Starting phenix.real_space_refine on Sat Aug 23 15:49:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gcd_29931/08_2025/8gcd_29931.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gcd_29931/08_2025/8gcd_29931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gcd_29931/08_2025/8gcd_29931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gcd_29931/08_2025/8gcd_29931.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gcd_29931/08_2025/8gcd_29931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gcd_29931/08_2025/8gcd_29931.map" } resolution = 2.97 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= -0.000 sd= 0.091 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: 7 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 100 5.16 5 C 7960 2.51 5 N 2163 2.21 5 O 2500 1.98 5 H 384 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13115 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7401 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 939, 7390 Classifications: {'peptide': 939} Link IDs: {'PCIS': 3, 'PTRANS': 59, 'TRANS': 876} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 939, 7390 Classifications: {'peptide': 939} Link IDs: {'PCIS': 3, 'PTRANS': 59, 'TRANS': 876} Chain breaks: 2 bond proxies already assigned to first conformer: 7545 Chain: "B" Number of atoms: 5507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 697, 5507 Classifications: {'peptide': 697} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 664} Chain breaks: 3 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 47 Unusual residues: {' CA': 5, 'NAG': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 78 residue: pdb=" N PRO B 605 " occ=0.75 ... (5 atoms not shown) pdb=" CD PRO B 605 " occ=0.75 residue: pdb=" N ASP B 606 " occ=0.75 ... (6 atoms not shown) pdb=" OD2 ASP B 606 " occ=0.75 residue: pdb=" N ALA B 607 " occ=0.75 ... (3 atoms not shown) pdb=" CB ALA B 607 " occ=0.75 residue: pdb=" N CYS B 608 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS B 608 " occ=0.75 residue: pdb=" N THR B 609 " occ=0.75 ... (5 atoms not shown) pdb=" CG2 THR B 609 " occ=0.75 residue: pdb=" N PHE B 610 " occ=0.75 ... (9 atoms not shown) pdb=" CZ PHE B 610 " occ=0.75 residue: pdb=" N LYS B 611 " occ=0.75 ... (7 atoms not shown) pdb=" NZ LYS B 611 " occ=0.75 residue: pdb=" N LYS B 612 " occ=0.75 ... (7 atoms not shown) pdb=" NZ LYS B 612 " occ=0.75 residue: pdb=" N GLU B 613 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU B 613 " occ=0.75 residue: pdb=" N CYS B 614 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS B 614 " occ=0.75 residue: pdb=" N VAL B 615 " occ=0.75 ... (5 atoms not shown) pdb=" CG2 VAL B 615 " occ=0.75 residue: pdb=" N GLU B 616 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU B 616 " occ=0.75 ... (remaining 66 not shown) Time building chain proxies: 3.85, per 1000 atoms: 0.29 Number of scatterers: 13115 At special positions: 0 Unit cell: (94.16, 153.01, 148.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 7 19.99 S 100 16.00 Mg 1 11.99 O 2500 8.00 N 2163 7.00 C 7960 6.00 H 384 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS A 473 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 602 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 890 " distance=2.02 Simple disulfide: pdb=" SG CYS A 880 " - pdb=" SG CYS A 885 " distance=2.03 Simple disulfide: pdb=" SG CYS B 5 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 435 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 38 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 49 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 433 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 460 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 508 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 528 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 547 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 558 " distance=2.01 Simple disulfide: pdb=" SG CYS B 560 " - pdb=" SG CYS B 583 " distance=2.04 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 588 " - pdb=" SG CYS B 598 " distance=2.05 Simple disulfide: pdb=" SG CYS B 601 " - pdb=" SG CYS B 604 " distance=2.10 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 655 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 631 " distance=2.03 Simple disulfide: pdb=" SG CYS B 663 " - pdb=" SG CYS B 687 " 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 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " BMA C 3 " - " BMA C 5 " NAG-ASN " NAG A1106 " - " ASN A 15 " " NAG A1107 " - " ASN A 570 " " NAG A1108 " - " ASN A 249 " " NAG C 1 " - " ASN B 320 " " NAG D 1 " - " ASN B 371 " " NAG E 1 " - " ASN B 559 " " NAG F 1 " - " ASN B 99 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 600.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2998 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 30 sheets defined 14.2% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.681A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 259 through 264 removed outlier: 3.648A pdb=" N THR A 263 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.768A pdb=" N ARG A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 558 removed outlier: 3.509A pdb=" N PHE A 558 " --> pdb=" O GLU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 606 removed outlier: 3.873A pdb=" N ASP A 605 " --> pdb=" O CYS A 602 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 606 " --> pdb=" O GLY A 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 602 through 606' Processing helix chain 'A' and resid 666 through 670 removed outlier: 3.692A pdb=" N PHE A 669 " --> pdb=" O VAL A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 removed outlier: 4.373A pdb=" N GLY A 714 " --> pdb=" O GLU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 915 removed outlier: 3.767A pdb=" N LEU A 914 " --> pdb=" O TRP A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 985 Processing helix chain 'B' and resid 12 through 20 removed outlier: 4.241A pdb=" N SER B 20 " --> pdb=" O CYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 126 through 134 removed outlier: 3.584A pdb=" N TRP B 129 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B 131 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN B 132 " --> pdb=" O TRP B 129 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN B 133 " --> pdb=" O SER B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.572A pdb=" N GLN B 141 " --> pdb=" O LYS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.637A pdb=" N LEU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 removed outlier: 4.019A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.600A pdb=" N VAL B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.716A pdb=" N ARG B 261 