Starting phenix.real_space_refine on Sun Apr 7 08:23:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppu_20447/04_2024/6ppu_20447_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppu_20447/04_2024/6ppu_20447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppu_20447/04_2024/6ppu_20447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppu_20447/04_2024/6ppu_20447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppu_20447/04_2024/6ppu_20447_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ppu_20447/04_2024/6ppu_20447_updated.pdb" } resolution = 3.5 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= 0.003 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 Fe 4 7.16 5 P 29 5.49 5 Mg 1 5.21 5 S 32 5.16 5 C 6299 2.51 5 N 1867 2.21 5 O 1872 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B ARG 597": "NH1" <-> "NH2" Residue "B PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 692": "NH1" <-> "NH2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "B ARG 746": "NH1" <-> "NH2" Residue "B ARG 751": "NH1" <-> "NH2" Residue "B GLU 784": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A ARG 751": "NH1" <-> "NH2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 914": "NH1" <-> "NH2" Residue "A ARG 990": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1033": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10104 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 5359 Classifications: {'peptide': 752} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 705} Chain breaks: 17 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 508 Unresolved non-hydrogen dihedrals: 320 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 1, 'GLU:plan': 29, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 301 Chain: "A" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4144 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 567} Chain breaks: 23 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 421 Unresolved non-hydrogen angles: 547 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 14, 'TYR:plan': 1, 'UNK:plan-1': 51, 'HIS:plan': 3, 'GLU:plan': 21, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 308 Chain: "X" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MG': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.22, per 1000 atoms: 0.62 Number of scatterers: 10104 At special positions: 0 Unit cell: (123.166, 95.6043, 112.83, 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) Fe 4 26.01 S 32 16.00 P 29 15.00 Mg 1 11.99 O 1872 8.00 N 1867 7.00 C 6299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.95 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1102 " pdb="FE4 SF4 A1102 " - pdb=" SG CYS A 807 " pdb="FE1 SF4 A1102 " - pdb=" SG CYS A1030 " pdb="FE2 SF4 A1102 " - pdb=" SG CYS A1036 " Number of angles added : 9 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 6 sheets defined 39.5% alpha, 5.2% beta 4 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'B' and resid 32 through 35 No H-bonds generated for 'chain 'B' and resid 32 through 35' Processing helix chain 'B' and resid 53 through 55 No H-bonds generated for 'chain 'B' and resid 53 through 55' Processing helix chain 'B' and resid 57 through 62 removed outlier: 3.903A pdb=" N TRP B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 97 removed outlier: 4.101A pdb=" N LEU B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 4.124A pdb=" N GLY B 124 " --> pdb=" O HIS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 removed outlier: 3.751A pdb=" N LEU B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 154 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 179 No H-bonds generated for 'chain 'B' and resid 176 through 179' Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.505A pdb=" N HIS B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 201 through 205' Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.543A pdb=" N MET B 225 " --> pdb=" O TRP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 243 through 246 No H-bonds generated for 'chain 'B' and resid 243 through 246' Processing helix chain 'B' and resid 254 through 261 removed outlier: 3.953A pdb=" N MET B 258 " --> pdb=" O PHE B 254 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 278 removed outlier: 3.579A pdb=" N LEU B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 295 through 301 removed outlier: 3.943A pdb=" N SER B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 403 through 415 removed outlier: 3.690A pdb=" N ALA B 411 " --> pdb=" O ARG B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 451 Processing helix chain 'B' and resid 470 