Starting phenix.real_space_refine on Tue Jun 24 20:37:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vun_43534/06_2025/8vun_43534.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vun_43534/06_2025/8vun_43534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vun_43534/06_2025/8vun_43534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vun_43534/06_2025/8vun_43534.map" model { file = "/net/cci-nas-00/data/ceres_data/8vun_43534/06_2025/8vun_43534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vun_43534/06_2025/8vun_43534.cif" } resolution = 4.01 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= 0.012 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 18362 2.51 5 N 4989 2.21 5 O 5286 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 2.30s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28765 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5751 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 33, 'TRANS': 755} Chain breaks: 2 Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 6, 'GLU:plan': 30, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 313 Chain: "B" Number of atoms: 5510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5510 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PTRANS': 30, 'TRANS': 750} Chain breaks: 2 Unresolved non-hydrogen bonds: 693 Unresolved non-hydrogen angles: 878 Unresolved non-hydrogen dihedrals: 572 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 23, 'PHE:plan': 11, 'GLU:plan': 31, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 431 Chain: "C" Number of atoms: 5601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 789, 5601 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 33, 'TRANS': 755} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 804 Unresolved non-hydrogen dihedrals: 533 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 20, 'PHE:plan': 9, 'GLU:plan': 35, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 396 Chain: "D" Number of atoms: 5473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 5473 Classifications: {'peptide': 781} Incomplete info: {'truncation_to_alanine': 213} Link IDs: {'PTRANS': 30, 'TRANS': 750} Chain breaks: 2 Unresolved non-hydrogen bonds: 727 Unresolved non-hydrogen angles: 917 Unresolved non-hydrogen dihedrals: 591 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 26, 'PHE:plan': 11, 'GLU:plan': 27, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 434 Chain: "G" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 209} Chain: "I" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1572 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Chain: "K" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1643 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 209} Chain: "L" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1572 Classifications: {'peptide': 209} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 193} Time building chain proxies: 18.81, per 1000 atoms: 0.65 Number of scatterers: 28765 At special positions: 0 Unit cell: (136.104, 152.368, 224.272, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 5286 8.00 N 4989 7.00 C 18362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 779 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 780 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 779 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 455 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 725 " - pdb=" SG CYS D 780 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 149 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 193 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 149 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 91 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 193 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.18 Conformation dependent library (CDL) restraints added in 3.8 seconds 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7444 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 59 sheets defined 34.9% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 4.289A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE A 42 " --> pdb=" O HIS A 38 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 3.848A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 99 through 103 removed outlier: 4.199A pdb=" N PHE A 102 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR A 103 " --> pdb=" O ASP A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 145 through 157 removed outlier: 3.904A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.862A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.990A pdb=" N MET A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.548A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A 260 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 261 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 262' Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.785A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.888A pdb=" N PHE A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.888A pdb=" N ASP A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 462 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 559 through 582 removed outlier: 3.582A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 595 Processing helix chain 'A' and resid 607 through 638 Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 669 through 676 removed outlier: 3.648A pdb=" N ARG A 676 " --> pdb=" O ILE A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 679 No H-bonds generated for 'chain 'A' and resid 677 through 679' Processing helix chain 'A' and resid 680 through 689 removed outlier: 3.634A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LYS