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 314 through 323 removed outlier: 3.673A pdb=" N GLU B 323 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.502A pdb=" N GLN B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 534 through 538 removed outlier: 3.558A pdb=" N SER B 537 " --> pdb=" O GLU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 611 removed outlier: 3.828A pdb=" N PHE B 610 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 606 through 611' Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 694 through 712 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.694A pdb=" N THR A 9 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 28 removed outlier: 4.449A pdb=" N ASP A 28 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 87 removed outlier: 3.696A pdb=" N HIS A 112 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 125 " --> pdb=" O TRP A 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 239 through 242 removed outlier: 3.772A pdb=" N ILE A 269 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS A 278 " --> pdb=" O ILE A 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 296 removed outlier: 3.503A pdb=" N THR A 296 " --> pdb=" O ASP A 305 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 345 " --> pdb=" O LEU A 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AB1, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.556A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.313A pdb=" N SER A 483 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 544 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.502A pdb=" N CYS A 490 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL A 454 " --> pdb=" O HIS A 587 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 530 through 536 Processing sheet with id=AB5, first strand: chain 'A' and resid 612 through 619 removed outlier: 3.993A pdb=" N GLU A 632 " --> pdb=" O THR A 619 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 697 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 704 " --> pdb=" O ARG A 661 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER A 706 " --> pdb=" O TYR A 659 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TYR A 659 " --> pdb=" O SER A 706 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 623 through 624 removed outlier: 6.085A pdb=" N LEU A 623 " --> pdb=" O ARG A 743 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLN A 720 " --> pdb=" O HIS A 652 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A 647 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 689 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 651 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 683 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 748 through 749 removed outlier: 3.927A pdb=" N HIS A 787 " --> pdb=" O GLU A 749 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 758 through 761 Processing sheet with id=AB9, first strand: chain 'A' and resid 797 through 798 Processing sheet with id=AC1, first strand: chain 'A' and resid 801 through 804 Processing sheet with id=AC2, first strand: chain 'A' and resid 815 through 818 removed outlier: 5.666A pdb=" N LEU A 906 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.645A pdb=" N TRP B 25 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 61 through 65 removed outlier: 6.834A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 88 " --> pdb=" O GLN B 428 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE B 414 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 97 through 100 removed outlier: 3.551A pdb=" N ALA B 401 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AC7, first strand: chain 'B' and resid 194 through 197 removed outlier: 5.900A pdb=" N THR B 195 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE B 153 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET B 118 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 156 " --> pdb=" O MET B 118 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS B 244 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE B 307 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 246 " --> pdb=" O ILE B 307 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.503A pdb=" N VAL B 355 " --> pdb=" O CYS B 386 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS B 386 " --> pdb=" O VAL B 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 499 through 502 Processing sheet with id=AD1, first strand: chain 'B' and resid 540 through 543 removed outlier: 3.569A pdb=" N GLN B 541 " --> pdb=" O LEU B 548 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 579 through 582 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 658 removed outlier: 4.058A pdb=" N TYR B 657 " --> pdb=" O VAL B 665 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 665 " --> pdb=" O TYR B 657 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 795 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: 2.26 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 384 1.04 - 1.24: 1308 1.24 - 1.43: 4188 1.43 - 1.63: 7359 1.63 - 1.83: 129 Bond restraints: 13368 Sorted by residual: bond pdb=" C VAL A 742 " pdb=" N ARG A 743 " ideal model delta sigma weight residual 1.328 1.515 -0.187 1.04e-02 9.25e+03 3.23e+02 bond pdb=" CA ARG A 743 " pdb=" C ARG A 743 " ideal model delta sigma weight residual 1.528 1.707 -0.179 1.23e-02 6.61e+03 2.12e+02 bond pdb=" C ARG A 743 " pdb=" N ALA A 744 " ideal model delta sigma weight residual 1.331 1.510 -0.179 1.30e-02 5.92e+03 1.90e+02 bond pdb=" C ALA A 744 " pdb=" N GLU A 745 " ideal model delta sigma weight residual 1.332 1.525 -0.192 1.40e-02 5.10e+03 1.89e+02 bond pdb=" N ALA A 744 " pdb=" CA ALA A 744 " ideal model delta sigma weight residual 1.455 1.630 -0.174 1.32e-02 5.74e+03 1.74e+02 ... (remaining 13363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.57: 18403 4.57 - 9.13: 86 9.13 - 13.70: 12 13.70 - 18.26: 6 18.26 - 22.83: 4 Bond angle restraints: 18511 Sorted by residual: angle pdb=" N ALA A 744 " pdb=" CA ALA A 744 " pdb=" C ALA A 744 " ideal model delta sigma weight residual 108.74 128.84 -20.10 1.38e+00 5.25e-01 2.12e+02 angle pdb=" CA ARG A 743 " pdb=" C ARG A 743 " pdb=" N ALA A 744 " ideal model delta sigma weight residual 116.52 133.05 -16.53 1.17e+00 7.31e-01 2.00e+02 angle pdb=" N ARG A 743 " pdb=" CA ARG A 743 " pdb=" C ARG A 743 " ideal model delta sigma weight residual 108.23 127.35 -19.12 1.38e+00 5.25e-01 1.92e+02 angle pdb=" CA ALA A 744 " pdb=" C ALA A 744 " pdb=" N GLU A 745 " ideal model delta sigma weight residual 115.67 132.82 -17.15 1.36e+00 5.41e-01 1.59e+02 angle pdb=" CA PRO B 602 " pdb=" C PRO B 602 " pdb=" O PRO B 602 " ideal model delta sigma weight residual 120.60 97.77 22.83 1.82e+00 3.02e-01 1.57e+02 ... (remaining 18506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.00: 