through 480 removed outlier: 3.954A pdb=" N LEU B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.616A pdb=" N ALA B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 510 " --> pdb=" O ALA B 506 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 513 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 540 through 542 No H-bonds generated for 'chain 'B' and resid 540 through 542' Processing helix chain 'B' and resid 558 through 574 removed outlier: 3.613A pdb=" N THR B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B 570 " --> pdb=" O ARG B 566 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N HIS B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 589 removed outlier: 3.773A pdb=" N ARG B 588 " --> pdb=" O ALA B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 622 removed outlier: 3.668A pdb=" N PHE B 615 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 616 " --> pdb=" O LEU B 612 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP B 617 " --> pdb=" O ASP B 613 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 642 No H-bonds generated for 'chain 'B' and resid 639 through 642' Processing helix chain 'B' and resid 736 through 755 removed outlier: 3.519A pdb=" N LYS B 740 " --> pdb=" O SER B 736 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 745 " --> pdb=" O SER B 741 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 746 " --> pdb=" O LEU B 742 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 747 " --> pdb=" O ASP B 743 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 749 " --> pdb=" O ARG B 745 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 750 " --> pdb=" O ARG B 746 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG B 752 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU B 753 " --> pdb=" O GLU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 793 removed outlier: 3.649A pdb=" N THR B 791 " --> pdb=" O CYS B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 850 removed outlier: 3.612A pdb=" N GLN B 845 " --> pdb=" O HIS B 841 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 847 " --> pdb=" O GLY B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 875 removed outlier: 3.874A pdb=" N VAL B 868 " --> pdb=" O TRP B 864 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 869 " --> pdb=" O ALA B 865 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 873 " --> pdb=" O ASP B 869 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU B 874 " --> pdb=" O ALA B 870 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG B 875 " --> pdb=" O LEU B 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 184 removed outlier: 3.586A pdb=" N UNK A 183 " --> pdb=" O UNK A 180 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N UNK A 184 " --> pdb=" O UNK A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.977A pdb=" N UNK A 193 " --> pdb=" O UNK A 189 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N UNK A 194 " --> pdb=" O UNK A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.892A pdb=" N ILE A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 403 No H-bonds generated for 'chain 'A' and resid 401 through 403' Processing helix chain 'A' and resid 420 through 432 removed outlier: 3.705A pdb=" N LEU A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 446 Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.684A pdb=" N ARG A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 486 removed outlier: 3.656A pdb=" N VAL A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 removed outlier: 3.577A pdb=" N LEU A 500 " --> pdb=" O HIS A 496 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 503 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 506 " --> pdb=" O ARG A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 530 removed outlier: 3.508A pdb=" N TRP A 528 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 530 " --> pdb=" O GLN A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 539 No H-bonds generated for 'chain 'A' and resid 536 through 539' Processing helix chain 'A' and resid 548 through 568 removed outlier: 3.518A pdb=" N ARG A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 557 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL A 564 " --> pdb=" O THR A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 585 removed outlier: 4.165A pdb=" N ASP A 582 " --> pdb=" O ARG A 578 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 629 No H-bonds generated for 'chain 'A' and resid 626 through 629' Processing helix chain 'A' and resid 643 through 646 No H-bonds generated for 'chain 'A' and resid 643 through 646' Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.944A pdb=" N LEU A 672 " --> pdb=" O GLU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 728 through 739 removed outlier: 3.512A pdb=" N VAL A 732 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG A 736 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 737 " --> pdb=" O GLY A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 764 removed outlier: 3.609A pdb=" N GLN A 757 " --> pdb=" O CYS A 753 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 removed outlier: 3.662A pdb=" N LEU A 801 " --> pdb=" O PRO A 798 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN A 802 " --> pdb=" O SER A 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 798 through 802' Processing helix chain 'A' and resid 810 through 814 Processing helix chain 'A' and resid 824 through 826 No H-bonds generated for 'chain 'A' and resid 824 through 826' Processing helix chain 'A' and resid 829 through 835 removed outlier: 3.696A pdb=" N HIS A 833 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 829 through 835' Processing helix chain 'A' and resid 843 through 853 removed outlier: 3.614A pdb=" N VAL A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 872 removed outlier: 4.570A pdb=" N LEU A 869 " --> pdb=" O SER A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 883 removed outlier: 4.145A pdb=" N THR A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 960 removed outlier: 3.960A pdb=" N LEU A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1000 No H-bonds generated for 'chain 'A' and resid 997 through 1000' Processing helix chain 'A' and resid 1004 through 1014 removed outlier: 3.719A pdb=" N GLY A1008 " --> pdb=" O LEU A1004 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 42 through 46 removed outlier: 7.779A pdb=" N ILE B 45 " --> pdb=" O PRO B 349 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 351 " --> pdb=" O ILE B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 116 through 118 removed outlier: 7.614A pdb=" N SER B 117 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLY B 76 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL B 281 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU B 77 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 283 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 311 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LEU B 284 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR B 313 " --> pdb=" O LEU B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 395 through 397 removed outlier: 6.946A pdb=" N LEU B 765 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 675 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 676 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 349 through 354 removed outlier: 6.754A pdb=" N VAL A 684 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ARG A 352 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 686 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA A 354 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ALA A 688 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 619 " --> pdb=" O MET A 685 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR A 687 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 621 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N VAL A 689 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ALA A 604 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL A 386 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 606 " --> pdb=" O VAL A 386 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 930 through 933 removed outlier: 3.567A pdb=" N ARG A 921 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A 894 " --> pdb=" O LEU A 922 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARG A 924 " --> pdb=" O GLU A 892 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLU A 892 " --> pdb=" O ARG A 924 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 974 through 978 removed outlier: 3.621A pdb=" N GLN A 992 " --> pdb=" O GLY A 974 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 978 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR A 988 " --> pdb=" O TYR A 978 " (cutoff:3.500A) 189 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 4180 1.43 - 1.64: 6087 1.64 - 1.85: 45 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 10324 Sorted by residual: bond pdb=" N THR A 795 " pdb=" CA THR A 795 " ideal model delta sigma weight residual 1.457 1.508 -0.051 1.29e-02 6.01e+03 1.56e+01 bond pdb=" N VAL A 794 " pdb=" CA VAL A 794 " ideal model delta sigma weight residual 1.460 1.506 -0.046 1.19e-02 7.06e+03 1.48e+01 bond pdb=" N VAL A 