A 689 " --> pdb=" O ARG A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 704 removed outlier: 3.581A pdb=" N ASP A 704 " --> pdb=" O GLN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 724 Processing helix chain 'A' and resid 749 through 773 removed outlier: 7.549A pdb=" N MET A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N GLU A 767 " --> pdb=" O ASN A 763 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 769 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 786 removed outlier: 4.131A pdb=" N ASN A 784 " --> pdb=" O THR A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 813 removed outlier: 4.530A pdb=" N LEU A 791 " --> pdb=" O GLY A 787 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE A 800 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS A 812 " --> pdb=" O ALA A 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 108 through 121 removed outlier: 3.991A pdb=" N MET B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.671A pdb=" N MET B 133 " --> pdb=" O GLY B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 166 removed outlier: 3.951A pdb=" N MET B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.809A pdb=" N LYS B 221 " --> pdb=" O GLN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 246 removed outlier: 4.505A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.727A pdb=" N GLY B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 Processing helix chain 'B' and resid 459 through 472 removed outlier: 3.639A pdb=" N ARG B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.576A pdb=" N VAL B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR B 502 " --> pdb=" O GLY B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 522 Processing helix chain 'B' and resid 555 through 578 removed outlier: 3.735A pdb=" N VAL B 559 " --> pdb=" O ALA B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 605 through 634 Processing helix chain 'B' and resid 668 through 678 Processing helix chain 'B' and resid 678 through 686 removed outlier: 3.957A pdb=" N HIS B 682 " --> pdb=" O TYR B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 703 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 723 through 726 removed outlier: 4.493A pdb=" N LYS B 726 " --> pdb=" O GLU B 723 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 723 through 726' Processing helix chain 'B' and resid 751 through 765 Processing helix chain 'B' and resid 766 through 776 removed outlier: 3.645A pdb=" N GLU B 770 " --> pdb=" O GLY B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 789 Processing helix chain 'B' and resid 790 through 814 Processing helix chain 'C' and resid 35 through 53 removed outlier: 4.131A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE C 42 " --> pdb=" O HIS C 38 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 removed outlier: 4.158A pdb=" N ALA C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 99 through 103 removed outlier: 3.748A pdb=" N PHE C 102 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR C 103 " --> pdb=" O ASP C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 103' Processing helix chain 'C' and resid 105 through 114 removed outlier: 4.089A pdb=" N ALA C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 157 removed outlier: 4.044A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 188 removed outlier: 4.053A pdb=" N GLU C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 213 removed outlier: 4.325A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU C 213 " --> pdb=" O MET C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.509A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 removed outlier: 3.543A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLY C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN C 257 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 260 " --> pdb=" O ASN C 257 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA C 262 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.536A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 327 Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.127A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 470 removed outlier: 3.517A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.503A pdb=" N GLU C 504 " --> pdb=" O GLY C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 527 removed outlier: 3.875A pdb=" N TYR C 526 " --> pdb=" O GLU C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 580 removed outlier: 4.052A pdb=" N TRP C 563 " --> pdb=" O GLN C 559 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER C 569 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 580 " --> pdb=" O MET C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 595 removed outlier: 4.417A pdb=" N LEU C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 638 Processing helix chain 'C' and resid 650 through 655 Processing helix chain 'C' and resid 670 through 677 removed outlier: 3.532A pdb=" N GLN C 677 " --> pdb=" O TYR C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 688 removed outlier: 3.638A pdb=" N MET C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG C 685 " --> pdb=" O SER C 681 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N HIS C 686 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET C 687 " --> pdb=" O MET C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 704 removed outlier: 3.765A pdb=" N ARG C 703 " --> pdb=" O ILE C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 724 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 764 through 774 Processing helix chain 'C' and resid 788 through 813 removed outlier: 3.987A pdb=" N VAL