7350 24.00 - 47.99: 705 47.99 - 71.99: 120 71.99 - 95.98: 37 95.98 - 119.98: 29 Dihedral angle restraints: 8241 sinusoidal: 3549 harmonic: 4692 Sorted by residual: dihedral pdb=" CA LEU A 959 " pdb=" C LEU A 959 " pdb=" N GLU A 960 " pdb=" CA GLU A 960 " ideal model delta harmonic sigma weight residual -180.00 -101.22 -78.78 0 5.00e+00 4.00e-02 2.48e+02 dihedral pdb=" CB CYS B 575 " pdb=" SG CYS B 575 " pdb=" SG CYS B 586 " pdb=" CB CYS B 586 " ideal model delta sinusoidal sigma weight residual 93.00 179.55 -86.55 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS B 523 " pdb=" SG CYS B 523 " pdb=" SG CYS B 544 " pdb=" CB CYS B 544 " ideal model delta sinusoidal sigma weight residual 93.00 178.44 -85.44 1 1.00e+01 1.00e-02 8.84e+01 ... (remaining 8238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.966: 2013 0.966 - 1.931: 1 1.931 - 2.897: 0 2.897 - 3.862: 0 3.862 - 4.828: 1 Chirality restraints: 2015 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.64 -1.76 2.00e-02 2.50e+03 7.72e+03 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 559 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 2.43 -4.83 2.00e-01 2.50e+01 5.83e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-02 2.50e+03 5.66e+02 ... (remaining 2012 not shown) Planarity restraints: 2355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.299 2.00e-02 2.50e+03 2.56e-01 8.16e+02 pdb=" C7 NAG E 2 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.447 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.289 2.00e-02 2.50e+03 2.44e-01 7.45e+02 pdb=" C7 NAG E 1 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.405 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.291 2.00e-02 2.50e+03 2.39e-01 7.15e+02 pdb=" C7 NAG C 2 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.198 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.394 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " -0.012 2.00e-02 2.50e+03 ... (remaining 2352 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.83: 4 1.83 - 2.52: 718 2.52 - 3.21: 13683 3.21 - 3.91: 27185 3.91 - 4.60: 38193 Nonbonded interactions: 79783 Sorted by model distance: nonbonded pdb=" OD1 ASP A 817 " pdb=" ND2 ASN A 833 " model vdw 1.134 2.950 nonbonded pdb=" OD2 ASP A 245 " pdb=" OE2 GLU A 252 " model vdw 1.417 2.800 nonbonded pdb=" O CYS A 602 " pdb=" OE2 GLU A 642 " model vdw 1.742 2.800 nonbonded pdb=" OE1 GLU B 378 " pdb=" NE ARG B 633 " model vdw 1.796 2.950 nonbonded pdb=" O ILE A 964 " pdb=" H ILE A 966 " model vdw 1.956 2.450 ... (remaining 79778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.080 Extract box with map and model: 0.120 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.180 Find NCS groups from input model: 0.100 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.192 13036 Z= 0.473 Angle : 1.026 22.826 17763 Z= 0.618 Chirality : 0.129 4.828 2015 Planarity : 0.014 0.256 2305 Dihedral : 19.515 119.978 5008 Min Nonbonded Distance : 1.134 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 1.29 % Allowed : 7.71 % Favored : 91.00 % Rotamer: Outliers : 4.44 % Allowed : 24.59 % Favored : 70.97 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -2.48 (0.20), residues: 1623 helix: -1.10 (0.40), residues: 157 sheet: -1.04 (0.26), residues: 450 loop : -2.12 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 77 TYR 0.018 0.001 TYR B 318 PHE 0.012 0.001 PHE A 908 TRP 0.013 0.001 TRP A 968 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00672 (12984) covalent geometry : angle 1.00136 (17644) SS BOND : bond 0.01219 ( 37) SS BOND : angle 2.15207 ( 74) hydrogen bonds : bond 0.27148 ( 308) hydrogen bonds : angle 10.18447 ( 795) link_ALPHA1-3 : bond 0.00409 ( 1) link_ALPHA1-3 : angle 3.12283 ( 3) link_BETA1-4 : bond 0.00705 ( 6) link_BETA1-4 : angle 4.93112 ( 18) link_BETA1-6 : bond 0.00328 ( 1) link_BETA1-6 : angle 0.35199 ( 3) link_NAG-ASN : bond 0.01300 ( 7) link_NAG-ASN : angle 3.16266 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 153 time to evaluate : 0.482 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7089 (m-80) REVERT: A 535 LEU cc_start: 0.7543 (mm) cc_final: 0.7224 (mm) REVERT: A 648 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6489 (tm-30) REVERT: A 660 MET cc_start: 0.6789 (mmt) cc_final: 0.6399 (tpp) REVERT: A 670 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: A 703 MET cc_start: 0.5689 (tpt) cc_final: 0.5222 (tpt) REVERT: A 815 ILE cc_start: 0.5261 (OUTLIER) cc_final: 0.4929 (pt) REVERT: A 959 LEU cc_start: 0.2800 (OUTLIER) cc_final: 0.0861 (tp) REVERT: A 967 TRP cc_start: 0.4397 (OUTLIER) cc_final: 0.3638 (p-90) REVERT: B 62 ARG cc_start: 0.7372 (mtm110) cc_final: 0.7117 (mtp85) REVERT: B 66 ASP cc_start: 0.7021 (t0) cc_final: 0.6771 (t70) REVERT: B 109 ASP cc_start: 0.6562 (t70) cc_final: 0.6030 (t0) REVERT: B 241 ASP cc_start: 0.7741 (p0) cc_final: 0.7434 (p0) REVERT: B 375 LEU cc_start: 0.7714 (mt) cc_final: 0.7143 (pp) REVERT: B 387 MET cc_start: 0.7433 (mtt) cc_final: 0.7087 (mtm) REVERT: B 390 LYS cc_start: 0.7374 (pttp) cc_final: 0.6886 (ptmm) REVERT: B 535 MET cc_start: 0.7850 (ptp) cc_final: 0.7518 (ptm) REVERT: B 568 MET cc_start: 0.7476 (tpt) cc_final: 0.7240 (tpp) outliers start: 62 outliers final: 23 residues processed: 210 average time/residue: 0.4477 time to fit residues: 104.1409 Evaluate side-chains 132 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 669 PHE Chi-restraints excluded: chain A residue 670 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 897 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 916 GLN Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 921 GLN Chi-restraints excluded: chain A residue 957 ARG Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 967 TRP Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 600 LYS Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 669 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 0.0070 overall best weight: 1.