793 " pdb=" CA VAL A 793 " ideal model delta sigma weight residual 1.459 1.504 -0.044 1.29e-02 6.01e+03 1.19e+01 bond pdb=" N VAL A 904 " pdb=" CA VAL A 904 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" N VAL A 915 " pdb=" CA VAL A 915 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.00e+01 ... (remaining 10319 not shown) Histogram of bond angle deviations from ideal: 73.51 - 85.67: 12 85.67 - 97.82: 0 97.82 - 109.98: 2503 109.98 - 122.14: 9618 122.14 - 134.30: 2105 Bond angle restraints: 14238 Sorted by residual: angle pdb=" N VAL B 488 " pdb=" CA VAL B 488 " pdb=" C VAL B 488 " ideal model delta sigma weight residual 111.90 105.31 6.59 8.10e-01 1.52e+00 6.62e+01 angle pdb=" N VAL A 794 " pdb=" CA VAL A 794 " pdb=" C VAL A 794 " ideal model delta sigma weight residual 110.53 117.95 -7.42 9.40e-01 1.13e+00 6.23e+01 angle pdb=" N LEU B 476 " pdb=" CA LEU B 476 " pdb=" C LEU B 476 " ideal model delta sigma weight residual 113.12 104.52 8.60 1.25e+00 6.40e-01 4.73e+01 angle pdb=" N THR B 338 " pdb=" CA THR B 338 " pdb=" C THR B 338 " ideal model delta sigma weight residual 114.56 106.74 7.82 1.27e+00 6.20e-01 3.79e+01 angle pdb=" C THR B 449 " pdb=" N ALA B 450 " pdb=" CA ALA B 450 " ideal model delta sigma weight residual 120.28 127.80 -7.52 1.34e+00 5.57e-01 3.15e+01 ... (remaining 14233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 5884 35.58 - 71.16: 148 71.16 - 106.73: 5 106.73 - 142.31: 3 142.31 - 177.89: 2 Dihedral angle restraints: 6042 sinusoidal: 2182 harmonic: 3860 Sorted by residual: dihedral pdb=" CA ASP B 189 " pdb=" C ASP B 189 " pdb=" N THR B 190 " pdb=" CA THR B 190 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA SER B 362 " pdb=" C SER B 362 " pdb=" N THR B 363 " pdb=" CA THR B 363 " ideal model delta harmonic sigma weight residual 180.00 152.26 27.74 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA TYR A 859 " pdb=" C TYR A 859 " pdb=" N ASP A 860 " pdb=" CA ASP A 860 " ideal model delta harmonic sigma weight residual 180.00 154.24 25.76 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 6039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1366 0.071 - 0.143: 324 0.143 - 0.214: 65 0.214 - 0.286: 6 0.286 - 0.357: 2 Chirality restraints: 1763 Sorted by residual: chirality pdb=" CA THR A 795 " pdb=" N THR A 795 " pdb=" C THR A 795 " pdb=" CB THR A 795 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C3' DT X 2 " pdb=" C4' DT X 2 " pdb=" O3' DT X 2 " pdb=" C2' DT X 2 " both_signs ideal model delta sigma weight residual False -2.66 -2.32 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA ARG A 914 " pdb=" N ARG A 914 " pdb=" C ARG A 914 " pdb=" CB ARG A 914 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1760 not shown) Planarity restraints: 1715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 532 " -0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO B 533 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 533 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 533 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 217 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO B 218 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 435 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C VAL B 435 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL B 435 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG B 436 " -0.016 2.00e-02 2.50e+03 ... (remaining 1712 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 21 2.46 - 3.07: 5765 3.07 - 3.68: 14455 3.68 - 4.29: 20038 4.29 - 4.90: 33144 Nonbonded interactions: 73423 Sorted by model distance: nonbonded pdb=" O PHE B 336 " pdb=" OG1 THR B 337 " model vdw 1.855 2.440 nonbonded pdb=" O LEU B 522 " pdb=" OD2 ASP B 526 " model vdw 2.263 3.040 nonbonded pdb=" CG2 THR A 447 " pdb=" CG2 VAL A 453 " model vdw 2.269 3.880 nonbonded pdb=" CD2 HIS B 130 " pdb=" CG1 VAL B 271 " model vdw 2.310 3.680 nonbonded pdb=" OD2 ASP B 867 " pdb=" NH2 ARG A 724 " model vdw 2.341 2.520 ... (remaining 73418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.960 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 33.760 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.009 0.078 10324 Z= 0.563 Angle : 1.177 10.257 14238 Z= 0.695 Chirality : 0.065 0.357 1763 Planarity : 0.008 0.086 1715 Dihedral : 15.183 177.887 3508 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.10 % Allowed : 6.44 % Favored : 90.46 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 2.74 % 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: -5.80 (0.18), residues: 1226 helix: -4.40 (0.12), residues: 621 sheet: -2.73 (0.55), residues: 96 loop : -3.11 