C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE C 800 " --> pdb=" O ILE C 796 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE C 801 " --> pdb=" O VAL C 797 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 813 " --> pdb=" O TYR C 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 107 through 119 removed outlier: 4.144A pdb=" N GLN D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS D 119 " --> pdb=" O PHE D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 removed outlier: 3.984A pdb=" N MET D 133 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 Processing helix chain 'D' and resid 179 through 192 Processing helix chain 'D' and resid 215 through 220 removed outlier: 3.592A pdb=" N LYS D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 247 removed outlier: 3.768A pdb=" N LEU D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 310 removed outlier: 3.744A pdb=" N GLY D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU D 299 " --> pdb=" O GLY D 295 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR D 300 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 339 removed outlier: 4.206A pdb=" N VAL D 339 " --> pdb=" O HIS D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 415 No H-bonds generated for 'chain 'D' and resid 413 through 415' Processing helix chain 'D' and resid 443 through 447 Processing helix chain 'D' and resid 459 through 472 Processing helix chain 'D' and resid 496 through 502 Processing helix chain 'D' and resid 515 through 522 Processing helix chain 'D' and resid 556 through 578 removed outlier: 3.744A pdb=" N MET D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 593 Processing helix chain 'D' and resid 604 through 633 removed outlier: 3.551A pdb=" N MET D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 652 removed outlier: 3.897A pdb=" N ARG D 652 " --> pdb=" O LYS D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 678 Processing helix chain 'D' and resid 680 through 685 Processing helix chain 'D' and resid 686 through 689 removed outlier: 4.174A pdb=" N ASN D 689 " --> pdb=" O THR D 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 686 through 689' Processing helix chain 'D' and resid 692 through 702 removed outlier: 3.862A pdb=" N THR D 702 " --> pdb=" O VAL D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 712 through 721 Processing helix chain 'D' and resid 751 through 765 Processing helix chain 'D' and resid 767 through 776 Processing helix chain 'D' and resid 786 through 814 removed outlier: 3.560A pdb=" N MET D 796 " --> pdb=" O GLY D 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.014A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 removed outlier: 4.256A pdb=" N ALA G 106 " --> pdb=" O SER G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 194 through 198 removed outlier: 3.532A pdb=" N SER G 197 " --> pdb=" O PRO G 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 121 through 127 Processing helix chain 'I' and resid 181 through 188 removed outlier: 3.751A pdb=" N HIS I 188 " --> pdb=" O GLN I 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'K' and resid 165 through 167 No H-bonds generated for 'chain 'K' and resid 165 through 167' Processing helix chain 'K' and resid 194 through 198 removed outlier: 3.585A pdb=" N LEU K 198 " --> pdb=" O SER K 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 181 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.422A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 194 through 197 removed outlier: 3.534A pdb=" N LEU A 195 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 167 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE A 197 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 271 removed outlier: 3.602A pdb=" N ILE A 353 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 332 through 333 Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 341 removed outlier: 3.749A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASP A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA8, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA9, first strand: chain 'A' and resid 662 through 663 removed outlier: 7.175A pdb=" N ALA A 663 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 712 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 662 through 663 removed outlier: 7.175A pdb=" N ALA A 663 " --> pdb=" O ILE A 711 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 712 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 538 " --> pdb=" O PHE A 735 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE A 735 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.755A pdb=" N VAL B 99 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 124 through 125 removed outlier: 6.534A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 227 through 228 removed outlier: 5.917A pdb=" N ILE B 227 " --> pdb=" O ILE B 256 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 277 through 280 removed outlier: 3.847A pdb=" N ILE B 364 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 341 through 342 removed outlier: 3.820A pdb=" N VAL B 341 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB8, first strand: chain 'B' and resid 409 through 410 Processing sheet with id=AB9, first strand: chain 'B' and resid 417 through 419 Processing sheet with id=AC1, first strand: chain 'B' and resid 530 through 531 Processing sheet with id=AC2, first strand: chain 'B' and resid 533 through 536 removed outlier: 3.963A pdb=" N TYR B 710 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY B 663 " --> pdb=" O ILE B 709 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASP B 711 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 