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 HIS A 333 GLN A 395 GLN A 497 ASN A 595 GLN A 747 GLN A 782 HIS ** A 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 HIS ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 438 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.192626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123435 restraints weight = 23855.747| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.76 r_work: 0.3427 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13036 Z= 0.181 Angle : 0.739 19.142 17763 Z= 0.358 Chirality : 0.051 1.015 2015 Planarity : 0.005 0.080 2305 Dihedral : 13.269 108.791 2130 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.94 % Favored : 90.57 % Rotamer: Outliers : 5.81 % Allowed : 25.16 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.36 (0.20), residues: 1623 helix: -0.74 (0.42), residues: 165 sheet: -1.12 (0.24), residues: 485 loop : -2.02 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 77 TYR 0.015 0.001 TYR B 318 PHE 0.019 0.002 PHE A 19 TRP 0.013 0.001 TRP A 260 HIS 0.006 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00412 (12984) covalent geometry : angle 0.69853 (17644) SS BOND : bond 0.00366 ( 37) SS BOND : angle 1.88487 ( 74) hydrogen bonds : bond 0.04422 ( 308) hydrogen bonds : angle 7.21476 ( 795) link_ALPHA1-3 : bond 0.01557 ( 1) link_ALPHA1-3 : angle 4.09508 ( 3) link_BETA1-4 : bond 0.00568 ( 6) link_BETA1-4 : angle 2.77960 ( 18) link_BETA1-6 : bond 0.01030 ( 1) link_BETA1-6 : angle 2.02625 ( 3) link_NAG-ASN : bond 0.00529 ( 7) link_NAG-ASN : angle 5.43971 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 103 time to evaluate : 0.318 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: symmetry clash REVERT: A 77 ARG cc_start: 0.6932 (ptt180) cc_final: 0.6373 (ptt180) REVERT: A 91 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8313 (pt0) REVERT: A 102 ASP cc_start: 0.8564 (t0) cc_final: 0.8345 (OUTLIER) REVERT: A 180 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: A 278 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.7130 (t-170) REVERT: A 288 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: A 535 LEU cc_start: 0.7679 (mm) cc_final: 0.7431 (mm) REVERT: A 648 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: A 704 LEU cc_start: 0.7854 (tt) cc_final: 0.7566 (mp) REVERT: A 788 ASN cc_start: 0.5975 (m-40) cc_final: 0.5180 (t0) REVERT: A 895 MET cc_start: 0.4560 (tpp) cc_final: 0.3821 (ptt) REVERT: A 900 ARG cc_start: 0.5652 (OUTLIER) cc_final: 0.5411 (ptm160) REVERT: A 902 MET cc_start: 0.4844 (OUTLIER) cc_final: 0.4423 (ppp) REVERT: A 927 HIS cc_start: 0.3763 (OUTLIER) cc_final: 0.3431 (t70) REVERT: B 49 CYS cc_start: 0.5336 (OUTLIER) cc_final: 0.4954 (t) REVERT: B 66 ASP cc_start: 0.8521 (t0) cc_final: 0.8318 (t70) REVERT: B 109 ASP cc_start: 0.7252 (t70) cc_final: 0.6987 (t0) REVERT: B 241 ASP cc_start: 0.8140 (p0) cc_final: 0.7931 (p0) REVERT: B 375 LEU cc_start: 0.7452 (mt) cc_final: 0.7200 (pp) REVERT: B 387 MET cc_start: 0.8148 (mtt) cc_final: 0.7689 (mtm) REVERT: B 535 MET cc_start: 0.7855 (ptp) cc_final: 0.7148 (ptm) REVERT: B 568 MET cc_start: 0.7854 (tpt) cc_final: 0.7473 (tpp) outliers start: 81 outliers final: 36 residues processed: 172 average time/residue: 0.3991 time to fit residues: 77.0953 Evaluate side-chains 136 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 92 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 893 GLN Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 921 GLN Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 603 THR Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 669 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 128 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 136 optimal weight: 30.0000 chunk 131 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 7 GLN A 18 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 795 ASN A 899 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN B 509 HIS B 668 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.186671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122455 restraints weight = 20907.437| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.58 r_work: 0.3295 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 13036 Z= 0.381 Angle : 0.907 17.169 17763 Z= 0.445 Chirality : 0.056 0.844 2015 Planarity : 0.007 0.078 2305 Dihedral : 10.686 87.054 2088 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 32.31 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.65 % Favored : 87.98 % Rotamer: Outliers : 7.96 % Allowed : 23.94 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.80 (0.20), residues: 1623 helix: -1.20 (0.40), residues: 171 sheet: -1.14 (0.25), residues: 465 loop : -2.46 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 77 TYR 0.021 0.003 TYR A 237 PHE 0.031 0.003 PHE A 356 TRP 0.016 0.003 TRP A 952 HIS 0.007 0.002 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00913 (12984) covalent geometry : angle 0.87834 (17644) SS BOND : bond 0.00469 ( 37) SS BOND : angle 1.87030 ( 74) hydrogen bonds : bond 0.05034 ( 308) hydrogen bonds : angle 6.89312 ( 795) link_ALPHA1-3 : bond 0.01980 ( 1) link_ALPHA1-3 : angle 3.82292 ( 3) link_BETA1-4 : bond 0.00479 ( 6) link_BETA1-4 : angle 2.25545 ( 18) link_BETA1-6 : bond 0.00548 ( 1) link_BETA1-6 : angle 1.78662 ( 3) link_NAG-ASN : bond 0.00602 ( 7) link_NAG-ASN : angle 5.32211 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 87 time to evaluate : 0.504 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 1 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7036 (pt) REVERT: A 77 ARG cc_start: 0.7430 (ptt180) cc_final: 0.6836 (ptt180) REVERT: A 102 ASP cc_start: 0.8645 (t0) cc_final: 0.8434 (t0) REVERT: A 147 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8281 (mtt180) REVERT: A 223 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.5650 (m-80) REVERT: A 278 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7552 (m90) REVERT: A 288 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8087 (m-80) REVERT: A 400 ARG cc_start: 0.7161 (mtt90) cc_final: 0.6895 (mtp85) REVERT: A 459 GLN cc_start: 0.7790 (mp10) cc_final: 0.7140 (mp10) REVERT: A 497 ASN cc_start: 0.7351 (t0) cc_final: 0.7093 (m-40) REVERT: A 648 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6469 (tm-30) REVERT: A 747 GLN cc_start: 0.6774 (OUTLIER) cc_final: 0.6111 (pm20) REVERT: A 785 GLU cc_start: 0.5866 (OUTLIER) cc_final: 0.5324 (mp0) REVERT: A 895 MET cc_start: 0.4384 (tpp) cc_final: 0.3308 (tpp) REVERT: A 902 MET cc_start: 0.4649 (ppp) cc_final: 0.4325 (ppp) REVERT: A 914 LEU cc_start: 0.4576 (OUTLIER) cc_final: 0.4315 (pp) REVERT: A 927 HIS cc_start: 0.3922 (OUTLIER) cc_final: 0.3527 (t70) REVERT: B 49 CYS cc_start: 0.5301 (OUTLIER) cc_final: 0.5026 (t) REVERT: B 66 ASP cc_start: 0.8607 (t0) cc_final: 0.8385 (t70) REVERT: B 323 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: B 387 MET cc_start: 0.8276 (mtt) cc_final: 0.7915 (ptp) REVERT: B 535 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7152 (ptm) REVERT: B 568 MET cc_start: 0.7963 (tpt) cc_final: 0.7710 (tpp) outliers start: 111 outliers final: 47 residues processed: 185 average time/residue: 0.3986 time to fit residues: 83.2864 Evaluate side-chains 141 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 81 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 921 GLN Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 654 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 79 optimal weight: 0.9990 chunk 147 optimal weight: 0.2980 chunk 53 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 