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP B 497 HIS 0.010 0.002 HIS B 577 PHE 0.016 0.003 PHE B 685 TYR 0.027 0.003 TYR A 956 ARG 0.015 0.001 ARG B 572 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 819 ASP cc_start: 0.8103 (t0) cc_final: 0.7776 (t0) REVERT: A 913 VAL cc_start: 0.7818 (OUTLIER) cc_final: 0.7578 (t) REVERT: A 1025 ASN cc_start: 0.7729 (t0) cc_final: 0.7356 (t0) outliers start: 26 outliers final: 10 residues processed: 212 average time/residue: 0.2731 time to fit residues: 77.6778 Evaluate side-chains 125 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 441 SER Chi-restraints excluded: chain A residue 913 VAL Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 919 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 130 HIS B 294 GLN B 413 HIS B 770 HIS A 848 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10324 Z= 0.238 Angle : 0.670 11.055 14238 Z= 0.343 Chirality : 0.042 0.233 1763 Planarity : 0.005 0.054 1715 Dihedral : 16.798 173.781 1745 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.93 % Favored : 92.99 % Rotamer: Outliers : 3.93 % Allowed : 12.40 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -4.78 (0.20), residues: 1226 helix: -3.50 (0.15), residues: 607 sheet: -2.72 (0.52), residues: 103 loop : -2.62 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 497 HIS 0.005 0.001 HIS A 372 PHE 0.037 0.002 PHE B 68 TYR 0.014 0.001 TYR A 864 ARG 0.006 0.001 ARG B 683 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 777 MET cc_start: 0.8286 (mmm) cc_final: 0.8064 (mmm) REVERT: A 1025 ASN cc_start: 0.7531 (t0) cc_final: 0.7231 (t0) outliers start: 33 outliers final: 19 residues processed: 151 average time/residue: 0.2158 time to fit residues: 46.8544 Evaluate side-chains 122 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 671 GLU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 84 optimal weight: 0.0980 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 123 optimal weight: 0.0270 chunk 42 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10324 Z= 0.148 Angle : 0.574 7.280 14238 Z= 0.292 Chirality : 0.039 0.146 1763 Planarity : 0.004 0.047 1715 Dihedral : 16.454 175.142 1735 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.26 % Allowed : 15.49 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -3.79 (0.22), residues: 1226 helix: -2.61 (0.18), residues: 615 sheet: -2.30 (0.52), residues: 100 loop : -2.22 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 497 HIS 0.007 0.001 HIS A 372 PHE 0.018 0.001 PHE B 68 TYR 0.008 0.001 TYR A 859 ARG 0.004 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.107 Fit side-chains REVERT: B 642 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6504 (mt-10) REVERT: B 729 LYS cc_start: 0.7495 (ptmm) cc_final: 0.7212 (ptpt) REVERT: B 756 VAL cc_start: 0.9117 (OUTLIER) cc_final: 0.8896 (t) outliers start: 19 outliers final: 11 residues processed: 140 average time/residue: 0.2214 time to fit residues: 43.9464 Evaluate side-chains 106 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1014 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 0.4980 chunk 93 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 162 HIS B 243 HIS B 679 HIS B 771 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10324 Z= 0.356 Angle : 0.690 8.976 14238 Z= 0.349 Chirality : 0.045 0.177 1763 Planarity : 0.005 0.052 1715 Dihedral : 16.742 169.403 1726 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.24 % Allowed : 14.66 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -3.69 (0.22), residues: 1226 helix: -2.45 (0.19), residues: 609 sheet: -2.37 (0.52), residues: 103 loop : -2.25 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 497 HIS 0.010 0.001 HIS B 243 PHE 0.014 0.002 PHE B 340 TYR 0.020 0.002 TYR A 864 ARG 0.008 0.001 ARG A 871 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 96 time to evaluate : 1.116 Fit side-chains REVERT: B 66 ASN cc_start: 0.8200 (t160) cc_final: 0.7979 (t0) REVERT: B 68 PHE cc_start: 0.8413 (m-80) cc_final: 0.8141 (m-80) REVERT: B 497 TRP cc_start: 0.8753 (OUTLIER) cc_final: 0.8076 (p90) REVERT: B 829 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 577 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6912 (pp) REVERT: A 606 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8048 (pp) REVERT: A 789 GLU cc_start: 0.7693 (pm20) cc_final: 0.7026 (tp30) outliers start: 44 outliers final: 25 residues processed: 134 average time/residue: 0.2007 time to fit residues: 39.5543 Evaluate side-chains 128 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 946 ASP Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 