61 through 62 removed outlier: 3.787A pdb=" N ILE C 29 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N LEU C 91 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY C 30 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 167 removed outlier: 3.547A pdb=" N SER C 222 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 267 through 270 removed outlier: 6.954A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 332 through 333 Processing sheet with id=AC7, first strand: chain 'C' and resid 340 through 341 removed outlier: 3.613A pdb=" N ASN C 341 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ASP C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 401 through 402 removed outlier: 3.816A pdb=" N THR C 402 " --> pdb=" O HIS C 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 410 through 412 removed outlier: 3.630A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 487 through 489 removed outlier: 3.800A pdb=" N GLU C 488 " --> pdb=" O GLU C 497 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 541 through 542 removed outlier: 4.194A pdb=" N VAL C 542 " --> pdb=" O VAL C 728 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL C 728 " --> pdb=" O VAL C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'D' and resid 124 through 126 removed outlier: 5.956A pdb=" N ILE D 124 " --> pdb=" O PHE D 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 171 through 174 removed outlier: 7.930A pdb=" N SER D 171 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N TYR D 230 " --> pdb=" O SER D 171 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL D 173 " --> pdb=" O TYR D 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 277 through 280 removed outlier: 3.731A pdb=" N SER D 278 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE D 364 " --> pdb=" O SER D 278 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY D 376 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 341 through 342 removed outlier: 3.704A pdb=" N VAL D 341 " --> pdb=" O LEU D 348 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AD9, first strand: chain 'D' and resid 409 through 410 removed outlier: 3.669A pdb=" N THR D 410 " --> pdb=" O TYR D 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 417 through 420 removed outlier: 3.682A pdb=" N CYS D 455 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 533 through 535 Processing sheet with id=AE3, first strand: chain 'G' and resid 3 through 4 Processing sheet with id=AE4, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.685A pdb=" N GLU G 46 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 49 through 50 Processing sheet with id=AE6, first strand: chain 'G' and resid 68 through 69 Processing sheet with id=AE7, first strand: chain 'G' and resid 98 through 99 removed outlier: 4.225A pdb=" N LYS G 98 " --> pdb=" O ASP G 110 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP G 110 " --> pdb=" O LYS G 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 129 through 133 removed outlier: 3.837A pdb=" N GLY G 148 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA G 146 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL G 193 " --> pdb=" O ALA G 146 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLY G 148 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL G 191 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU G 150 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER G 189 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS G 152 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU G 187 " --> pdb=" O LYS G 152 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL G 190 " --> pdb=" O HIS G 173 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 129 through 133 removed outlier: 3.837A pdb=" N GLY G 148 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA G 146 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N VAL G 193 " --> pdb=" O ALA G 146 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLY G 148 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL G 191 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU G 150 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER G 189 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS G 152 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU G 187 " --> pdb=" O LYS G 152 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 159 through 163 Processing sheet with id=AF2, first strand: chain 'I' and resid 4 through 5 removed outlier: 3.707A pdb=" N VAL I 18 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE I 77 " --> pdb=" O SER I 64 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 9 through 11 removed outlier: 3.749A pdb=" N THR I 104 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP I 88 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN I 38 " --> pdb=" O THR I 47 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N THR I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 116 through 118 removed outlier: 3.507A pdb=" N THR I 116 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP I 138 " --> pdb=" O TYR I 172 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 116 through 118 removed outlier: 3.507A pdb=" N THR I 116 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP I 138 " --> pdb=" O TYR I 172 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR I 172 " --> pdb=" O ASP I 138 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 145 through 149 removed outlier: 3.600A pdb=" N LYS I 149 " --> pdb=" O SER I 192 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS I 204 " --> pdb=" O CYS I 193 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.932A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER K 25 " --> pdb=" O GLN K 3 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER K 78 " --> pdb=" O ASP K 73 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 58 through 60 removed outlier: 3.877A pdb=" N VAL K 40 " --> pdb=" O LYS K 43 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU K 45 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG K 38 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TRP K 47 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TRP K 36 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER K 49 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET K 34 " --> pdb=" O SER K 49 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL K 37 " --> pdb=" O TYR K 95 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 93 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL K 118 " --> pdb=" O ALA K 92 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 129 through 133 removed outlier: 3.810A pdb=" N GLY K 148 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU K 147 " --> pdb=" O VAL K 191 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS K 149 " --> pdb=" O SER K 189 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR K 185 " --> pdb=" O ASP K 153 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 160 through 163 removed outlier: 3.670A pdb=" N VAL K 216 " --> pdb=" O VAL K 207 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS K 209 " --> pdb=" O THR K 214 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR K 214 " --> pdb=" O HIS K 209 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.753A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.519A pdb=" N VAL L 18 " --> pdb=" O ILE L 78 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.528A pdb=" N SER L 114 " --> pdb=" O SER L 137 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE L 136 " --> pdb=" O ALA L 174 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER L 175 " --> pdb=" O THR L 163 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N THR L 163 " --> pdb=" O SER L 175 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR L 177 " --> pdb=" O THR L 161 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR L 161 " --> pdb=" O TYR L 177 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER L 179 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL L 159 " --> pdb=" O SER L 179 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.119A pdb=" N TRP L 148 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR L 145 " --> pdb=" O THR L 196 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR L 196 " --> pdb=" O THR L 145 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS L 204 " --> pdb=" O CYS L 193 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3018 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: 12.69 Time building geometry restraints manager: 8.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 50 1.23 - 1.38: 10397 1.38 - 1.53: 14558 1.53 - 1.67: 4219 1.67 - 1.82: 203 Bond restraints: 29427 Sorted by residual: bond pdb=" CG PRO D 546 " pdb=" CD PRO D 546 " ideal model delta sigma weight residual 1.503 1.157 0.346 3.40e-02 8.65e+02 1.03e+02 bond pdb=" CB PRO D 546 " pdb=" CG PRO D 546 " ideal model delta sigma weight residual 1.492 1.081 0.411 5.00e-02 4.00e+02 6.77e+01 bond pdb=" N PRO D 546 " pdb=" CA PRO D 546 " ideal model delta sigma weight residual 1.469 1.515 -0.046 1.28e-02 6.10e+03 1.31e+01 bond pdb=" CB ARG A 397 " pdb=" CG ARG A 397 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" C VAL D 257 " pdb=" N PRO D 258 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.25e-02 6.40e+03 1.44e+00 ... (remaining 29422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.07: 40192 7.07 - 14.14: 29 14.14 - 21.21: 1 21.21 - 28.27: 0 28.27 - 35.34: 3 Bond angle restraints: 40225 Sorted by residual: angle pdb=" N PRO D 546 " pdb=" CD PRO D 546 " pdb=" CG PRO D 546 " ideal model delta sigma weight residual 103.20 73.38 29.82 1.50e+00 4.44e-01 3.95e+02 angle pdb=" CA PRO D 546 " pdb=" CB PRO D 546 " pdb=" CG PRO D 546 " ideal model delta sigma weight residual 104.50 69.16 35.34 1.90e+00 2.77e-01 3.46e+02 angle pdb=" CB PRO D 546 " pdb=" CG PRO D 546 " pdb=" CD PRO D 546 " ideal model delta sigma weight residual 106.10 140.64 -34.54 3.20e+00 9.77e-02 1.17e+02 angle pdb=" CA PRO D 546 " pdb=" N PRO D 546 " pdb=" CD PRO D 546 " ideal model delta sigma weight residual 112.00 102.36 9.64 1.40e+00 5.10e-01 4.74e+01 angle pdb=" N PRO D 546 " pdb=" CA PRO D 546 " pdb=" CB PRO D 546 " ideal model delta sigma weight residual 103.25 96.66 6.59 1.05e+00 9.07e-01 3.94e+01 ... (remaining 40220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 14960 18.00 - 36.01: 1814 36.01 - 54.01: 443 54.01 - 72.02: 69 72.02 - 90.02: 28 Dihedral angle restraints: 17314 sinusoidal: 5762 harmonic: 11552 Sorted by residual: dihedral pdb=" CB CYS D 436 " pdb=" SG CYS D 436 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual -86.00 -174.17 88.17 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS D 87 " pdb=" SG CYS D 87 " pdb=" SG CYS D 320 " pdb=" CB CYS D 320 " ideal model delta sinusoidal sigma weight residual -86.00 1.23 -87.23 1 1.00e+01 1.00e-02 9.14e+01 dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 455 " pdb=" CB CYS A 455 " ideal model delta sinusoidal sigma weight residual 93.00 178.66 -85.66 1 1.00e+01 1.00e-02 8.87e+01 ... (remaining 17311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4097 0.063 - 0.127: 595 0.127 - 0.190: 23 0.190 - 0.254: 1 0.254 - 0.317: 1 Chirality restraints: 4717 Sorted by residual: chirality pdb=" CG LEU D 588 " pdb=" CB LEU D 588 " pdb=" CD1 LEU D 588 " pdb=" CD2 LEU D 588 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CB VAL D 430 " pdb=" CA VAL D 430 " pdb=" CG1 VAL D 430 " pdb=" CG2 VAL D 430 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB ILE D 313 " pdb=" CA ILE D 313 " pdb=" CG1 ILE D 313 " pdb=" CG2 ILE D 313 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 ... (remaining 4714 not shown) Planarity restraints: 5145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 443 " -0.049 5.00e-02 4.00e+02 7.30e-02 8.54e+00 pdb=" N PRO A 444 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 761 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.81e+00 pdb=" C HIS A 761 " 0.048 2.00e-02 2.50e+03 pdb=" O HIS A 761 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU A 762 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 446 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO A 447 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 447 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 447 " 0.038 5.00e-02 4.00e+02 ... (remaining 5142 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1574 2.72 - 3.26: 30462 3.26 - 3.81: 46814 3.81 - 4.35: 50999 4.35 - 4.90: 86471 Nonbonded interactions: 216320 Sorted by model distance: nonbonded pdb=" O GLU A 251 " pdb=" OG SER A 255 " model vdw 2.175 3.040 nonbonded pdb=" OG SER K 71 " pdb=" O TYR K 80 " model vdw 2.183 3.040 nonbonded pdb=" OG SER B 538 " pdb=" O LYS B 726 " model vdw 2.194 3.040 nonbonded pdb=" O THR B 215 " pdb=" N LEU B 219 " model vdw 2.194 3.120 nonbonded pdb=" OG SER B 225 " pdb=" O ASP B 252 " model vdw 2.198 3.040 ... (remaining 216315 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 'A' and (resid 25 through 393 or (resid 394 and (name N or name CA or nam \ e C or name O or name CB )) or resid 395 through 398 or (resid 399 and (name N o \ r name CA or name C or name O or name CB )) or resid 400 through 415 or (resid 4 \ 16 through 417 and (name N or name CA or name C or name O or name CB )) or resid \ 418 or (resid 419 and (name N or name CA or name C or name O or name CB )) or r \ esid 420 or (resid 421 through 424 and (name N or name CA or name C or name O or \ name CB )) or resid 425 through 426 or (resid 427 and (name N or name CA or nam \ e C or name O or name CB )) or resid 428 or (resid 429 and (name N or name CA or \ name C or name O or name CB )) or resid 430 through 445 or (resid 446 and (name \ N or name CA or name C or name O or name CB )) or resid 447 through 450 or (res \ id 451 and (name N or name CA or name C or name O or name CB )) or resid 452 thr \ ough 469 or (resid 470 and (name N or name CA or name C or name O or name CB )) \ or resid 471 through 488 or (resid 489 and (name N or name CA or name C or name \ O or name CB )) or resid 490 or (resid 491 through 492 and (name N or name CA or \ name C or name O or name CB )) or resid 493 or (resid 494 and (name N or name C \ A or name C or name O or name CB )) or resid 495 through 510 or (resid 511 and ( \ name N or name CA or name C or name O or name CB )) or resid 512 through 542 or \ (resid 543 through 546 and (name N or name CA or name C or name O or name CB )) \ or resid 547 through 550 or (resid 551 through 556 and (name N or name CA or nam \ e C or name O or name CB )) or resid 557 through 572 or (resid 573 through 577 a \ nd (name N or name CA or name C or name O or name CB )) or resid 578 or (resid 5 \ 79 through 582 and (name N or name CA or name C or name O or name CB )) or resid \ 583 or (resid 584 through 588 and (name N or name CA or name C or name O or nam \ e CB )) or resid 589 through 606 or (resid 607 through 613 and (name N or name C \ A or name C or name O or name CB )) or resid 614 through 634 or (resid 635 throu \ gh 640 and (name N or name CA or name C or name O or name CB )) or resid 641 thr \ ough 642 or (resid 643 and (name N or name CA or name C or name O or name CB )) \ or resid 644 or (resid 645 and (name N or name CA or name C or name O or name CB \ )) or resid 646 through 650 or (resid 651 and (name N or name CA or name C or n \ ame O or name CB )) or resid 652 or (resid 653 through 655 and (name N or name C \ A or name C or name O or name CB )) or resid 656 or (resid 657 through 659 and ( \ name N or name CA or name C or name O or name CB )) or resid 660 through 663 or \ (resid 664 through 667 and (name N or name CA or name C or name O or name CB )) \ or resid 668 through 675 or (resid 676 and (name N or name CA or name C or name \ O or name CB )) or resid 677 through 679 or (resid 680 and (name N or name CA or \ name C or name O or name CB )) or resid 681 through 684 or (resid 685 and (name \ N or name CA or name C or name O or name CB )) or resid 686 or (resid 687 throu \ gh 688 and (name N or name CA or name C or name O or name CB )) or resid 689 thr \ ough 692 or (resid 693 and (name N or name CA or name C or name O or name CB )) \ or resid 694 through 696 or (resid 697 through 698 and (name N or name CA or nam \ e C or name O or name CB )) or resid 699 through 703 or (resid 704 and (name N o \ r name CA or name C or name O or name CB )) or resid 705 through 723 or (resid 7 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 725 through \ 731 or (resid 732 and (name N or name CA or name C or name O or name CB )) or r \ esid 733 through 744 or (resid 745 through 746 and (name N or name CA or name C \ or name O or name CB )) or resid 747 through 750 or (resid 751 and (name N or na \ me CA or name C or name O or name CB )) or resid 752 through 761 or (resid 762 a \ nd (name N or name CA or name C or name O or name CB )) or resid 763 through 769 \ or (resid 770 through 771 and (name N or name CA or name C or name O or name CB \ )) or