921 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN B 313 ASN B 668 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.192290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121656 restraints weight = 28388.550| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.03 r_work: 0.3394 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3255 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3255 r_free = 0.3255 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3255 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13036 Z= 0.115 Angle : 0.605 15.292 17763 Z= 0.294 Chirality : 0.046 0.679 2015 Planarity : 0.005 0.061 2305 Dihedral : 8.908 96.109 2086 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 28.76 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.52 % Favored : 92.11 % Rotamer: Outliers : 4.66 % Allowed : 26.31 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.29 (0.20), residues: 1623 helix: -0.61 (0.42), residues: 166 sheet: -0.86 (0.25), residues: 455 loop : -2.09 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 900 TYR 0.014 0.001 TYR B 318 PHE 0.010 0.001 PHE B 56 TRP 0.008 0.001 TRP A 952 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00260 (12984) covalent geometry : angle 0.57308 (17644) SS BOND : bond 0.00283 ( 37) SS BOND : angle 1.28848 ( 74) hydrogen bonds : bond 0.02924 ( 308) hydrogen bonds : angle 6.10089 ( 795) link_ALPHA1-3 : bond 0.01711 ( 1) link_ALPHA1-3 : angle 3.54377 ( 3) link_BETA1-4 : bond 0.00445 ( 6) link_BETA1-4 : angle 2.51059 ( 18) link_BETA1-6 : bond 0.00942 ( 1) link_BETA1-6 : angle 1.86455 ( 3) link_NAG-ASN : bond 0.00610 ( 7) link_NAG-ASN : angle 4.46805 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 95 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6841 (pt) REVERT: A 68 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7898 (mt) REVERT: A 77 ARG cc_start: 0.7325 (ptt180) cc_final: 0.6619 (ptt180) REVERT: A 102 ASP cc_start: 0.8677 (t0) cc_final: 0.8418 (OUTLIER) REVERT: A 278 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.7422 (t70) REVERT: A 497 ASN cc_start: 0.7561 (t0) cc_final: 0.7082 (m-40) REVERT: A 535 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7534 (mm) REVERT: A 648 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: A 704 LEU cc_start: 0.7852 (tt) cc_final: 0.7581 (mp) REVERT: A 747 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6146 (pm20) REVERT: A 785 GLU cc_start: 0.5651 (mp0) cc_final: 0.4855 (pp20) REVERT: A 788 ASN cc_start: 0.6035 (m-40) cc_final: 0.5655 (m110) REVERT: A 895 MET cc_start: 0.4540 (tpp) cc_final: 0.3868 (tpp) REVERT: A 902 MET cc_start: 0.4855 (ppp) cc_final: 0.4612 (ppp) REVERT: A 927 HIS cc_start: 0.3568 (OUTLIER) cc_final: 0.3193 (t70) REVERT: B 49 CYS cc_start: 0.4543 (OUTLIER) cc_final: 0.4067 (t) REVERT: B 66 ASP cc_start: 0.8617 (t0) cc_final: 0.8307 (t0) REVERT: B 267 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: B 323 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: B 361 ASP cc_start: 0.7987 (t0) cc_final: 0.7673 (t0) REVERT: B 375 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6966 (pp) REVERT: B 387 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7649 (mtm) REVERT: B 535 MET cc_start: 0.7776 (ptp) cc_final: 0.6984 (ptm) REVERT: B 568 MET cc_start: 0.7903 (tpt) cc_final: 0.7651 (tpp) outliers start: 65 outliers final: 33 residues processed: 149 average time/residue: 0.3654 time to fit residues: 61.8588 Evaluate side-chains 128 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 84 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 654 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 103 optimal weight: 0.0040 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 153 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.190303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.127437 restraints weight = 20804.842| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.14 r_work: 0.3361 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13036 Z= 0.187 Angle : 0.676 18.826 17763 Z= 0.323 Chirality : 0.048 0.641 2015 Planarity : 0.005 0.059 2305 Dihedral : 8.281 84.367 2081 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 29.88 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.68 % Favored : 89.95 % Rotamer: Outliers : 5.95 % Allowed : 25.73 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.28 (0.21), residues: 1623 helix: -0.45 (0.43), residues: 165 sheet: -0.87 (0.25), residues: 482 loop : -2.13 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 900 TYR 0.013 0.001 TYR A 207 PHE 0.019 0.002 PHE A 19 TRP 0.009 0.001 TRP A 952 HIS 0.005 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00440 (12984) covalent geometry : angle 0.62752 (17644) SS BOND : bond 0.00328 ( 37) SS BOND : angle 1.32700 ( 74) hydrogen bonds : bond 0.03250 ( 308) hydrogen bonds : angle 6.00703 ( 795) link_ALPHA1-3 : bond 0.01856 ( 1) link_ALPHA1-3 : angle 3.80622 ( 3) link_BETA1-4 : bond 0.00415 ( 6) link_BETA1-4 : angle 2.25616 ( 18) link_BETA1-6 : bond 0.00966 ( 1) link_BETA1-6 : angle 1.76288 ( 3) link_NAG-ASN : bond 0.00506 ( 7) link_NAG-ASN : angle 6.55235 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 85 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6938 (pt) REVERT: A 77 ARG cc_start: 0.7417 (ptt180) cc_final: 0.6672 (ptt180) REVERT: A 486 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7453 (m-40) REVERT: A 497 ASN cc_start: 0.7666 (t0) cc_final: 0.7144 (m-40) REVERT: A 648 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6594 (tm-30) REVERT: A 703 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7301 (tpt) REVERT: A 704 LEU cc_start: 0.7946 (tt) cc_final: 0.7675 (mm) REVERT: A 747 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6281 (pm20) REVERT: A 785 GLU cc_start: 0.5813 (mp0) cc_final: 0.5021 (pp20) REVERT: A 895 MET cc_start: 0.4673 (tpp) cc_final: 0.3963 (tpp) REVERT: A 902 MET cc_start: 0.4619 (ppp) cc_final: 0.4403 (ppp) REVERT: A 927 HIS cc_start: 0.3790 (OUTLIER) cc_final: 0.3398 (t70) REVERT: B 49 CYS cc_start: 0.4602 (OUTLIER) cc_final: 0.4089 (t) REVERT: B 66 ASP cc_start: 0.8621 (t0) cc_final: 0.8396 (t0) REVERT: B 361 ASP cc_start: 0.8171 (t0) cc_final: 0.7834 (t0) REVERT: B 375 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6996 (pp) REVERT: B 387 MET cc_start: 0.8210 (mtt) cc_final: 0.7684 (mtm) REVERT: B 390 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6974 (ptmt) REVERT: B 508 CYS cc_start: 0.3015 (OUTLIER) cc_final: 0.2772 (p) REVERT: B 535 MET cc_start: 0.7786 (ptp) cc_final: 0.7001 (ptm) REVERT: B 568 MET cc_start: 0.7875 (tpt) cc_final: 0.7598 (tpp) REVERT: B 588 CYS cc_start: 0.1816 (OUTLIER) cc_final: 0.0498 (m) outliers start: 83 outliers final: 52 residues processed: 157 average