697 (ptpp) REVERT: F 380 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8686 (t0) REVERT: F 395 ASP cc_start: 0.8560 (t70) cc_final: 0.7998 (t0) REVERT: F 479 TRP cc_start: 0.9043 (t-100) cc_final: 0.8838 (t-100) REVERT: B 209 ASP cc_start: 0.8734 (p0) cc_final: 0.8509 (p0) REVERT: B 319 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6104 (mp0) REVERT: B 342 GLU cc_start: 0.8132 (pm20) cc_final: 0.7528 (mp0) REVERT: B 343 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: B 459 LYS cc_start: 0.8735 (tptt) cc_final: 0.8233 (tppt) REVERT: B 495 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7300 (mtmm) REVERT: B 594 PHE cc_start: 0.7716 (m-80) cc_final: 0.7375 (m-80) outliers start: 81 outliers final: 65 residues processed: 235 average time/residue: 0.1160 time to fit residues: 42.1050 Evaluate side-chains 234 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 162 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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 510 MET Chi-restraints excluded: chain A residue 537 ILE 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 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 811 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 28 CYS Chi-restraints excluded: chain F residue 38 CYS Chi-restraints excluded: chain F residue 59 VAL 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 315 LYS 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 380 ASN 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 548 ASP Chi-restraints excluded: chain F residue 615 CYS 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 642 ARG 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 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 292 TYR Chi-restraints excluded: chain B residue 295 LEU 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 141 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 51 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 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 = 0.4005 r_free = 0.4005 target = 0.135805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100438 restraints weight = 83598.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.104759 restraints weight = 28368.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107421 restraints weight = 12947.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.107660 restraints weight = 8528.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.107915 restraints weight = 7771.049| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1986 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 : 0.594 10.931 22760 Z= 0.303 Chirality : 0.042 0.163 2378 Planarity : 0.004 0.051 3002 Dihedral : 5.759 57.379 2352 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.65 % Favored : 94.31 % Rotamer: Outliers : 4.63 % Allowed : 26.27 % 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: -0.97 (0.18), residues: 2096 helix: -0.35 (0.32), residues: 254 sheet: -0.31 (0.19), residues: 692 loop : -0.86 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 239 TYR 0.037 0.001 TYR B 563 PHE 0.023 0.001 PHE F 627 TRP 0.022 0.001 TRP F 27 HIS 0.004 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (16815) covalent geometry : angle 0.59363 / 0.30 (22714) SS BOND : bond 0.00281 / 0.18 ( 23) SS BOND : angle 0.65161 / 0.43 ( 46) hydrogen bonds : bond 0.03088 / 2.13 ( 595) hydrogen bonds : angle 5.80387 / 4.11 ( 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 249 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 170 time to evaluate : 0.705 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 50 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7437 (mtt90) REVERT: A 114 ASP cc_start: 0.8261 (t0) cc_final: 0.7958 (t0) REVERT: A 154 SER cc_start: 0.9274 (m) cc_final: 0.8810 (t) REVERT: A 510 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7104 (tmm) REVERT: A 755 TRP cc_start: 0.5549 (OUTLIER) cc_final: 0.5193 (p90) REVERT: A 817 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8082 (mm-30) REVERT: A 832 SER cc_start: 0.9183 (p) cc_final: 0.8786 (m) REVERT: A 833 ARG cc_start: 0.7994 (mmm160) cc_final: 0.7338 (mtm110) REVERT: F 69 ARG cc_start: 0.8430 (ptm160) cc_final: 0.8112 (ptm-80) REVERT: F 264 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: F 315 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7878 (mtmm) REVERT: F 395 ASP cc_start: 0.8542 (t70) cc_final: 0.7971 (t0) REVERT: B 209 ASP cc_start: 0.8724 (p0) cc_final: 0.8503 (p0) REVERT: B 319 GLU cc_start: 0.7497 (tm-30) cc_final: 0.6084 (mp0) REVERT: B 342 GLU cc_start: 0.8115 (pm20) cc_final: 0.7533 (mp0) REVERT: B 343 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: B 495 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7294 (mtmm) REVERT: B 594 PHE cc_start: 0.7630 (m-80) cc_final: 0.7299 (m-80) outliers start: 79 outliers final: 58 residues processed: 235 average time/residue: 0.1391 time to fit residues: 50.3223 Evaluate side-chains 228 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 164 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 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 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 811 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 264 GLN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 315 LYS Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain F residue 374 CYS 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 548 ASP 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 642 ARG 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 76 GLU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 295 LEU 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 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 696 THR 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: 8.9990 chunk 54 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN ** F 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN F 623 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.130805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.094244 restraints weight = 79823.