Starting phenix.real_space_refine on Thu Jul 31 04:35:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gcd_29931/07_2025/8gcd_29931.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gcd_29931/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gcd_29931/07_2025/8gcd_29931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gcd_29931/07_2025/8gcd_29931.map" model { file = "/net/cci-nas-00/data/ceres_data/8gcd_29931/07_2025/8gcd_29931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gcd_29931/07_2025/8gcd_29931.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.27, per 1000 atoms: 0.86 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: 3.69 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.57 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: 4.98 Time building geometry restraints manager: 4.34 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: 0.010 Normalize map: mean=0, sd=1: 1.770 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: 0.360 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.480 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.080 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:14.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.900 ------------------------------------------------------------------------------- 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 : 16.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP A 968 HIS 0.004 0.001 HIS B 192 PHE 0.012 0.001 PHE A 908 TYR 0.018 0.001 TYR B 318 ARG 0.010 0.000 ARG A 77 Details of bonding type rmsd link_NAG-ASN : bond 0.01300 ( 7) link_NAG-ASN : angle 3.16266 ( 21) link_BETA1-4 : bond 0.00705 ( 6) link_BETA1-4 : angle 4.93112 ( 18) link_ALPHA1-3 : bond 0.00409 ( 1) link_ALPHA1-3 : angle 3.12283 ( 3) hydrogen bonds : bond 0.27148 ( 308) hydrogen bonds : angle 10.18447 ( 795) link_BETA1-6 : bond 0.00328 ( 1) link_BETA1-6 : angle 0.35199 ( 3) SS BOND : bond 0.01219 ( 37) SS BOND : angle 2.15207 ( 74) covalent geometry : bond 0.00672 (12984) covalent geometry : angle 1.00136 (17644) *********************** 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 : 1.475 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: 0.7225 (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: 0.6397 (tpp) REVERT: A 670 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: A 703 MET cc_start: 0.5689 (tpt) cc_final: 0.5224 (tpt) REVERT: A 815 ILE cc_start: 0.5261 (OUTLIER) cc_final: 0.4930 (pt) REVERT: A 959 LEU cc_start: 0.2800 (OUTLIER) cc_final: 0.0862 (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: 0.6772 (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: 0.7142 (pp) REVERT: B 387 MET cc_start: 0.7433 (mtt) cc_final: 0.7086 (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: 1.0809 time to fit residues: 251.9935 Evaluate side-chains 131 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 136 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 0.0060 chunk 82 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 126 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 147 optimal weight: 0.0170 overall best weight: 3.2040 ------------------------------------------------------------------------------- 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 112 HIS A 333 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.189855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123604 restraints weight = 20687.856| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.18 r_work: 0.3365 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13036 Z= 0.288 Angle : 0.847 19.099 17763 Z= 0.413 Chirality : 0.054 0.927 2015 Planarity : 0.006 0.086 2305 Dihedral : 13.140 103.483 2130 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 27.44 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.43 % Favored : 90.07 % Rotamer: Outliers : 6.81 % Allowed : 24.30 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.20), residues: 1623 helix: -1.16 (0.40), residues: 174 sheet: -1.16 (0.24), residues: 482 loop : -2.25 (0.18), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 260 HIS 0.007 0.002 HIS B 255 PHE 0.023 0.002 PHE A 356 TYR 0.019 0.002 TYR A 207 ARG 0.009 0.001 ARG A 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 7) link_NAG-ASN : angle 5.51276 ( 21) link_BETA1-4 : bond 0.00647 ( 6) link_BETA1-4 : angle 2.84410 ( 18) link_ALPHA1-3 : bond 0.01409 ( 1) link_ALPHA1-3 : angle 4.33035 ( 3) hydrogen bonds : bond 0.04600 ( 308) hydrogen bonds : angle 7.23506 ( 795) link_BETA1-6 : bond 0.00760 ( 1) link_BETA1-6 : angle 2.18621 ( 3) SS BOND : bond 0.00414 ( 37) SS BOND : angle 1.93168 ( 74) covalent geometry : bond 0.00669 (12984) covalent geometry : angle 0.81180 (17644) *********************** 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 194 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 99 time to evaluate : 1.416 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: 0.7349 (ptt180) cc_final: 0.6751 (ptt180) REVERT: A 91 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8461 (pt0) REVERT: A 172 SER cc_start: 0.8984 (OUTLIER) cc_final: 0.8764 (t) REVERT: A 288 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8025 (m-80) REVERT: A 535 LEU cc_start: 0.7648 (mm) cc_final: 0.7244 (mm) REVERT: A 593 GLN cc_start: 0.8583 (pm20) cc_final: 0.8259 (tt0) REVERT: A 648 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6839 (tm-30) REVERT: A 704 LEU cc_start: 0.7817 (tt) cc_final: 0.7533 (mp) REVERT: A 895 MET cc_start: 0.4582 (tpp) cc_final: 0.3520 (tpp) REVERT: A 902 MET cc_start: 0.4861 (OUTLIER) cc_final: 0.4599 (ppp) REVERT: A 927 HIS cc_start: 0.3912 (OUTLIER) cc_final: 0.3533 (t70) REVERT: B 49 CYS cc_start: 0.5252 (OUTLIER) cc_final: 0.4943 (t) REVERT: B 66 ASP cc_start: 0.8648 (t0) cc_final: 0.8417 (t70) REVERT: B 387 MET cc_start: 0.8302 (mtt) cc_final: 0.7850 (mtm) REVERT: B 505 GLN cc_start: 0.5844 (tt0) cc_final: 0.5444 (pp30) REVERT: B 535 MET cc_start: 0.7813 (ptp) cc_final: 0.7089 (ptm) REVERT: B 568 MET cc_start: 0.7897 (tpt) cc_final: 0.7541 (tpp) REVERT: B 614 CYS cc_start: 0.2364 (OUTLIER) cc_final: 0.1896 (m) outliers start: 95 outliers final: 37 residues processed: 182 average time/residue: 0.9020 time to fit residues: 185.5895 Evaluate side-chains 132 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 87 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 SER 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 174 VAL Chi-restraints excluded: chain A residue 249 ASN 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 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 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 102 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 434 ASP 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 614 CYS 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 43 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 141 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 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 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS B 668 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.191812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121518 restraints weight = 26560.673| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.93 r_work: 0.3395 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13036 Z= 0.140 Angle : 0.631 15.930 17763 Z= 0.306 Chirality : 0.047 0.778 2015 Planarity : 0.005 0.063 2305 Dihedral : 10.172 97.941 2088 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 26.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.20 % Favored : 91.43 % Rotamer: Outliers : 5.16 % Allowed : 25.95 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.20), residues: 1623 helix: -0.76 (0.42), residues: 168 sheet: -0.96 (0.25), residues: 477 loop : -2.03 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 967 HIS 0.003 0.001 HIS B 192 PHE 0.016 0.001 PHE A 922 TYR 0.013 0.001 TYR B 318 ARG 0.006 0.000 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 7) link_NAG-ASN : angle 4.72448 ( 21) link_BETA1-4 : bond 0.00495 ( 6) link_BETA1-4 : angle 2.33611 ( 18) link_ALPHA1-3 : bond 0.01781 ( 1) link_ALPHA1-3 : angle 3.35611 ( 3) hydrogen bonds : bond 0.03560 ( 308) hydrogen bonds : angle 6.41089 ( 795) link_BETA1-6 : bond 0.00788 ( 1) link_BETA1-6 : angle 1.68024 ( 3) SS BOND : bond 0.00231 ( 37) SS BOND : angle 1.33730 ( 74) covalent geometry : bond 0.00324 (12984) covalent geometry : angle 0.59904 (17644) *********************** 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 164 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 92 time to evaluate : 1.552 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: 0.7365 (ptt180) cc_final: 0.6805 (ptt180) REVERT: A 91 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8275 (pt0) REVERT: A 102 ASP cc_start: 0.8539 (t0) cc_final: 0.8310 (t0) REVERT: A 278 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.7123 (t-170) REVERT: A 288 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: A 459 GLN cc_start: 0.7802 (mp10) cc_final: 0.7209 (mp10) REVERT: A 535 LEU cc_start: 0.7721 (mm) cc_final: 0.7407 (mm) REVERT: A 593 GLN cc_start: 0.8570 (pm20) cc_final: 0.8362 (tt0) REVERT: A 704 LEU cc_start: 0.7801 (tt) cc_final: 0.7563 (mp) REVERT: A 785 GLU cc_start: 0.6978 (tt0) cc_final: 0.6287 (pp20) REVERT: A 788 ASN cc_start: 0.5906 (m-40) cc_final: 0.4949 (t0) REVERT: A 880 CYS cc_start: -0.1243 (OUTLIER) cc_final: -0.1453 (t) REVERT: A 895 MET cc_start: 0.4480 (tpp) cc_final: 0.3636 (ppp) REVERT: A 902 MET cc_start: 0.4898 (ppp) cc_final: 0.4425 (ppp) REVERT: A 914 LEU cc_start: 0.4298 (OUTLIER) cc_final: 0.3973 (pp) REVERT: A 927 HIS cc_start: 0.3669 (OUTLIER) cc_final: 0.3330 (t70) REVERT: B 49 CYS cc_start: 0.4853 (OUTLIER) cc_final: 0.4410 (t) REVERT: B 66 ASP cc_start: 0.8605 (t0) cc_final: 0.8367 (t70) REVERT: B 323 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: B 375 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7115 (pp) REVERT: B 387 MET cc_start: 0.8203 (mtt) cc_final: 0.7719 (mtm) REVERT: B 535 MET cc_start: 0.7744 (ptp) cc_final: 0.7009 (ptm) REVERT: B 568 MET cc_start: 0.7871 (tpt) cc_final: 0.7563 (tpp) outliers start: 72 outliers final: 33 residues processed: 153 average time/residue: 0.8896 time to fit residues: 154.8381 Evaluate side-chains 127 