time/residue: 0.3867 time to fit residues: 68.8036 Evaluate side-chains 145 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 82 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 486 ASN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 105 optimal weight: 2.9990 chunk 156 optimal weight: 0.0980 chunk 123 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 ASN B 668 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.191967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121876 restraints weight = 23590.717| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.78 r_work: 0.3398 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13036 Z= 0.126 Angle : 0.581 13.133 17763 Z= 0.282 Chirality : 0.045 0.575 2015 Planarity : 0.004 0.054 2305 Dihedral : 7.766 81.453 2080 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 29.88 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.14 % Favored : 91.49 % Rotamer: Outliers : 4.73 % Allowed : 26.67 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.09 (0.21), residues: 1623 helix: -0.23 (0.43), residues: 165 sheet: -0.72 (0.25), residues: 481 loop : -2.03 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 900 TYR 0.011 0.001 TYR B 318 PHE 0.010 0.001 PHE B 56 TRP 0.007 0.001 TRP A 952 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00295 (12984) covalent geometry : angle 0.54754 (17644) SS BOND : bond 0.00232 ( 37) SS BOND : angle 0.96774 ( 74) hydrogen bonds : bond 0.02821 ( 308) hydrogen bonds : angle 5.77796 ( 795) link_ALPHA1-3 : bond 0.01755 ( 1) link_ALPHA1-3 : angle 3.62233 ( 3) link_BETA1-4 : bond 0.00422 ( 6) link_BETA1-4 : angle 2.17199 ( 18) link_BETA1-6 : bond 0.01031 ( 1) link_BETA1-6 : angle 1.70274 ( 3) link_NAG-ASN : bond 0.00600 ( 7) link_NAG-ASN : angle 4.89267 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 87 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6942 (pt) REVERT: A 41 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7565 (mtm180) REVERT: A 77 ARG cc_start: 0.7367 (ptt180) cc_final: 0.6823 (ptt180) REVERT: A 223 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.5484 (m-80) REVERT: A 272 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.8143 (p) REVERT: A 278 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7407 (t70) REVERT: A 459 GLN cc_start: 0.7750 (mp10) cc_final: 0.7095 (mp10) REVERT: A 497 ASN cc_start: 0.7634 (t0) cc_final: 0.7150 (m-40) REVERT: A 535 LEU cc_start: 0.7743 (mm) cc_final: 0.7537 (mm) REVERT: A 704 LEU cc_start: 0.7941 (tt) cc_final: 0.7688 (mm) REVERT: A 747 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6221 (pm20) REVERT: A 785 GLU cc_start: 0.5639 (mp0) cc_final: 0.4968 (pp20) REVERT: A 895 MET cc_start: 0.4683 (tpp) cc_final: 0.3961 (tpp) REVERT: A 902 MET cc_start: 0.4695 (ppp) cc_final: 0.4470 (ppp) REVERT: A 927 HIS cc_start: 0.3754 (OUTLIER) cc_final: 0.3337 (t70) REVERT: B 49 CYS cc_start: 0.4657 (OUTLIER) cc_final: 0.4143 (t) REVERT: B 66 ASP cc_start: 0.8555 (t0) cc_final: 0.8242 (t0) REVERT: B 361 ASP cc_start: 0.8116 (t0) cc_final: 0.7775 (t0) REVERT: B 375 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6798 (pp) REVERT: B 387 MET cc_start: 0.8206 (mtt) cc_final: 0.7715 (mtm) REVERT: B 390 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6868 (ptmt) REVERT: B 535 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7021 (ptm) REVERT: B 568 MET cc_start: 0.7902 (tpt) cc_final: 0.7661 (tpp) REVERT: B 588 CYS cc_start: 0.0898 (OUTLIER) cc_final: 0.0080 (m) REVERT: B 638 GLU cc_start: 0.5389 (OUTLIER) cc_final: 0.5006 (pm20) outliers start: 66 outliers final: 37 residues processed: 144 average time/residue: 0.4285 time to fit residues: 69.3897 Evaluate side-chains 134 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 84 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 638 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 122 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.2980 chunk 125 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 18 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN ** B 86 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 = 0.4350 r_free = 0.4350 target = 0.191030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119804 restraints weight = 27992.369| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.99 r_work: 0.3370 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13036 Z= 0.160 Angle : 0.603 12.003 17763 Z= 0.295 Chirality : 0.045 0.534 2015 Planarity : 0.004 0.055 2305 Dihedral : 7.399 74.684 2075 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 30.35 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.43 % Favored : 90.20 % Rotamer: Outliers : 5.59 % Allowed : 25.88 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.08 (0.21), residues: 1623 helix: -0.15 (0.44), residues: 165 sheet: -0.73 (0.25), residues: 483 loop : -2.03 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 900 TYR 0.011 0.001 TYR A 207 PHE 0.016 0.001 PHE A 19 TRP 0.008 0.001 TRP B 25 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00378 (12984) covalent geometry : angle 0.57313 (17644) SS BOND : bond 0.00264 ( 37) SS BOND : angle 1.18788 ( 74) hydrogen bonds : bond 0.02930 ( 308) hydrogen bonds : angle 5.68914 ( 795) link_ALPHA1-3 : bond 0.01815 ( 1) link_ALPHA1-3 : angle 3.68245 ( 3) link_BETA1-4 : bond 0.00442 ( 6) link_BETA1-4 : angle 1.95223 ( 18) link_BETA1-6 : bond 0.00904 ( 1) link_BETA1-6 : angle 1.73506 ( 3) link_NAG-ASN : bond 0.00491 ( 7) link_NAG-ASN : angle 4.59104 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 89 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7021 (pt) REVERT: A 18 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8361 (mt0) REVERT: A 41 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7787 (mtp85) REVERT: A 77 ARG cc_start: 0.7608 (ptt180) cc_final: 0.6818 (ptt90) REVERT: A 223 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.5491 (m-80) REVERT: A 272 SER cc_start: 0.8527 (OUTLIER) cc_final: 0.8317 (p) REVERT: A 278 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.7459 (t70) REVERT: A 397 GLU cc_start: 0.7795 (mp0) cc_final: 0.7324 (tm-30) REVERT: A 459 GLN cc_start: 0.7709 (mp10) cc_final: 0.7054 (mp10) REVERT: A 497 ASN cc_start: 0.7690 (t0) cc_final: 0.7201 (m-40) REVERT: A 535 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7578 (mm) REVERT: A 661 ARG cc_start: 0.7390 (ttp-110) cc_final: 0.6677 (ttp-170) REVERT: A 704 LEU cc_start: 0.7956 (tt) cc_final: 0.7673 (mm) REVERT: A 747 GLN cc_start: 0.6899 (OUTLIER) cc_final: 0.6206 (pm20) REVERT: A 785 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.5156 (pp20) REVERT: A 895 MET cc_start: 0.4402 (tpp) cc_final: 0.3748 (tpp) REVERT: A 900 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.5904 (ptt180) REVERT: A 