resid 772 through 775 or (resid 776 through 778 and (name N or name CA or \ name C or name O or name CB )) or resid 779 through 789 or (resid 790 through 7 \ 93 and (name N or name CA or name C or name O or name CB )) or (resid 794 throug \ h 801 and (name N or name CA or name C or name O or name CB )) or resid 802 or ( \ resid 803 through 813 and (name N or name CA or name C or name O or name CB )))) \ selection = (chain 'C' and (resid 25 through 411 or (resid 412 and (name N or name CA or nam \ e C or name O or name CB )) or resid 413 through 447 or (resid 448 and (name N o \ r name CA or name C or name O or name CB )) or resid 449 through 482 or (resid 4 \ 83 and (name N or name CA or name C or name O or name CB )) or resid 484 through \ 485 or (resid 486 and (name N or name CA or name C or name O or name CB )) or r \ esid 487 through 501 or (resid 502 and (name N or name CA or name C or name O or \ name CB )) or resid 503 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 563 through 565 or (resid 566 and (name N o \ r name CA or name C or name O or name CB )) or resid 567 or (resid 568 through 5 \ 69 and (name N or name CA or name C or name O or name CB )) or resid 570 through \ 584 or (resid 585 through 588 and (name N or name CA or name C or name O or nam \ e CB )) or resid 589 through 591 or (resid 592 and (name N or name CA or name C \ or name O or name CB )) or resid 593 through 611 or (resid 612 through 613 and ( \ name N or name CA or name C or name O or name CB )) or resid 614 through 619 or \ (resid 620 through 624 and (name N or name CA or name C or name O or name CB )) \ or resid 625 through 677 or (resid 678 through 680 and (name N or name CA or nam \ e C or name O or name CB )) or resid 681 through 690 or (resid 691 and (name N o \ r name CA or name C or name O or name CB )) or resid 692 through 726 or (resid 7 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 728 through \ 766 or (resid 767 and (name N or name CA or name C or name O or name CB )) or r \ esid 768 through 774 or (resid 775 through 778 and (name N or name CA or name C \ or name O or name CB )) or resid 779 through 784 or (resid 785 through 786 and ( \ name N or name CA or name C or name O or name CB )) or resid 787 through 813)) } ncs_group { reference = (chain 'B' and (resid 34 through 396 or (resid 397 through 400 and (name N or na \ me CA or name C or name O or name CB )) or resid 401 through 402 or (resid 403 a \ nd (name N or name CA or name C or name O or name CB )) or resid 404 through 419 \ or (resid 420 through 421 and (name N or name CA or name C or name O or name CB \ )) or resid 422 or (resid 423 and (name N or name CA or name C or name O or nam \ e CB )) or resid 424 or (resid 425 and (name N or name CA or name C or name O or \ name CB )) or resid 426 or (resid 427 through 428 and (name N or name CA or nam \ e C or name O or name CB )) or resid 429 through 437 or (resid 438 and (name N o \ r name CA or name C or name O or name CB )) or resid 439 or (resid 440 through 4 \ 48 and (name N or name CA or name C or name O or name CB )) or resid 449 through \ 471 or (resid 472 and (name N or name CA or name C or name O or name CB )) or r \ esid 473 or (resid 474 and (name N or name CA or name C or name O or name CB )) \ or resid 475 through 480 or (resid 481 through 482 and (name N or name CA or nam \ e C or name O or name CB )) or resid 483 or (resid 484 and (name N or name CA or \ name C or name O or name CB )) or resid 485 through 493 or (resid 494 and (name \ N or name CA or name C or name O or name CB )) or resid 495 through 510 or (res \ id 511 and (name N or name CA or name C or name O or name CB )) or resid 512 thr \ ough 522 or (resid 523 and (name N or name CA or name C or name O or name CB )) \ or resid 524 or (resid 525 and (name N or name CA or name C or name O or name CB \ )) or resid 526 through 535 or (resid 536 and (name N or name CA or name C or n \ ame O or name CB )) or resid 537 or (resid 538 and (name N or name CA or name C \ or name O or name CB )) or resid 539 through 540 or (resid 541 and (name N or na \ me CA or name C or name O or name CB )) or resid 542 through 590 or (resid 591 t \ hrough 593 and (name N or name CA or name C or name O or name CB )) or resid 594 \ through 606 or (resid 607 through 609 and (name N or name CA or name C or name \ O or name CB )) or resid 610 through 618 or (resid 619 through 621 and (name N o \ r name CA or name C or name O or name CB )) or resid 622 through 627 or (resid 6 \ 28 through 631 and (name N or name CA or name C or name O or name CB )) or resid \ 632 through 640 or (resid 641 through 643 and (name N or name CA or name C or n \ ame O or name CB )) or resid 644 through 646 or (resid 647 and (name N or name C \ A or name C or name O or name CB )) or resid 648 through 663 or (resid 664 throu \ gh 665 and (name N or name CA or name C or name O or name CB )) or resid 666 thr \ ough 669 or (resid 670 and (name N or name CA or name C or name O or name CB )) \ or resid 671 through 676 or (resid 677 and (name N or name CA or name C or name \ O or name CB )) or resid 678 through 682 or (resid 683 and (name N or name CA or \ name C or name O or name CB )) or resid 684 through 685 or (resid 686 through 6 \ 87 and (name N or name CA or name C or name O or name CB )) or resid 688 or (res \ id 689 and (name N or name CA or name C or name O or name CB )) or resid 690 thr \ ough 696 or (resid 697 through 698 and (name N or name CA or name C or name O or \ name CB )) or resid 699 through 700 or (resid 701 through 702 and (name N or na \ me CA or name C or name O or name CB )) or (resid 703 through 707 and (name N or \ name CA or name