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 LEU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 182 VAL 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 384 SER Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 633 LEU 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 825 GLN Chi-restraints excluded: chain A residue 880 CYS 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 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 212 VAL Chi-restraints excluded: chain B residue 304 ILE 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 432 ASP Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 614 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 5 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 22 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 ** 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 509 HIS B 668 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.190335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124502 restraints weight = 22858.570| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.26 r_work: 0.3347 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13036 Z= 0.202 Angle : 0.675 15.203 17763 Z= 0.328 Chirality : 0.048 0.713 2015 Planarity : 0.005 0.060 2305 Dihedral : 8.478 83.656 2083 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 28.96 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.19 % Favored : 90.44 % Rotamer: Outliers : 6.16 % Allowed : 24.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.20), residues: 1623 helix: -0.70 (0.42), residues: 170 sheet: -1.00 (0.25), residues: 472 loop : -2.08 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 952 HIS 0.004 0.001 HIS A 291 PHE 0.020 0.002 PHE A 19 TYR 0.015 0.002 TYR B 318 ARG 0.007 0.001 ARG A 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00449 ( 7) link_NAG-ASN : angle 4.65861 ( 21) link_BETA1-4 : bond 0.00378 ( 6) link_BETA1-4 : angle 2.33551 ( 18) link_ALPHA1-3 : bond 0.01785 ( 1) link_ALPHA1-3 : angle 3.79819 ( 3) hydrogen bonds : bond 0.03486 ( 308) hydrogen bonds : angle 6.16566 ( 795) link_BETA1-6 : bond 0.00924 ( 1) link_BETA1-6 : angle 1.77689 ( 3) SS BOND : bond 0.00300 ( 37) SS BOND : angle 1.30934 ( 74) covalent geometry : bond 0.00475 (12984) covalent geometry : angle 0.64582 (17644) *********************** 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 180 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 94 time to evaluate : 1.341 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 102 ASP cc_start: 0.8528 (t0) cc_final: 0.8205 (OUTLIER) REVERT: A 147 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.8062 (mtt180) REVERT: A 180 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8030 (mm-30) REVERT: A 223 PHE cc_start: 0.6417 (OUTLIER) cc_final: 0.5555 (m-80) REVERT: A 288 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: A 459 GLN cc_start: 0.7668 (mp10) cc_final: 0.7011 (mp10) REVERT: A 497 ASN cc_start: 0.7377 (t0) cc_final: 0.7053 (m-40) REVERT: A 535 LEU cc_start: 0.7648 (mm) cc_final: 0.7316 (mm) REVERT: A 704 LEU cc_start: 0.7819 (tt) cc_final: 0.7545 (mp) REVERT: A 785 GLU cc_start: 0.7058 (tt0) cc_final: 0.6348 (pp20) REVERT: A 895 MET cc_start: 0.4450 (tpp) cc_final: 0.3877 (tpp) REVERT: A 902 MET cc_start: 0.4746 (ppp) cc_final: 0.4362 (ppp) REVERT: A 914 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.4085 (pp) REVERT: A 927 HIS cc_start: 0.3530 (OUTLIER) cc_final: 0.3155 (t70) REVERT: B 66 ASP cc_start: 0.8537 (t0) cc_final: 0.8319 (t0) REVERT: B 323 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: B 387 MET cc_start: 0.8125 (mtt) cc_final: 0.7624 (mtm) REVERT: B 535 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.6965 (ptm) REVERT: B 568 MET cc_start: 0.7864 (tpt) cc_final: 0.7552 (tpp) outliers start: 86 outliers final: 54 residues processed: 167 average time/residue: 0.9200 time to fit residues: 173.1516 Evaluate side-chains 148 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 87 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 LEU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 147 ARG 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 180 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 223 PHE 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 482 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 663 LEU 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 810 SER 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 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 212 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 323 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 437 CYS 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 567 CYS Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 701 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 139 optimal weight: 0.7980 chunk 79 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 147 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 486 ASN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.192334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128580 restraints weight = 19387.293| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.39 r_work: 0.3388 