927 HIS cc_start: 0.3902 (OUTLIER) cc_final: 0.3463 (t-170) REVERT: B 49 CYS cc_start: 0.4651 (OUTLIER) cc_final: 0.4141 (t) REVERT: B 66 ASP cc_start: 0.8592 (t0) cc_final: 0.8392 (t70) REVERT: B 361 ASP cc_start: 0.8247 (t0) cc_final: 0.7919 (t0) REVERT: B 375 LEU cc_start: 0.7171 (mt) cc_final: 0.6627 (pp) REVERT: B 387 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7760 (mtm) REVERT: B 390 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6913 (ptmt) REVERT: B 508 CYS cc_start: 0.2973 (OUTLIER) cc_final: 0.2756 (p) REVERT: B 535 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7067 (ptm) REVERT: B 568 MET cc_start: 0.7882 (tpt) cc_final: 0.7633 (tpp) REVERT: B 638 GLU cc_start: 0.5566 (OUTLIER) cc_final: 0.5120 (pm20) outliers start: 78 outliers final: 46 residues processed: 153 average time/residue: 0.3544 time to fit residues: 61.7322 Evaluate side-chains 147 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 84 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 785 GLU Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 638 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 80 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 15 optimal weight: 0.0870 chunk 138 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 133 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.189297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118452 restraints weight = 26562.279| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.89 r_work: 0.3345 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13036 Z= 0.257 Angle : 0.683 12.076 17763 Z= 0.336 Chirality : 0.048 0.544 2015 Planarity : 0.005 0.056 2305 Dihedral : 7.622 77.808 2075 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 32.47 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.91 % Favored : 88.72 % Rotamer: Outliers : 5.52 % Allowed : 26.31 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.27 (0.21), residues: 1623 helix: -0.34 (0.43), residues: 165 sheet: -0.67 (0.25), residues: 480 loop : -2.26 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 900 TYR 0.015 0.002 TYR A 288 PHE 0.019 0.002 PHE A 356 TRP 0.011 0.002 TRP A 952 HIS 0.006 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00609 (12984) covalent geometry : angle 0.65617 (17644) SS BOND : bond 0.00329 ( 37) SS BOND : angle 1.27565 ( 74) hydrogen bonds : bond 0.03433 ( 308) hydrogen bonds : angle 5.87526 ( 795) link_ALPHA1-3 : bond 0.01997 ( 1) link_ALPHA1-3 : angle 3.88601 ( 3) link_BETA1-4 : bond 0.00323 ( 6) link_BETA1-4 : angle 1.88843 ( 18) link_BETA1-6 : bond 0.00764 ( 1) link_BETA1-6 : angle 1.99806 ( 3) link_NAG-ASN : bond 0.00543 ( 7) link_NAG-ASN : angle 4.59226 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 79 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7123 (pt) REVERT: A 41 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7542 (mtm180) REVERT: A 77 ARG cc_start: 0.7697 (ptt180) cc_final: 0.6974 (ptt180) REVERT: A 223 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.5467 (m-80) REVERT: A 272 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8324 (p) REVERT: A 400 ARG cc_start: 0.7287 (mtt90) cc_final: 0.6922 (mtp85) REVERT: A 459 GLN cc_start: 0.7758 (mp10) cc_final: 0.7088 (mp10) REVERT: A 497 ASN cc_start: 0.7777 (t0) cc_final: 0.7438 (m-40) REVERT: A 535 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7571 (mm) REVERT: A 549 MET cc_start: 0.7739 (mpp) cc_final: 0.7269 (tpp) REVERT: A 704 LEU cc_start: 0.7969 (tt) cc_final: 0.7698 (mm) REVERT: A 747 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6203 (pm20) REVERT: A 785 GLU cc_start: 0.5834 (mp0) cc_final: 0.5222 (pp20) REVERT: A 895 MET cc_start: 0.4416 (tpp) cc_final: 0.3861 (tpp) REVERT: A 900 ARG cc_start: 0.6188 (OUTLIER) cc_final: 0.5950 (ptt180) REVERT: A 927 HIS cc_start: 0.4032 (OUTLIER) cc_final: 0.3605 (t-170) REVERT: B 49 CYS cc_start: 0.4670 (OUTLIER) cc_final: 0.4133 (t) REVERT: B 66 ASP cc_start: 0.8652 (t0) cc_final: 0.8451 (t0) REVERT: B 361 ASP cc_start: 0.8345 (t0) cc_final: 0.7977 (t0) REVERT: B 375 LEU cc_start: 0.7029 (mt) cc_final: 0.6773 (pp) REVERT: B 387 MET cc_start: 0.8300 (mtt) cc_final: 0.7819 (mtm) REVERT: B 390 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6891 (ptmt) REVERT: B 508 CYS cc_start: 0.3171 (OUTLIER) cc_final: 0.2888 (p) REVERT: B 535 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7044 (ptm) REVERT: B 568 MET cc_start: 0.7914 (tpt) cc_final: 0.7681 (tpp) outliers start: 77 outliers final: 53 residues processed: 144 average time/residue: 0.3577 time to fit residues: 58.4948 Evaluate side-chains 143 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 78 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 516 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 638 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 39 optimal weight: 0.0570 chunk 1 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 18 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 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 = 0.4364 r_free = 0.4364 target = 0.192596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.130619 restraints weight = 18369.378| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.49 r_work: 0.3411 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13036 Z= 0.101 Angle : 0.545 11.568 17763 Z= 0.266 Chirality : 0.043 0.497 2015 Planarity : 0.004 0.057 2305 Dihedral : 7.133 77.147 2075 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 30.35 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.40 % Favored : 92.29 % Rotamer: Outliers : 3.51 % Allowed : 28.17 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -1.98 (0.21), residues: 1623 helix: 0.09 (0.44), residues: 165 sheet: -0.72 (0.24), residues: 509 loop : -1.99 (0.19), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 900 TYR 0.011 0.001 TYR B 318 PHE 0.011 0.001 PHE B 56 TRP 0.006 0.001 TRP A 58 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00236 (12984) covalent geometry : angle 0.51854 (17644) SS BOND : bond 0.00200 ( 37) SS BOND : angle 0.94693 ( 74) hydrogen bonds : bond 0.02464 ( 308) hydrogen bonds : angle 5.45879 ( 795) link_ALPHA1-3 : bond 0.01641 ( 1) link_ALPHA1-3 : angle 3.20282 ( 3) link_BETA1-4 : bond 0.00433 ( 6) link_BETA1-4 : angle 1.85505 ( 18) link_BETA1-6 : bond 0.00905 ( 1) link_BETA1-6 : angle 1.85500 ( 3) link_NAG-ASN : bond 0.00572 ( 7) link_NAG-ASN : angle 4.13865 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 86 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7558 (ptt180) cc_final: 0.6777 (ptt180) REVERT: A 272 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8312 (p) REVERT: A 278 HIS cc_start: 0.7514 (OUTLIER) cc_final: 0.7284 (t70) REVERT: A 397 GLU cc_start: 0.7756 (mp0) cc_final: 0.7423 (tm-30) REVERT: A 459 GLN cc_start: 0.7589 (mp10) cc_final: 0.6893 (mp10) REVERT: A 497 ASN cc_start: 0.7786 (t0) cc_final: 0.7249 (m-40) REVERT: A 549 MET cc_start: 0.7894 (mpp) cc_final: 0.7498 (tpp) REVERT: A 704 LEU cc_start: 0.7947 (tt) cc_final: 0.7713 (mm) REVERT: A 747 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.6207 (pm20) REVERT: A 785 GLU cc_start: 0.5775 (mp0) cc_final: 0.5482 (mp0) REVERT: A 895 MET cc_start: 0.4143 (tpp) cc_final: 0.3614 (tpp) REVERT: A 900 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.6011 (ptt180) REVERT: A 927 HIS cc_start: 0.3889 (OUTLIER) cc_final: 0.3543 (t70) REVERT: B 49 CYS cc_start: 0.4631 (OUTLIER) cc_final: 0.3994 (t) REVERT: B 66 ASP cc_start: 0.8641 (t0) cc_final: 0.8307 (t0) REVERT: B 361 ASP cc_start: 0.8129 (t0) cc_final: 0.7811 (t0) REVERT: B 375 LEU cc_start: 0.7012 (mt) cc_final: 0.6797 (pp) REVERT: B 387 MET cc_start: 0.8088 (mtt) cc_final: 0.7588 (mtm) REVERT: B 390 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6851 (ptmt) REVERT: B 508 CYS cc_start: 0.2806 (OUTLIER) cc_final: 0.2558 (p) REVERT: B 535 MET cc_start: 0.7760 (ptp) cc_final: 0.6972 (ptm) REVERT: B 568 MET cc_start: 0.7870 (tpt) cc_final: 0.7618 (tpp) outliers start: 49 outliers final: 31 residues processed: 125 average time/residue: 0.3991 time to fit residues: 56.5947 Evaluate side-chains 122 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 83 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 693 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 0.0040 chunk 43 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.191359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127362 restraints weight = 22599.572| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.42 r_work: 0.3387 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13036 Z= 0.147 Angle : 0.584 11.585 17763 Z= 0.284 Chirality : 0.044 0.496 2015 Planarity : 0.004 0.059 2305 Dihedral : 6.973 72.015 2072 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 31.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.25 % Favored : 90.44 % Rotamer: Outliers : 3.66 % Allowed : 28.53 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -1.97 (0.21), residues: 1623 helix: 0.10 (0.44), residues: 165 sheet: -0.61 (0.25), residues: 494 loop : -2.02 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 900 TYR 0.011 0.001 TYR B 318 PHE 0.016 0.001 PHE A 19 TRP 0.008 0.001 TRP A 952 HIS 0.004 0.001 HIS A 291 Details of bonding type rmsd covalent geometry : bond 0.00348 (12984) covalent geometry : angle 0.55847 (17644) SS BOND : bond 0.00241 ( 37) SS BOND : angle 1.02410 ( 74) hydrogen bonds : bond 0.02746 ( 308) hydrogen bonds : angle 5.45643 ( 795) link_ALPHA1-3 : bond 0.01577 ( 1) link_ALPHA1-3 : angle 3.34245 ( 3) link_BETA1-4 : bond 0.00383 ( 6) link_BETA1-4 : angle 1.72774 ( 18) link_BETA1-6 : bond 0.00758 ( 1) link_BETA1-6 : angle 1.87544 ( 3) link_NAG-ASN : bond 0.00526 ( 7) link_NAG-ASN : angle 4.22487 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 85 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7254 (pt) REVERT: A 77 ARG cc_start: 0.7578 (ptt180) cc_final: 0.6995 (ptt180) REVERT: A 223 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.5478 (m-80) REVERT: A 272 SER cc_start: 0.8461 (OUTLIER) cc_final: 0.8221 (p) REVERT: A 459 GLN cc_start: 0.7560 (mp10) cc_final: 0.6852 (mp10) REVERT: A 497 ASN cc_start: 0.7652 (t0) cc_final: 0.7269 (m-40) REVERT: A 549 MET cc_start: 0.7870 (mpp) cc_final: 0.7481 (tpp) REVERT: A 704 LEU cc_start: 0.7947 (tt) cc_final: 0.7692 (mm) REVERT: A 747 GLN cc_start: 0.6894 (OUTLIER) cc_final: 0.6238 (pm20) REVERT: A 785 GLU cc_start: 0.5956 (mp0) cc_final: 0.5674 (mp0) REVERT: A 895 MET cc_start: 0.4259 (tpp) cc_final: 0.3527 (tpp) REVERT: A 900 ARG cc_start: 0.6173 (OUTLIER) cc_final: 0.5957 (ptt180) REVERT: A 927 HIS cc_start: 0.3810 (OUTLIER) cc_final: 0.3476 (t70) REVERT: B 49 CYS cc_start: 0.4795 (OUTLIER) cc_final: 0.4115 (t) REVERT: B 66 ASP cc_start: 0.8399 (t0) cc_final: 0.8188 (t70) REVERT: B 361 ASP cc_start: 0.8117 (t0) cc_final: 0.7790 (t0) REVERT: B 375 LEU cc_start: 0.7125 (mt) cc_final: 0.6923 (pp) REVERT: B 387 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7626 (mtm) REVERT: B 390 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6796 (ptmt) REVERT: B 508 CYS cc_start: 0.2751 (OUTLIER) cc_final: 0.2496 (p) REVERT: B 535 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7118 (ptm) REVERT: B 568 MET cc_start: 0.7844 (tpt) cc_final: 0.7597 (tpp) outliers start: 51 outliers final: 37 residues processed: 126 average time/residue: 0.4392 time to fit residues: 62.3176 Evaluate side-chains 127 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 79 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 LEU Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 30 HIS Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 PHE Chi-restraints excluded: chain A residue 747 GLN Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 900 ARG Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 693 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 113 optimal weight: 0.1980 chunk 142 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 ASN ** B 86 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 = 0.4372 r_free = 0.4372 target = 0.193452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.126331 restraints weight = 26401.061| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 3.70 r_work: 0.3394 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13036 Z= 0.092 Angle : 0.535 11.572 17763 Z= 0.260 Chirality : 0.043 0.473 2015 Planarity : 0.004 0.059 2305 Dihedral : 6.524 61.217 2072 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 30.51 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.21 % Favored : 92.54 % Rotamer: Outliers : 2.94 % Allowed : 29.32 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -1.81 (0.21), residues: 1623 helix: 0.29 (0.44), residues: 166 sheet: -0.64 (0.24), residues: 513 loop : -1.87 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 900 TYR 0.011 0.001 TYR B 318 PHE 0.013 0.001 PHE B 56 TRP 0.006 0.001 TRP A 967 HIS 0.003 0.000 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00218 (12984) covalent geometry : angle 0.50973 (17644) SS BOND : bond 0.00194 ( 37) SS BOND : angle 0.86731 ( 74) hydrogen bonds : bond 0.02315 ( 308) hydrogen bonds : angle 5.21439 ( 795) link_ALPHA1-3 : bond 0.01440 ( 1) link_ALPHA1-3 : angle 2.77990 ( 3) link_BETA1-4 : bond 0.00413 ( 6) link_BETA1-4 : angle 1.67847 ( 18) link_BETA1-6 : bond 0.00826 ( 1) link_BETA1-6 : angle 1.83444 ( 3) link_NAG-ASN : bond 0.00521 ( 7) link_NAG-ASN : angle 4.09798 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5284.37 seconds wall clock time: 90 minutes 25.84 seconds (5425.84 seconds total)