Starting phenix.real_space_refine on Sun Nov 17 06:44:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcd_29931/11_2024/8gcd_29931.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcd_29931/11_2024/8gcd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcd_29931/11_2024/8gcd_29931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcd_29931/11_2024/8gcd_29931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcd_29931/11_2024/8gcd_29931.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcd_29931/11_2024/8gcd_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-5513/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: 11.52, per 1000 atoms: 0.88 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: 3.81 Conformation dependent library (CDL) restraints added in 2.5 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: 1.82 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: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 384 1.04 - 1.24: 1308 1.24 - 1.43: 4188 1.43 - 1.63: 7359 1.63 - 1.83: 129 Bond restraints: 13368 Sorted by residual: bond pdb=" C VAL A 742 " pdb=" N ARG A 743 " ideal model delta sigma weight residual 1.328 1.515 -0.187 1.04e-02 9.25e+03 3.23e+02 bond pdb=" CA ARG A 743 " pdb=" C ARG A 743 " ideal model delta sigma weight residual 1.528 1.707 -0.179 1.23e-02 6.61e+03 2.12e+02 bond pdb=" C ARG A 743 " pdb=" N ALA A 744 " ideal model delta sigma weight residual 1.331 1.510 -0.179 1.30e-02 5.92e+03 1.90e+02 bond pdb=" C ALA A 744 " pdb=" N GLU A 745 " ideal model delta sigma weight residual 1.332 1.525 -0.192 1.40e-02 5.10e+03 1.89e+02 bond pdb=" N ALA A 744 " pdb=" CA ALA A 744 " ideal model delta sigma weight residual 1.455 1.630 -0.174 1.32e-02 5.74e+03 1.74e+02 ... (remaining 13363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.57: 18403 4.57 - 9.13: 86 9.13 - 13.70: 12 13.70 - 18.26: 6 18.26 - 22.83: 4 Bond angle restraints: 18511 Sorted by residual: angle pdb=" N ALA A 744 " pdb=" CA ALA A 744 " pdb=" C ALA A 744 " ideal model delta sigma weight residual 108.74 128.84 -20.10 1.38e+00 5.25e-01 2.12e+02 angle pdb=" CA ARG A 743 " pdb=" C ARG A 743 " pdb=" N ALA A 744 " ideal model delta sigma weight residual 116.52 133.05 -16.53 1.17e+00 7.31e-01 2.00e+02 angle pdb=" N ARG A 743 " pdb=" CA ARG A 743 " pdb=" C ARG A 743 " ideal model delta sigma weight residual 108.23 127.35 -19.12 1.38e+00 5.25e-01 1.92e+02 angle pdb=" CA ALA A 744 " pdb=" C ALA A 744 " pdb=" N GLU A 745 " ideal model delta sigma weight residual 115.67 132.82 -17.15 1.36e+00 5.41e-01 1.59e+02 angle pdb=" CA PRO B 602 " pdb=" C PRO B 602 " pdb=" O PRO B 602 " ideal model delta sigma weight residual 120.60 97.77 22.83 1.82e+00 3.02e-01 1.57e+02 ... (remaining 18506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.00: 7350 24.00 - 47.99: 705 47.99 - 71.99: 120 71.99 - 95.98: 37 95.98 - 119.98: 29 Dihedral angle restraints: 8241 sinusoidal: 3549 harmonic: 4692 Sorted by residual: dihedral pdb=" CA LEU A 959 " pdb=" C LEU A 959 " pdb=" N GLU A 960 " pdb=" CA GLU A 960 " ideal model delta harmonic sigma weight residual -180.00 -101.22 -78.78 0 5.00e+00 4.00e-02 2.48e+02 dihedral pdb=" CB CYS B 575 " pdb=" SG CYS B 575 " pdb=" SG CYS B 586 " pdb=" CB CYS B 586 " ideal model delta sinusoidal sigma weight residual 93.00 179.55 -86.55 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS B 523 " pdb=" SG CYS B 523 " pdb=" SG CYS B 544 " pdb=" CB CYS B 544 " ideal model delta sinusoidal sigma weight residual 93.00 178.44 -85.44 1 1.00e+01 1.00e-02 8.84e+01 ... (remaining 8238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.966: 2013 0.966 - 1.931: 1 1.931 - 2.897: 0 2.897 - 3.862: 0 3.862 - 4.828: 1 Chirality restraints: 2015 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.64 -1.76 2.00e-02 2.50e+03 7.72e+03 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 559 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 2.43 -4.83 2.00e-01 2.50e+01 5.83e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-02 2.50e+03 5.66e+02 ... (remaining 2012 not shown) Planarity restraints: 2355 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.299 2.00e-02 2.50e+03 2.56e-01 8.16e+02 pdb=" C7 NAG E 2 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.447 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.289 2.00e-02 2.50e+03 2.44e-01 7.45e+02 pdb=" C7 NAG E 1 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.405 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.213 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.291 2.00e-02 2.50e+03 2.39e-01 7.15e+02 pdb=" C7 NAG C 2 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.198 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.394 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " -0.012 2.00e-02 2.50e+03 ... (remaining 2352 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.83: 4 1.83 - 2.52: 718 2.52 - 3.21: 13683 3.21 - 3.91: 27185 3.91 - 4.60: 38193 Nonbonded interactions: 79783 Sorted by model distance: nonbonded pdb=" OD1 ASP A 817 " pdb=" ND2 ASN A 833 " model vdw 1.134 2.950 nonbonded pdb=" OD2 ASP A 245 " pdb=" OE2 GLU A 252 " model vdw 1.417 2.800 nonbonded pdb=" O CYS A 602 " pdb=" OE2 GLU A 642 " model vdw 1.742 2.800 nonbonded pdb=" OE1 GLU B 378 " pdb=" NE ARG B 633 " model vdw 1.796 2.950 nonbonded pdb=" O ILE A 964 " pdb=" H ILE A 966 " model vdw 1.956 2.450 ... (remaining 79778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.400 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.550 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.780 ------------------------------------------------------------------------------- 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 12984 Z= 0.429 Angle : 1.001 22.826 17644 Z= 0.613 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 *********************** 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 : 1.342 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: 1.0964 time to fit residues: 255.7566 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 : 1.808 ------------------------------------------------------------------------------- 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: 7.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 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: 3.0040 ------------------------------------------------------------------------------- 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 43 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12984 Z= 0.413 Angle : 0.782 16.026 17644 Z= 0.390 Chirality : 0.054 0.985 2015 Planarity : 0.006 0.083 2305 Dihedral : 13.380 105.166 2130 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 25.73 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.43 % Favored : 90.07 % Rotamer: Outliers : 6.81 % Allowed : 24.16 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.58 (0.20), residues: 1623 helix: -1.11 (0.40), residues: 174 sheet: -1.14 (0.24), residues: 485 loop : -2.21 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 260 HIS 0.006 0.001 HIS B 255 PHE 0.023 0.002 PHE A 19 TYR 0.018 0.002 TYR B 318 ARG 0.009 0.001 ARG A 77 *********************** 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 196 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 101 time to evaluate : 1.380 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: A 48 GLU cc_start: 0.6531 (pm20) cc_final: 0.6328 (pm20) REVERT: A 91 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7815 (pt0) REVERT: A 288 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: A 535 LEU cc_start: 0.7365 (mm) cc_final: 0.7089 (mm) REVERT: A 648 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: A 649 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7735 (tt) REVERT: A 704 LEU cc_start: 0.8094 (tt) cc_final: 0.7652 (mp) REVERT: A 895 MET cc_start: 0.4916 (tpp) cc_final: 0.3943 (tpp) REVERT: A 899 GLN cc_start: 0.6697 (mm-40) cc_final: 0.6387 (mm110) REVERT: A 967 TRP cc_start: 0.3988 (OUTLIER) cc_final: 0.3447 (p-90) REVERT: B 66 ASP cc_start: 0.7530 (t0) cc_final: 0.7246 (t70) REVERT: B 109 ASP cc_start: 0.6774 (t70) cc_final: 0.6444 (t0) REVERT: B 387 MET cc_start: 0.7541 (mtt) cc_final: 0.7173 (mtm) REVERT: B 434 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.6208 (t70) REVERT: B 505 GLN cc_start: 0.6213 (tt0) cc_final: 0.5935 (pp30) REVERT: B 535 MET cc_start: 0.7888 (ptp) cc_final: 0.7302 (ptm) REVERT: B 568 MET cc_start: 0.7739 (tpt) cc_final: 0.7344 (tpp) outliers start: 95 outliers final: 41 residues processed: 182 average time/residue: 0.9852 time to fit residues: 202.3956 Evaluate side-chains 137 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 90 time to evaluate : 1.566 ------------------------------------------------------------------------------- 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 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 174 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 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 649 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 893 GLN Chi-restraints excluded: chain A residue 897 ARG 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 959 LEU Chi-restraints excluded: chain A residue 967 TRP 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 102 ILE 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 419 VAL 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 81 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 122 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12984 Z= 0.216 Angle : 0.599 11.048 17644 Z= 0.300 Chirality : 0.047 0.766 2015 Planarity : 0.005 0.062 2305 Dihedral : 10.250 98.802 2096 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.26 % Favored : 91.37 % Rotamer: Outliers : 4.73 % Allowed : 26.31 % Favored : 68.96 % 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: -2.25 (0.20), residues: 1623 helix: -0.59 (0.43), residues: 163 sheet: -0.95 (0.25), residues: 477 loop : -2.01 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 967 HIS 0.003 0.001 HIS B 255 PHE 0.011 