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13036 Z= 0.134 Angle : 0.629 18.068 17763 Z= 0.300 Chirality : 0.046 0.622 2015 Planarity : 0.004 0.053 2305 Dihedral : 7.923 77.838 2081 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 29.00 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.20 % Favored : 91.43 % Rotamer: Outliers : 5.02 % Allowed : 26.16 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.21), residues: 1623 helix: -0.43 (0.43), residues: 165 sheet: -0.86 (0.25), residues: 465 loop : -1.96 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 952 HIS 0.003 0.001 HIS A 291 PHE 0.010 0.001 PHE A 19 TYR 0.012 0.001 TYR B 318 ARG 0.005 0.000 ARG A 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 7) link_NAG-ASN : angle 6.45843 ( 21) link_BETA1-4 : bond 0.00417 ( 6) link_BETA1-4 : angle 2.33761 ( 18) link_ALPHA1-3 : bond 0.01739 ( 1) link_ALPHA1-3 : angle 3.62985 ( 3) hydrogen bonds : bond 0.02879 ( 308) hydrogen bonds : angle 5.89776 ( 795) link_BETA1-6 : bond 0.01088 ( 1) link_BETA1-6 : angle 1.62248 ( 3) SS BOND : bond 0.00271 ( 37) SS BOND : angle 1.38164 ( 74) covalent geometry : bond 0.00315 (12984) covalent geometry : angle 0.57681 (17644) *********************** 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 160 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 90 time to evaluate : 2.052 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 102 ASP cc_start: 0.8628 (t0) cc_final: 0.8250 (OUTLIER) REVERT: A 180 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: A 223 PHE cc_start: 0.6479 (OUTLIER) cc_final: 0.5492 (m-80) REVERT: A 278 HIS cc_start: 0.7536 (OUTLIER) cc_final: 0.7104 (t-170) REVERT: A 459 GLN cc_start: 0.7763 (mp10) cc_final: 0.7090 (mp10) REVERT: A 486 ASN cc_start: 0.7746 (OUTLIER) cc_final: 0.7500 (m-40) REVERT: A 497 ASN cc_start: 0.7636 (t0) cc_final: 0.7131 (m-40) REVERT: A 704 LEU cc_start: 0.7865 (tt) cc_final: 0.7612 (mm) REVERT: A 785 GLU cc_start: 0.7085 (tt0) cc_final: 0.6332 (pp20) REVERT: A 895 MET cc_start: 0.4508 (tpp) cc_final: 0.3929 (tpp) REVERT: A 902 MET cc_start: 0.4760 (ppp) cc_final: 0.4289 (ppp) REVERT: A 927 HIS cc_start: 0.3566 (OUTLIER) cc_final: 0.3202 (t70) REVERT: B 66 ASP cc_start: 0.8647 (t0) cc_final: 0.8400 (t70) REVERT: B 267 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: B 335 MET cc_start: 0.7122 (mmt) cc_final: 0.6900 (mmt) REVERT: B 361 ASP cc_start: 0.8013 (t0) cc_final: 0.7700 (t0) REVERT: B 387 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7691 (mtm) REVERT: B 434 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6242 (t70) REVERT: B 535 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6996 (ptm) REVERT: B 568 MET cc_start: 0.7898 (tpt) cc_final: 0.7622 (tpp) REVERT: B 588 CYS cc_start: 0.1776 (OUTLIER) cc_final: 0.0417 (m) outliers start: 70 outliers final: 46 residues processed: 150 average time/residue: 0.9429 time to fit residues: 160.2099 Evaluate side-chains 137 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 82 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 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 180 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 223 PHE 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 486 ASN Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 705 VAL 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 921 GLN Chi-restraints excluded: chain A residue 927 HIS Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 20 SER 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 212 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 267 GLN 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 432 ASP Chi-restraints excluded: chain B residue 434 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 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 654 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 69 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 486 ASN ** 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 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS B 654 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 = 0.4315 r_free = 0.4315 target = 0.187560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118443 restraints weight = 23058.473| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.17 r_work: 0.3317 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 13036 Z= 0.325 Angle : 0.797 13.657 17763 Z= 0.391 Chirality : 0.052 0.640 2015 Planarity : 0.006 0.063 2305 Dihedral : 8.072 77.851 2079 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 33.86 Ramachandran Plot: Outliers : 0.37 % Allowed : 11.34 % Favored : 88.29 % Rotamer: Outliers : 6.38 % Allowed : 25.