1 optimal weight: 0.0030 chunk 98 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 10324 Z= 0.388 Angle : 0.706 9.578 14238 Z= 0.354 Chirality : 0.046 0.172 1763 Planarity : 0.005 0.056 1715 Dihedral : 16.738 166.248 1726 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 5.36 % Allowed : 15.85 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -3.53 (0.22), residues: 1226 helix: -2.30 (0.19), residues: 611 sheet: -2.04 (0.56), residues: 95 loop : -2.28 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 497 HIS 0.010 0.001 HIS A 775 PHE 0.018 0.002 PHE B 340 TYR 0.017 0.002 TYR A 864 ARG 0.009 0.001 ARG A 871 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 97 time to evaluate : 1.047 Fit side-chains REVERT: B 66 ASN cc_start: 0.8236 (t160) cc_final: 0.7962 (t0) REVERT: B 68 PHE cc_start: 0.8376 (m-80) cc_final: 0.8143 (m-80) REVERT: B 497 TRP cc_start: 0.8857 (OUTLIER) cc_final: 0.8285 (p90) REVERT: B 829 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8319 (mp) REVERT: A 577 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6718 (pp) REVERT: A 606 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8065 (pp) outliers start: 45 outliers final: 35 residues processed: 133 average time/residue: 0.2069 time to fit residues: 40.5402 Evaluate side-chains 131 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 92 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 756 VAL Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 946 ASP Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10324 Z= 0.169 Angle : 0.573 7.648 14238 Z= 0.290 Chirality : 0.040 0.143 1763 Planarity : 0.004 0.047 1715 Dihedral : 16.431 175.561 1726 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.17 % Allowed : 17.88 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -2.86 (0.23), residues: 1226 helix: -1.79 (0.20), residues: 600 sheet: -1.63 (0.55), residues: 101 loop : -1.92 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 497 HIS 0.004 0.001 HIS B 130 PHE 0.010 0.001 PHE B 340 TYR 0.009 0.001 TYR A 859 ARG 0.005 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 1.062 Fit side-chains REVERT: B 497 TRP cc_start: 0.8815 (OUTLIER) cc_final: 0.8182 (p90) REVERT: B 829 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8124 (mp) REVERT: A 577 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6676 (pp) REVERT: A 789 GLU cc_start: 0.7400 (pm20) cc_final: 0.7199 (tp30) outliers start: 35 outliers final: 25 residues processed: 127 average time/residue: 0.1850 time to fit residues: 35.1136 Evaluate side-chains 126 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1024 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10324 Z= 0.305 Angle : 0.646 8.347 14238 Z= 0.326 Chirality : 0.043 0.161 1763 Planarity : 0.005 0.053 1715 Dihedral : 16.511 173.026 1726 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 5.01 % Allowed : 17.64 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -3.02 (0.23), residues: 1226 helix: -1.82 (0.20), residues: 618 sheet: -1.81 (0.57), residues: 96 loop : -2.11 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 497 HIS 0.007 0.001 HIS A 775 PHE 0.025 0.002 PHE B 68 TYR 0.013 0.002 TYR A 859 ARG 0.006 0.000 ARG A 871 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 94 time to evaluate : 1.199 Fit side-chains REVERT: B 497 TRP cc_start: 0.8829 (OUTLIER) cc_final: 0.8159 (p90) REVERT: B 829 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 577 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6702 (pp) REVERT: A 606 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8012 (pp) REVERT: A 789 GLU cc_start: 0.7342 (pm20) cc_final: 0.7133 (tp30) outliers start: 42 outliers final: 30 residues processed: 124 average time/residue: 0.2014 time to fit residues: 36.9978 Evaluate side-chains 125 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 91 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 253 ASP Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 920 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1024 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 25 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 103 optimal weight: 8.9990 chunk 120 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10324 Z= 0.143 Angle : 0.545 7.839 14238 Z= 0.276 Chirality : 0.039 0.140 1763 Planarity : 0.004 0.048 1715 Dihedral : 16.182 179.137 1726 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.81 % Allowed : 18.83 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -2.49 (0.24), residues: 1226 helix: -1.42 (0.21), residues: 620 sheet: -1.42 (0.56), residues: 102 loop : -1.83 