0.001 PHE A 417 TYR 0.013 0.001 TYR B 318 ARG 0.006 0.000 ARG A 900 *********************** 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 160 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 94 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: A 91 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7776 (pt0) REVERT: A 288 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: A 459 GLN cc_start: 0.7495 (mp10) cc_final: 0.7144 (mp10) REVERT: A 704 LEU cc_start: 0.8004 (tt) cc_final: 0.7652 (mp) REVERT: A 788 ASN cc_start: 0.2286 (m-40) cc_final: 0.1962 (t0) REVERT: A 967 TRP cc_start: 0.3949 (OUTLIER) cc_final: 0.3525 (p-90) REVERT: B 66 ASP cc_start: 0.7482 (t0) cc_final: 0.7215 (t70) REVERT: B 109 ASP cc_start: 0.6696 (t70) cc_final: 0.6459 (t0) REVERT: B 323 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: B 387 MET cc_start: 0.7481 (mtt) cc_final: 0.7098 (mtm) REVERT: B 535 MET cc_start: 0.7882 (ptp) cc_final: 0.7356 (ptm) REVERT: B 568 MET cc_start: 0.7667 (tpt) cc_final: 0.7312 (tpp) outliers start: 66 outliers final: 34 residues processed: 151 average time/residue: 0.9168 time to fit residues: 157.5787 Evaluate side-chains 126 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 88 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 91 GLN Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 249 ASN 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 897 ARG 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 967 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 102 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 200 VAL 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 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 654 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 156 optimal weight: 0.0980 chunk 77 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12984 Z= 0.240 Angle : 0.602 10.620 17644 Z= 0.298 Chirality : 0.047 0.696 2015 Planarity : 0.004 0.057 2305 Dihedral : 8.587 87.117 2087 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.26 % Favored : 91.37 % Rotamer: Outliers : 4.95 % Allowed : 25.95 % Favored : 69.10 % 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: -2.20 (0.21), residues: 1623 helix: -0.59 (0.42), residues: 167 sheet: -0.89 (0.25), residues: 472 loop : -1.99 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 967 HIS 0.004 0.001 HIS A 291 PHE 0.016 0.001 PHE A 19 TYR 0.014 0.001 TYR B 318 ARG 0.005 0.000 ARG A 900 *********************** 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 161 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 92 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ARG cc_start: 0.6800 (ptt180) cc_final: 0.6591 (ptt180) REVERT: A 223 PHE cc_start: 0.6688 (OUTLIER) cc_final: 0.5860 (m-80) REVERT: A 288 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: A 459 GLN cc_start: 0.7503 (mp10) cc_final: 0.7115 (mp10) REVERT: A 660 MET cc_start: 0.7052 (mmt) cc_final: 0.6760 (tpp) REVERT: A 704 LEU cc_start: 0.8032 (tt) cc_final: 0.7747 (mm) REVERT: A 967 TRP cc_start: 0.4227 (OUTLIER) cc_final: 0.3797 (p-90) REVERT: B 227 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7093 (tpp) REVERT: B 387 MET cc_start: 0.7513 (mtt) cc_final: 0.7129 (mtm) REVERT: B 434 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.6170 (t70) REVERT: B 535 MET cc_start: 0.7891 (ptp) cc_final: 0.7263 (ptm) REVERT: B 568 MET cc_start: 0.7681 (tpt) cc_final: 0.7315 (tpp) outliers start: 69 outliers final: 41 residues processed: 150 average time/residue: 0.9787 time to fit residues: 165.7505 Evaluate side-chains 130 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 84 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 182 VAL Chi-restraints excluded: chain A residue 223 PHE 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 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 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 967 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 145 LEU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 THR 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 334 SER 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 509 HIS 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 654 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 140 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN ** 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 668 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 12984 Z= 0.475 Angle : 0.759 12.615 17644 Z= 0.376 Chirality : 0.052 0.678 2015 Planarity : 0.006 0.063 2305 Dihedral : 8.410 80.578 2078 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 33.11 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.91 % Favored : 88.72 % Rotamer: Outliers : 5.73 % Allowed : 25.81 % 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: -2.48 (0.20), residues: 1623 helix: -0.82 (0.41), residues: 169 sheet: -0.87 (0.25), residues: 462 loop : -2.29 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 910 HIS 0.006 0.001 HIS