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.20), residues: 1623 helix: -0.79 (0.42), residues: 166 sheet: -0.98 (0.25), residues: 471 loop : -2.35 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 910 HIS 0.007 0.001 HIS A 291 PHE 0.025 0.003 PHE A 356 TYR 0.019 0.002 TYR A 288 ARG 0.007 0.001 ARG A 77 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 7) link_NAG-ASN : angle 5.47063 ( 21) link_BETA1-4 : bond 0.00346 ( 6) link_BETA1-4 : angle 2.10673 ( 18) link_ALPHA1-3 : bond 0.02004 ( 1) link_ALPHA1-3 : angle 4.14461 ( 3) hydrogen bonds : bond 0.04145 ( 308) hydrogen bonds : angle 6.24429 ( 795) link_BETA1-6 : bond 0.00652 ( 1) link_BETA1-6 : angle 2.01994 ( 3) SS BOND : bond 0.00423 ( 37) SS BOND : angle 1.52533 ( 74) covalent geometry : bond 0.00773 (12984) covalent geometry : angle 0.76518 (17644) *********************** 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 168 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 79 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8742 (t0) cc_final: 0.8492 (OUTLIER) REVERT: A 147 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8253 (mtt180) REVERT: A 223 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.5528 (m-80) REVERT: A 288 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8172 (m-80) REVERT: A 400 ARG cc_start: 0.7364 (mtt90) cc_final: 0.7038 (mtp85) REVERT: A 459 GLN cc_start: 0.7847 (mp10) cc_final: 0.7162 (mp10) REVERT: A 486 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7495 (m-40) REVERT: A 497 ASN cc_start: 0.7657 (t0) cc_final: 0.7389 (m-40) REVERT: A 703 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7432 (tpt) REVERT: A 704 LEU cc_start: 0.7906 (tt) cc_final: 0.7653 (mm) REVERT: A 785 GLU cc_start: 0.7326 (tt0) cc_final: 0.6611 (pp20) REVERT: A 895 MET cc_start: 0.4704 (tpp) cc_final: 0.4111 (tpp) REVERT: A 902 MET cc_start: 0.4837 (ppp) cc_final: 0.4405 (ppp) REVERT: A 927 HIS cc_start: 0.3982 (OUTLIER) cc_final: 0.3538 (t-170) REVERT: B 319 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: B 323 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: B 335 MET cc_start: 0.7256 (mmt) cc_final: 0.6894 (mmt) REVERT: B 361 ASP cc_start: 0.8392 (t0) cc_final: 0.8069 (t0) REVERT: B 387 MET cc_start: 0.8367 (mtt) cc_final: 0.7892 (mtm) REVERT: B 535 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7089 (ptm) REVERT: B 568 MET cc_start: 0.7932 (tpt) cc_final: 0.7667 (tpp) REVERT: B 588 CYS cc_start: 0.1351 (OUTLIER) cc_final: 0.0211 (m) outliers start: 89 outliers final: 62 residues processed: 157 average time/residue: 1.3260 time to fit residues: 236.9545 Evaluate side-chains 145 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 74 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 147 ARG 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 288 TYR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 373 ASP 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 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 547 THR Chi-restraints excluded: chain A residue 597 ARG 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 810 SER 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 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 145 LEU Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 319 GLN 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 394 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 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 563 ARG Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 588 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 25 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 142 optimal weight: 0.0030 chunk 137 optimal weight: 20.0000 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 GLN 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 = 0.192551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128857 restraints weight = 20586.498| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.45 r_work: 0.3393 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3303 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= 0.098 Angle : 0.570 13.111 17763 Z= 0.278 Chirality : 0.044 0.547 2015 Planarity : 0.004 0.054 2305 Dihedral : 7.435 81.175 2076 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 30.75 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.72 % Favored : 92.91 % Rotamer: Outliers : 4.01 % Allowed : 27.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.21), residues: 1623 helix: -0.35 (0.43), residues: 165 sheet: -0.80 (0.25), residues: 466 loop : -2.03 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 910 HIS 0.002 0.000 HIS B 192 PHE 0.009 0.001 PHE B 56 TYR 0.012 0.001 TYR B 318 ARG 0.003 0.000 ARG A 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00626 ( 7) link_NAG-ASN : angle 4.54358 ( 21) link_BETA1-4 : bond 0.00466 ( 6) link_BETA1-4 : angle 2.06966 ( 18) link_ALPHA1-3 : bond 0.01721 ( 1) link_ALPHA1-3 : angle 3.48237 ( 3) hydrogen bonds : bond 0.02661 ( 308) hydrogen bonds : angle 5.73972 ( 795) link_BETA1-6 : bond 0.01049 ( 1) link_BETA1-6 : angle 1.76608 ( 3) SS BOND : bond 0.00232 ( 37) SS BOND : angle 1.13041 ( 74) covalent geometry : bond 0.00225 (12984) covalent geometry : angle 0.53824 (17644) *********************** 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 145 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 89 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8681 (t0) cc_final: 0.8390 (OUTLIER) REVERT: A 147 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8059 (mtt180) REVERT: A 223 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.5531 (m-80) REVERT: A 459 GLN cc_start: 0.7701 (mp10) cc_final: 0.7017 (mp10) REVERT: A 497 ASN cc_start: 0.7702 (t0) cc_final: 0.7169 (m-40) REVERT: A 535 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7398 (mm) REVERT: A 704 LEU cc_start: 0.7851 (tt) cc_final: 0.7574 (mm) REVERT: A 743 ARG cc_start: 0.4231 (ttt180) cc_final: 0.3953 (ttt-90) REVERT: A 895 MET cc_start: 0.4388 (tpp) cc_final: 0.3894 (tpp) REVERT: A 902 MET cc_start: 0.5092 (ppp) cc_final: 0.4868 (ppp) REVERT: A 927 HIS cc_start: 0.3812 (OUTLIER) cc_final: 0.3427 (t70) REVERT: B 319 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8471 (mt0) REVERT: B 335 MET cc_start: 0.7032 (mmt) cc_final: 0.6705 (mmt) REVERT: B 361 ASP cc_start: 0.8101 (t0) cc_final: 0.7738 (t0) REVERT: B 387 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7676 (mtm) REVERT: B 390 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.6684 (ptmt) REVERT: B 393 ASP cc_start: 0.8279 (m-30) cc_final: 0.8008 (m-30) REVERT: B 508 CYS cc_start: 0.2944 (OUTLIER) cc_final: 0.2676 (p) REVERT: B 535 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6913 (ptm) REVERT: B 568 MET cc_start: 0.7873 (tpt) cc_final: 0.7608 (tpp) outliers start: 56 outliers final: 38 residues processed: 135 average time/residue: 0.9912 time to fit residues: 150.1120 Evaluate side-chains 124 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 78 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 147 ARG 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 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 466 LEU 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 597 ARG Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 705 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 939 VAL Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 319 GLN 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 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 561 THR Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 567 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 39 optimal weight: 0.0040 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 70 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.6798 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.190952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119401 restraints weight = 27955.222| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.01 r_work: 0.3369 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13036 Z= 0.157 Angle : 0.591 12.092 17763 Z= 0.289 Chirality : 0.045 0.538 2015 Planarity : 0.004 0.056 2305 Dihedral : 7.252 74.996 2073 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 31.51 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.06 % Favored : 90.57 % Rotamer: Outliers : 4.23 % Allowed : 27.31 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.21), residues: 1623 helix: -0.31 (0.43), residues: 167 sheet: -0.70 (0.25), residues: 485 loop : -2.07 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 952 HIS 0.004 0.001 HIS A 291 PHE 0.013 0.001 PHE A 19 TYR 0.011 0.001 TYR B 318 ARG 0.004 0.000 ARG A 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00565 ( 7) link_NAG-ASN : angle 4.44457 ( 21) link_BETA1-4 : bond 0.00391 ( 6) link_BETA1-4 : angle 1.86677 ( 18) link_ALPHA1-3 : bond 0.01717 ( 1) link_ALPHA1-3 : angle 3.64112 ( 3) hydrogen bonds : bond 0.02879 ( 308) hydrogen bonds : angle 5.70063 ( 795) link_BETA1-6 : bond 0.00867 ( 1) link_BETA1-6 : angle 1.79011 ( 3) SS BOND : bond 0.00247 ( 37) SS BOND : angle 1.10272 ( 74) covalent geometry : bond 0.00372 (12984) covalent geometry : angle 0.56265 (17644) *********************** 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 144 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 85 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8811 (t0) cc_final: 0.8547 (OUTLIER) REVERT: A 147 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8009 (mtt180) REVERT: A 223 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.5449 (m-80) REVERT: A 459 GLN cc_start: 0.7709 (mp10) cc_final: 0.7057 (mp10) REVERT: A 497 ASN cc_start: 0.7680 (t0) cc_final: 0.7150 (m-40) REVERT: A 594 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7606 (tp30) REVERT: A 704 LEU cc_start: 0.7856 (tt) cc_final: 0.7607 (mm) REVERT: A 743 ARG cc_start: 0.4397 (ttt180) cc_final: 0.4049 (ttt-90) REVERT: A 785 GLU cc_start: 0.7212 (tt0) cc_final: 0.6514 (pp20) REVERT: A 895 MET cc_start: 0.4427 (tpp) cc_final: 0.3913 (tpp) REVERT: A 902 MET cc_start: 0.5041 (ppp) cc_final: 0.4655 (ppp) REVERT: A 927 HIS cc_start: 0.3902 (OUTLIER) cc_final: 0.3510 (t70) REVERT: B 335 MET cc_start: 0.7114 (mmt) cc_final: 0.6778 (mmt) REVERT: B 361 ASP cc_start: 0.8233 (t0) cc_final: 0.7883 (t0) REVERT: B 387 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7732 (mtm) REVERT: B 390 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.6428 (ptmm) REVERT: B 393 ASP cc_start: 0.8273 (m-30) cc_final: 0.7954 (m-30) REVERT: B 434 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.6189 (t70) REVERT: B 508 CYS cc_start: 0.3073 (OUTLIER) cc_final: 0.2797 (p) REVERT: B 535 MET cc_start: 0.7792 (OUTLIER) cc_final: 0.7014 (ptm) REVERT: B 568 MET cc_start: 0.7879 (tpt) cc_final: 0.7638 (tpp) outliers start: 59 outliers final: 43 residues processed: 132 average time/residue: 0.9682 time to fit residues: 143.9068 Evaluate side-chains 132 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 81 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 147 ARG 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 288 TYR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 597 ARG 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 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 939 VAL Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 10 VAL 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 212 VAL Chi-restraints excluded: chain B residue 287 MET 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 434 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 53 optimal weight: 0.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.190716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.124978 restraints weight = 28275.510| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.43 r_work: 0.3353 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13036 Z= 0.161 Angle : 0.595 11.765 17763 Z= 0.291 Chirality : 0.045 0.515 2015 Planarity : 0.004 0.056 2305 Dihedral : 7.154 74.125 2073 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 31.39 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.25 % Favored : 90.44 % Rotamer: Outliers : 4.09 % Allowed : 27.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.21), residues: 1623 helix: -0.27 (0.43), residues: 167 sheet: -0.65 (0.25), residues: 483 loop : -2.07 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 910 HIS 0.004 0.001 HIS A 291 PHE 0.013 0.001 PHE A 19 TYR 0.011 0.001 TYR A 329 ARG 0.011 0.000 ARG A 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 7) link_NAG-ASN : angle 4.32580 ( 21) link_BETA1-4 : bond 0.00386 ( 6) link_BETA1-4 : angle 1.80901 ( 18) link_ALPHA1-3 : bond 0.01677 ( 1) link_ALPHA1-3 : angle 3.43545 ( 3) hydrogen bonds : bond 0.02870 ( 308) hydrogen bonds : angle 5.64497 ( 795) link_BETA1-6 : bond 0.00779 ( 1) link_BETA1-6 : angle 1.93528 ( 3) SS BOND : bond 0.00264 ( 37) SS BOND : angle 1.06909 ( 74) covalent geometry : bond 0.00380 (12984) covalent geometry : angle 0.56820 (17644) *********************** 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 142 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 85 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8639 (t0) cc_final: 0.8389 (OUTLIER) REVERT: A 147 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7940 (mtt180) REVERT: A 223 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.5447 (m-80) REVERT: A 497 ASN cc_start: 0.7585 (t0) cc_final: 0.7148 (m-40) REVERT: A 535 LEU cc_start: 0.7655 (mm) cc_final: 0.7418 (mm) REVERT: A 594 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: A 704 LEU cc_start: 0.7863 (tt) cc_final: 0.7632 (mm) REVERT: A 743 ARG cc_start: 0.4484 (ttt180) cc_final: 0.4127 (ttt-90) REVERT: A 785 GLU cc_start: 0.7144 (tt0) cc_final: 0.6388 (pp20) REVERT: A 895 MET cc_start: 0.4117 (tpp) cc_final: 0.3556 (tpp) REVERT: A 902 MET cc_start: 0.4928 (ppp) cc_final: 0.4637 (ppp) REVERT: A 927 HIS cc_start: 0.3963 (OUTLIER) cc_final: 0.3588 (t70) REVERT: B 335 MET cc_start: 0.6967 (mmt) cc_final: 0.6628 (mmt) REVERT: B 361 ASP cc_start: 0.8072 (t0) cc_final: 0.7785 (t0) REVERT: B 387 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7675 (mtm) REVERT: B 390 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.6475 (ptmm) REVERT: B 393 ASP cc_start: 0.8082 (m-30) cc_final: 0.7767 (m-30) REVERT: B 434 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.6189 (t70) REVERT: B 508 CYS cc_start: 0.2957 (OUTLIER) cc_final: 0.2664 (p) REVERT: B 535 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6993 (ptm) REVERT: B 568 MET cc_start: 0.7868 (tpt) cc_final: 0.7639 (tpp) outliers start: 57 outliers final: 45 residues processed: 131 average time/residue: 0.9485 time to fit residues: 140.7926 Evaluate side-chains 135 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 82 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 147 ARG 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 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 633 LEU 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 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 939 VAL Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 10 VAL 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 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 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 434 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 132 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 161 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.192734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122335 restraints weight = 28178.293| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.98 r_work: 0.3394 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13036 Z= 0.097 Angle : 0.535 11.763 17763 Z= 0.262 Chirality : 0.043 0.476 2015 Planarity : 0.004 0.059 2305 Dihedral : 6.691 64.736 2073 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 31.