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 497 HIS 0.004 0.001 HIS B 130 PHE 0.022 0.001 PHE B 68 TYR 0.006 0.001 TYR A 859 ARG 0.005 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.064 Fit side-chains REVERT: B 497 TRP cc_start: 0.8784 (OUTLIER) cc_final: 0.8089 (p90) REVERT: A 577 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6721 (pp) REVERT: A 606 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7830 (pp) outliers start: 32 outliers final: 23 residues processed: 125 average time/residue: 0.2075 time to fit residues: 37.8830 Evaluate side-chains 118 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 497 TRP Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1024 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9990 chunk 123 optimal weight: 0.0000 chunk 126 optimal weight: 0.3980 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 116 optimal weight: 0.0980 chunk 122 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10324 Z= 0.134 Angle : 0.525 7.712 14238 Z= 0.266 Chirality : 0.038 0.141 1763 Planarity : 0.004 0.046 1715 Dihedral : 15.947 178.981 1726 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.10 % Allowed : 19.67 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -2.08 (0.24), residues: 1226 helix: -1.03 (0.21), residues: 626 sheet: -1.18 (0.56), residues: 101 loop : -1.73 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 497 HIS 0.007 0.001 HIS B 130 PHE 0.021 0.001 PHE B 68 TYR 0.008 0.001 TYR A 859 ARG 0.006 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 1.101 Fit side-chains REVERT: B 672 TRP cc_start: 0.7589 (m-90) cc_final: 0.7277 (m-90) REVERT: A 577 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6827 (pp) REVERT: A 606 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7838 (pp) outliers start: 26 outliers final: 22 residues processed: 108 average time/residue: 0.1884 time to fit residues: 31.1929 Evaluate side-chains 113 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1024 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 0.1980 chunk 136 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10324 Z= 0.349 Angle : 0.660 7.567 14238 Z= 0.332 Chirality : 0.045 0.167 1763 Planarity : 0.005 0.051 1715 Dihedral : 16.396 176.279 1726 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.22 % Allowed : 19.90 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % 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: -2.45 (0.23), residues: 1226 helix: -1.29 (0.20), residues: 624 sheet: -1.30 (0.54), residues: 108 loop : -1.98 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 497 HIS 0.010 0.002 HIS A 775 PHE 0.033 0.002 PHE B 68 TYR 0.015 0.002 TYR A 864 ARG 0.007 0.001 ARG B 587 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 1.049 Fit side-chains REVERT: B 97 ARG cc_start: 0.7640 (ttm110) cc_final: 0.7277 (mtp85) REVERT: B 185 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7606 (tp30) REVERT: A 577 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6926 (pp) REVERT: A 606 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7954 (pp) outliers start: 27 outliers final: 22 residues processed: 112 average time/residue: 0.1902 time to fit residues: 32.5753 Evaluate side-chains 113 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 89 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 931 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1003 TRP Chi-restraints excluded: chain A residue 1024 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 16 optimal weight: 0.0030 chunk 30 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 111 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.157181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.130317 restraints weight = 14197.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.130578 restraints weight = 16734.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.131671 restraints weight = 14832.965| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10324 Z= 0.148 Angle : 0.551 9.215 14238 Z= 0.277 Chirality : 0.039 0.143 1763 Planarity : 0.004 0.048 1715 Dihedral : 16.080 177.965 1726 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.86 % Allowed : 19.90 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.24), residues: 1226 helix: -0.86 (0.21), residues: 627 sheet: -1.17 (0.57), residues: 102 loop : -1.74 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 497 HIS 0.009 0.001 HIS B 130 PHE 0.030 0.001 PHE B 68 TYR 0.007 0.001 TYR A 859 ARG 0.006 0.000 ARG B 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1990.29 seconds wall clock time: 36 minutes 49.86 seconds (2209.86 seconds total)