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.098813 restraints weight = 28127.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.100894 restraints weight = 13370.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101516 restraints weight = 8903.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.101734 restraints weight = 8139.070| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16838 Z= 0.187 Angle : 0.642 12.639 22760 Z= 0.331 Chirality : 0.044 0.196 2378 Planarity : 0.004 0.052 3002 Dihedral : 5.847 57.962 2348 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.36 % Favored : 93.59 % Rotamer: Outliers : 4.86 % Allowed : 26.22 % Favored : 68.92 % 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: -1.04 (0.18), residues: 2096 helix: -0.34 (0.33), residues: 254 sheet: -0.38 (0.20), residues: 678 loop : -0.91 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 239 TYR 0.052 0.002 TYR B 563 PHE 0.028 0.002 PHE F 627 TRP 0.057 0.002 TRP F 479 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (16815) covalent geometry : angle 0.64089 / 0.33 (22714) SS BOND : bond 0.00517 / 0.30 ( 23) SS BOND : angle 1.00854 / 0.61 ( 46) hydrogen bonds : bond 0.03446 / 2.36 ( 595) hydrogen bonds : angle 5.90944 / 4.16 ( 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 251 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 168 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7447 (mtt90) REVERT: A 114 ASP cc_start: 0.8291 (t0) cc_final: 0.7958 (t0) REVERT: A 154 SER cc_start: 0.9280 (m) cc_final: 0.8842 (t) REVERT: A 510 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7084 (tmm) REVERT: A 817 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8131 (mm-30) REVERT: A 832 SER cc_start: 0.9164 (p) cc_final: 0.8780 (m) REVERT: A 833 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7260 (mtm110) REVERT: F 69 ARG cc_start: 0.8383 (ptm160) cc_final: 0.8073 (ptm-80) REVERT: F 264 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7105 (pm20) REVERT: F 380 ASN cc_start: 0.9022 (OUTLIER) cc_final: 0.8781 (t0) REVERT: F 395 ASP cc_start: 0.8641 (t70) cc_final: 0.8075 (t0) REVERT: B 209 ASP cc_start: 0.8755 (p0) cc_final: 0.8505 (p0) REVERT: B 319 GLU cc_start: 0.7583 (tm-30) cc_final: 0.6073 (mp0) REVERT: B 342 GLU cc_start: 0.8150 (pm20) cc_final: 0.7573 (mp0) REVERT: B 343 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: B 460 PHE cc_start: 0.7751 (p90) cc_final: 0.7486 (p90) REVERT: B 495 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7396 (mtmm) REVERT: B 594 PHE cc_start: 0.7878 (m-80) cc_final: 0.7545 (m-80) outliers start: 83 outliers final: 70 residues processed: 236 average time/residue: 0.1350 time to fit residues: 49.1950 Evaluate side-chains 235 residues out of total 1755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 160 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 69 SER Chi-restraints excluded: chain A residue 73 VAL 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 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 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 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 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 38 CYS Chi-restraints excluded: chain F residue 59 VAL 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 380 ASN 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 548 ASP 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 629 SER Chi-restraints excluded: chain F residue 638 PHE 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 687 SER Chi-restraints excluded: chain F residue 695 PHE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 295 LEU 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 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 696 THR 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: 0.0770 chunk 208 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 195 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 184 optimal weight: 0.0770 chunk 171 optimal weight: 0.6980 overall best weight: 1.1498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 GLN ** 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 = 0.3951 r_free = 0.3951 target = 0.130836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.094685 restraints weight = 73488.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.099341 restraints weight = 26665.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.101628 restraints weight = 12565.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.101828 restraints weight = 8881.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.102273 restraints weight = 7834.843| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16838 Z= 0.189 Angle : 0.834 59.187 22760 Z= 0.471 Chirality : 0.044 0.217 2378 Planarity : 0.004 0.052 3002 Dihedral : 5.865 57.889 2348 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.22 % Favored : 93.73 % Rotamer: Outliers : 4.75 % Allowed : 26.22 % Favored : 69.04 % Cbeta Deviations : 0.05 % 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: -1.05 (0.18), residues: 2096 helix: -0.37 (0.33), residues: 254 sheet: -0.39 (0.20), residues: 680 loop : -0.90 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 564 TYR 0.038 0.002 TYR B 563 PHE 0.022 0.002 PHE F 627 TRP 0.046 0.002 TRP F 479 HIS 0.005 0.001 HIS A 440 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (16815) covalent geometry : angle 0.83133 / 0.47 (22714) SS BOND : bond 0.00527 / 0.28 ( 23) SS BOND : angle 1.77513 / 1.06 ( 46) hydrogen bonds : bond 0.03430 / 2.34 ( 595) hydrogen bonds : angle 5.91555 / 4.17 ( 1584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3142.08 seconds wall clock time: 55 minutes 13.14 seconds (3313.14 seconds total)