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.26 % Favored : 91.43 % Rotamer: Outliers : 3.08 % Allowed : 28.46 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.21), residues: 1623 helix: 0.03 (0.44), residues: 166 sheet: -0.59 (0.25), residues: 487 loop : -1.95 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 967 HIS 0.003 0.000 HIS B 192 PHE 0.015 0.001 PHE B 56 TYR 0.011 0.001 TYR B 318 ARG 0.004 0.000 ARG A 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 7) link_NAG-ASN : angle 4.10953 ( 21) link_BETA1-4 : bond 0.00431 ( 6) link_BETA1-4 : angle 1.72896 ( 18) link_ALPHA1-3 : bond 0.01549 ( 1) link_ALPHA1-3 : angle 3.01358 ( 3) hydrogen bonds : bond 0.02399 ( 308) hydrogen bonds : angle 5.32663 ( 795) link_BETA1-6 : bond 0.00819 ( 1) link_BETA1-6 : angle 1.83618 ( 3) SS BOND : bond 0.00199 ( 37) SS BOND : angle 0.92985 ( 74) covalent geometry : bond 0.00232 (12984) covalent geometry : angle 0.50955 (17644) ********************** 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 131 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 88 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8670 (t0) cc_final: 0.8446 (OUTLIER) REVERT: A 397 GLU cc_start: 0.7716 (mp0) cc_final: 0.7436 (tm-30) REVERT: A 459 GLN cc_start: 0.7681 (mp10) cc_final: 0.6991 (mp10) REVERT: A 497 ASN cc_start: 0.7705 (t0) cc_final: 0.7191 (m-40) REVERT: A 535 LEU cc_start: 0.7684 (mm) cc_final: 0.7406 (mm) REVERT: A 704 LEU cc_start: 0.7892 (tt) cc_final: 0.7641 (mm) REVERT: A 743 ARG cc_start: 0.4293 (ttt180) cc_final: 0.3921 (ttt-90) REVERT: A 895 MET cc_start: 0.4000 (tpp) cc_final: 0.3594 (tpp) REVERT: A 902 MET cc_start: 0.5171 (ppp) cc_final: 0.4882 (ppp) REVERT: A 927 HIS cc_start: 0.3866 (OUTLIER) cc_final: 0.3525 (t70) REVERT: A 939 VAL cc_start: 0.5364 (OUTLIER) cc_final: 0.4944 (p) REVERT: B 335 MET cc_start: 0.7176 (mmt) cc_final: 0.6843 (mmt) REVERT: B 361 ASP cc_start: 0.8153 (t0) cc_final: 0.7849 (t0) REVERT: B 387 MET cc_start: 0.8138 (mtt) cc_final: 0.7690 (mtm) REVERT: B 390 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7162 (pptt) REVERT: B 434 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6061 (t70) REVERT: B 508 CYS cc_start: 0.2788 (OUTLIER) cc_final: 0.2534 (p) REVERT: B 535 MET cc_start: 0.7762 (ptp) cc_final: 0.7159 (ptm) REVERT: B 568 MET cc_start: 0.7879 (tpt) cc_final: 0.7612 (tpp) outliers start: 43 outliers final: 30 residues processed: 123 average time/residue: 0.9889 time to fit residues: 136.6352 Evaluate side-chains 120 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 1.338 ------------------------------------------------------------------------------- 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 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 288 TYR Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 ARG Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 705 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 939 VAL Chi-restraints excluded: chain A residue 968 TRP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 322 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 434 ASP Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 508 CYS Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 567 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 156 optimal weight: 10.0000 chunk 6 optimal weight: 0.0270 chunk 111 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- 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 ** 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 486 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN ** B 376 ASN ** 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 = 0.4349 r_free = 0.4349 target = 0.191070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127168 restraints weight = 19078.926| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.49 r_work: 0.3393 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13036 Z= 0.154 Angle : 0.582 11.429 17763 Z= 0.284 Chirality : 0.044 0.477 2015 Planarity : 0.004 0.059 2305 Dihedral : 6.595 57.201 2072 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 31.99 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.31 % Favored : 90.38 % Rotamer: Outliers : 3.01 % Allowed : 28.60 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.21), residues: 1623 helix: -0.04 (0.44), residues: 166 sheet: -0.51 (0.25), residues: 474 loop : -2.01 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 952 HIS 0.004 0.001 HIS A 291 PHE 0.013 0.001 PHE A 19 TYR 0.011 0.001 TYR B 318 ARG 0.006 0.000 ARG A 900 Details of bonding type rmsd link_NAG-ASN : bond 0.00521 ( 7) link_NAG-ASN : angle 4.39996 ( 21) link_BETA1-4 : bond 0.00370 ( 6) link_BETA1-4 : angle 1.62736 ( 18) link_ALPHA1-3 : bond 0.01541 ( 1) link_ALPHA1-3 : angle 3.15918 ( 3) hydrogen bonds : bond 0.02771 ( 308) hydrogen bonds : angle 5.38458 ( 795) link_BETA1-6 : bond 0.00694 ( 1) link_BETA1-6 : angle 1.93524 ( 3) SS BOND : bond 0.00248 ( 37) SS BOND : angle 1.00616 ( 74) covalent geometry : bond 0.00367 (12984) covalent geometry : angle 0.55535 (17644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13217.81 seconds wall clock time: 234 minutes 28.34 seconds (14068.34 seconds total)