A 291 PHE 0.024 0.002 PHE A 356 TYR 0.018 0.002 TYR A 288 ARG 0.004 0.001 ARG A 327 *********************** 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 163 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 83 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7324 (mtt180) REVERT: A 223 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.5714 (m-80) REVERT: A 288 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: A 459 GLN cc_start: 0.7603 (mp10) cc_final: 0.7133 (mp10) REVERT: A 660 MET cc_start: 0.6947 (mmt) cc_final: 0.6682 (tpp) REVERT: A 704 LEU cc_start: 0.8053 (tt) cc_final: 0.7770 (mm) REVERT: A 967 TRP cc_start: 0.4408 (OUTLIER) cc_final: 0.3951 (p-90) REVERT: B 323 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 335 MET cc_start: 0.6510 (mmt) cc_final: 0.6179 (mmt) REVERT: B 387 MET cc_start: 0.7552 (mtt) cc_final: 0.7206 (ptp) REVERT: B 535 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7257 (ptm) REVERT: B 568 MET cc_start: 0.7780 (tpt) cc_final: 0.7512 (tpp) REVERT: B 588 CYS cc_start: 0.2120 (OUTLIER) cc_final: 0.0964 (m) outliers start: 80 outliers final: 52 residues processed: 151 average time/residue: 0.9396 time to fit residues: 160.9176 Evaluate side-chains 138 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 79 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN 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 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 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 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 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 939 VAL Chi-restraints excluded: chain A residue 967 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 112 VAL 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 304 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 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 516 ILE Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 567 CYS Chi-restraints excluded: chain B residue 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 52 optimal weight: 4.9990 chunk 141 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 overall best weight: 0.8642 ------------------------------------------------------------------------------- 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 278 HIS ** 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 654 ASN B 668 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12984 Z= 0.165 Angle : 0.543 10.891 17644 Z= 0.271 Chirality : 0.044 0.572 2015 Planarity : 0.004 0.056 2305 Dihedral : 7.659 83.887 2077 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 30.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.64 % Favored : 91.99 % Rotamer: Outliers : 3.94 % Allowed : 27.74 % 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: -2.13 (0.21), residues: 1623 helix: -0.38 (0.43), residues: 165 sheet: -0.80 (0.25), residues: 473 loop : -1.99 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 967 HIS 0.002 0.001 HIS B 255 PHE 0.010 0.001 PHE A 191 TYR 0.012 0.001 TYR B 318 ARG 0.013 0.000 ARG A 77 *********************** 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 143 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 88 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.5667 (m-80) REVERT: A 459 GLN cc_start: 0.7458 (mp10) cc_final: 0.7040 (mp10) REVERT: A 660 MET cc_start: 0.6957 (mmt) cc_final: 0.6714 (tpp) REVERT: A 704 LEU cc_start: 0.8122 (tt) cc_final: 0.7805 (mm) REVERT: B 267 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: B 335 MET cc_start: 0.6458 (mmt) cc_final: 0.6131 (mmt) REVERT: B 387 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7066 (mtm) REVERT: B 535 MET cc_start: 0.7877 (ptp) cc_final: 0.7255 (ptm) REVERT: B 568 MET cc_start: 0.7709 (tpt) cc_final: 0.7486 (tpp) REVERT: B 588 CYS cc_start: 0.1581 (OUTLIER) cc_final: 0.1033 (m) outliers start: 55 outliers final: 35 residues processed: 135 average time/residue: 1.0710 time to fit residues: 164.8564 Evaluate side-chains 119 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 325 VAL 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 547 THR Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 967 TRP 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 267 GLN 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 432 ASP Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 561 THR Chi-restraints excluded: chain B residue 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 151 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 156 optimal weight: 0.0040 chunk 97 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 72 optimal weight: 0.0270 overall best weight: 0.7454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12984 Z= 0.156 Angle : 0.522 11.353 17644 Z= 0.261 Chirality : 0.043 0.508 2015 Planarity : 0.004 0.056 2305 Dihedral : 7.113 70.583 2075 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 30.55 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.08 % Favored : 91.55 % Rotamer: Outliers : 3.44 % Allowed : 28.10 % 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: -0.08 (0.44), residues: 165 sheet: -0.65 (0.25), residues: 487 loop : -1.88 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 967 HIS 0.003 0.001 HIS B 509 PHE 0.010 0.001 PHE A 19 TYR 0.011 0.001 TYR B 318 ARG 0.013 0.000 ARG A 77 *********************** 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 137 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 89 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLN cc_start: 0.7398 (mp10) cc_final: 0.6977 (mp10) REVERT: A 660 MET cc_start: 0.6984 (mmt) cc_final: 0.6735 (tpp) REVERT: A 703 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7111 (tpt) REVERT: A 704 LEU cc_start: 0.8038 (tt) cc_final: 0.7749 (mm) REVERT: B 335 MET cc_start: 0.6480 (mmt) cc_final: 0.6146 (mmt) REVERT: B 387 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7071 (mtm) REVERT: B 509 HIS cc_start: 0.4804 (OUTLIER) cc_final: 0.4471 (m-70) REVERT: B 535 MET cc_start: 0.7878 (ptp) cc_final: 0.7248 (ptm) REVERT: B 568 MET cc_start: 0.7638 (tpt) cc_final: 0.7355 (tpp) outliers start: 48 outliers final: 36 residues processed: 128 average time/residue: 1.0142 time to fit residues: 146.0543 Evaluate side-chains 122 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 83 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 182 VAL 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 547 THR Chi-restraints excluded: chain A residue 597 ARG 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 761 VAL Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 967 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 102 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 249 THR 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 432 ASP Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 454 THR Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 537 SER 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 96 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12984 Z= 0.314 Angle : 0.619 11.704 17644 Z= 0.309 Chirality : 0.046 0.514 2015 Planarity : 0.005 0.056 2305 Dihedral : 7.215 65.589 2074 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.80 % Favored : 89.83 % Rotamer: Outliers : 4.66 % Allowed : 27.38 % Favored : 67.96 % 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: -2.04 (0.21), residues: 1623 helix: -0.23 (0.43), residues: 165 sheet: -0.66 (0.25), residues: 491 loop : -2.02 (0.19), residues: 967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 952 HIS 0.005 0.001 HIS A 291 PHE 0.017 0.002 PHE A 19 TYR 0.013 0.002 TYR A 288 ARG 0.008 0.001 ARG A 77 *********************** 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 150 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 85 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 PHE cc_start: 0.6962 (OUTLIER) cc_final: 0.5605 (m-80) REVERT: A 301 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7881 (p0) REVERT: A 459 GLN cc_start: 0.7436 (mp10) cc_final: 0.7009 (mp10) REVERT: A 660 MET cc_start: 0.7007 (mmt) cc_final: 0.6751 (tpp) REVERT: A 703 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7191 (tpt) REVERT: A 704 LEU cc_start: 0.8044 (tt) cc_final: 0.7766 (mm) REVERT: B 335 MET cc_start: 0.6529 (mmt) cc_final: 0.6186 (mmt) REVERT: B 387 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7121 (mtm) REVERT: B 535 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7278 (ptm) REVERT: B 568 MET cc_start: 0.7745 (tpt) cc_final: 0.7484 (tpp) outliers start: 65 outliers final: 44 residues processed: 142 average time/residue: 0.9853 time to fit residues: 159.0798 Evaluate side-chains 130 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 81 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 482 VAL 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 597 ARG 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 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 939 VAL Chi-restraints excluded: chain A residue 967 TRP 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 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 329 THR 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 567 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 114 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN B 313 ASN ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12984 Z= 0.325 Angle : 0.619 11.814 17644 Z= 0.311 Chirality : 0.046 0.512 2015 Planarity : 0.005 0.061 2305 Dihedral : 7.233 67.862 2074 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 33.03 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.80 % Favored : 89.83 % Rotamer: Outliers : 4.16 % Allowed : 27.81 % Favored : 68.03 % 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: -2.13 (0.21), residues: 1623 helix: -0.27 (0.43), residues: 165 sheet: -0.64 (0.25), residues: 484 loop : -2.13 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 910 HIS 0.005 0.001 HIS A 291 PHE 0.017 0.002 PHE A 19 TYR 0.012 0.002 TYR A 207 ARG 0.014 0.001 ARG A 77 *********************** 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 139 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 81 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.5649 (m-80) REVERT: A 660 MET cc_start: 0.7139 (mmt) cc_final: 0.6896 (tpp) REVERT: A 703 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7162 (tpt) REVERT: A 704 LEU cc_start: 0.8068 (tt) cc_final: 0.7774 (mm) REVERT: B 335 MET cc_start: 0.6528 (mmt) cc_final: 0.6202 (mmt) REVERT: B 387 MET cc_start: 0.7434 (mtt) cc_final: 0.7030 (mtm) REVERT: B 434 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6254 (t70) REVERT: B 535 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7268 (ptm) REVERT: B 568 MET cc_start: 0.7723 (tpt) cc_final: 0.7499 (tpp) outliers start: 58 outliers final: 45 residues processed: 129 average time/residue: 0.8946 time to fit residues: 133.6482 Evaluate side-chains 128 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 79 time to evaluate : 1.663 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 384 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 597 ARG 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 939 VAL Chi-restraints excluded: chain A residue 967 TRP Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 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 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 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 567 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12984 Z= 0.179 Angle : 0.543 11.677 17644 Z= 0.272 Chirality : 0.043 0.488 2015 Planarity : 0.004 0.058 2305 Dihedral : 6.715 60.778 2070 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 32.47 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.14 % Favored : 91.49 % Rotamer: Outliers : 3.44 % Allowed : 28.53 % Favored : 68.03 % 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: -1.91 (0.21), residues: 1623 helix: -0.02 (0.44), residues: 166 sheet: -0.61 (0.24), residues: 500 loop : -1.94 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 967 HIS 0.003 0.001 HIS B 192 PHE 0.012 0.001 PHE B 56 TYR 0.012 0.001 TYR B 318 ARG 0.007 0.000 ARG A 77 ********************** 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: 48 poor density : 83 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 GLN cc_start: 0.7421 (mp10) cc_final: 0.6975 (mp10) REVERT: A 660 MET cc_start: 0.7008 (mmt) cc_final: 0.6758 (tpp) REVERT: A 703 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7190 (tpt) REVERT: A 704 LEU cc_start: 0.8041 (tt) cc_final: 0.7748 (mm) REVERT: A 815 ILE cc_start: 0.5981 (OUTLIER) cc_final: 0.5653 (pt) REVERT: B 335 MET cc_start: 0.6494 (mmt) cc_final: 0.6233 (mmt) REVERT: B 387 MET cc_start: 0.7326 (mtt) cc_final: 0.6981 (mtm) REVERT: B 434 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6203 (t70) REVERT: B 535 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7236 (ptm) REVERT: B 568 MET cc_start: 0.7704 (tpt) cc_final: 0.7445 (tpp) outliers start: 48 outliers final: 40 residues processed: 122 average time/residue: 0.9355 time to fit residues: 130.2762 Evaluate side-chains 124 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 80 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 335 ARG Chi-restraints excluded: chain A residue 482 VAL 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 597 ARG 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 785 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 915 TYR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 967 TRP Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 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 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 437 CYS Chi-restraints excluded: chain B residue 509 HIS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 537 SER Chi-restraints excluded: chain B residue 567 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 118 optimal weight: 0.0050 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.192120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128868 restraints weight = 22354.341| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 3.55 r_work: 0.3421 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12984 Z= 0.151 Angle : 0.519 10.160 17644 Z= 0.261 Chirality : 0.043 0.470 2015 Planarity : 0.004 0.058 2305 Dihedral : 6.280 56.784 2070 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 32.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.83 % Favored : 91.92 % Rotamer: Outliers : 2.94 % Allowed : 28.96 % 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: -1.79 (0.21), residues: 1623 helix: 0.19 (0.44), residues: 166 sheet: -0.54 (0.24), residues: 499 loop : -1.88 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 967 HIS 0.003 0.001 HIS B 192 PHE 0.014 0.001 PHE B 56 TYR 0.011 0.001 TYR B 318 ARG 0.023 0.000 ARG A 900 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4503.47 seconds wall clock time: 81 minutes 44.01 seconds (4904.01 seconds total)