C or name O or name CB )) or resid 708 through 720 or (resid 72 \ 1 through 723 and (name N or name CA or name C or name O or name CB )) or resid \ 724 through 733 or (resid 734 through 737 and (name N or name CA or name C or na \ me O or name CB )) or resid 738 through 766 or (resid 767 and (name N or name CA \ or name C or name O or name CB )) or resid 768 through 780 or (resid 781 throug \ h 791 and (name N or name CA or name C or name O or name CB )) or resid 792 thro \ ugh 793 or (resid 794 through 814 and (name N or name CA or name C or name O or \ name CB )))) selection = (chain 'D' and (resid 34 through 399 or (resid 400 and (name N or name CA or nam \ e C or name O or name CB )) or resid 401 through 411 or (resid 412 through 414 a \ nd (name N or name CA or name C or name O or name CB )) or resid 415 through 519 \ or (resid 520 and (name N or name CA or name C or name O or name CB )) or resid \ 521 through 553 or (resid 554 through 557 and (name N or name CA or name C or n \ ame O or name CB )) or resid 558 through 563 or (resid 564 and (name N or name C \ A or name C or name O or name CB )) or resid 565 through 566 or (resid 567 and ( \ name N or name CA or name C or name O or name CB )) or resid 568 through 575 or \ (resid 576 through 579 and (name N or name CA or name C or name O or name CB )) \ or resid 580 or (resid 581 and (name N or name CA or name C or name O or name CB \ )) or resid 582 through 591 or (resid 592 through 593 and (name N or name CA or \ name C or name O or name CB )) or resid 594 through 619 or (resid 620 through 6 \ 21 and (name N or name CA or name C or name O or name CB )) or resid 622 through \ 641 or (resid 642 through 643 and (name N or name CA or name C or name O or nam \ e CB )) or resid 644 through 655 or (resid 656 through 657 and (name N or name C \ A or name C or name O or name CB )) or resid 658 through 694 or (resid 695 throu \ gh 698 and (name N or name CA or name C or name O or name CB )) or resid 699 thr \ ough 746 or (resid 747 and (name N or name CA or name C or name O or name CB )) \ or resid 748 through 752 or (resid 753 and (name N or name CA or name C or name \ O or name CB )) or resid 754 through 768 or (resid 769 through 770 and (name N o \ r name CA or name C or name O or name CB )) or resid 771 through 773 or (resid 7 \ 74 and (name N or name CA or name C or name O or name CB )) or resid 775 through \ 778 or (resid 779 and (name N or name CA or name C or name O or name CB )) or r \ esid 780 through 794 or (resid 795 through 814 and (name N or name CA or name C \ or name O or name CB )))) } ncs_group { reference = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'I' selection = chain 'L' } 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: 34.880 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: 0.040 Extract box with map and model: 1.370 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 67.560 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.150 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.004 0.411 29451 Z= 0.157 Angle : 0.725 35.343 40273 Z= 0.372 Chirality : 0.042 0.317 4717 Planarity : 0.004 0.073 5145 Dihedral : 16.749 90.023 9798 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.06 % Favored : 86.56 % Rotamer: Outliers : 0.47 % Allowed : 37.71 % Favored : 61.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -1.46 (0.14), residues: 3966 helix: 1.23 (0.15), residues: 1190 sheet: -0.94 (0.22), residues: 666 loop : -2.41 (0.14), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 614 HIS 0.007 0.001 HIS A 146 PHE 0.026 0.001 PHE A 472 TYR 0.015 0.001 TYR D 286 ARG 0.007 0.000 ARG L 62 Details of bonding type rmsd hydrogen bonds : bond 0.20758 ( 1065) hydrogen bonds : angle 7.30231 ( 3018) SS BOND : bond 0.00202 ( 24) SS BOND : angle 0.95007 ( 48) covalent geometry : bond 0.00437 (29427) covalent geometry : angle 0.72449 (40225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 267 LEU cc_start: 0.8812 (mp) cc_final: 0.8319 (tp) REVERT: D 496 MET cc_start: 0.7513 (tpp) cc_final: 0.7238 (tpt) REVERT: D 564 MET cc_start: 0.0946 (tpt) cc_final: -0.0272 (mtt) outliers start: 13 outliers final: 11 residues processed: 250 average time/residue: 0.3669 time to fit residues: 156.3448 Evaluate side-chains 247 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 236 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 20.0000 chunk 300 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 310 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 231 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 371 HIS A 405 GLN A 761 HIS C 28 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 168 HIS D 676 ASN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN L 32 ASN L 39 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.119733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.085912 restraints weight = 114849.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082419 restraints weight = 77780.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082836 restraints weight = 88913.865| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 29451 Z= 0.263 Angle : 0.758 12.507 40273 Z= 0.400 Chirality : 0.047 0.261 4717 Planarity : 0.005 0.066 5145 Dihedral : 5.292 29.111 4229 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.38 % Allowed : 14.07 % Favored : 85.55 % Rotamer: Outliers : 0.18 % Allowed : 6.28 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -1.73 (0.14), residues: 3966 helix: 0.93 (0.15), residues: 1215 sheet: -1.31 (0.21), residues: 705 loop : -2.49 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 104 HIS 0.013 0.002 HIS A 761 PHE 0.031 0.002 PHE C 472 TYR 0.031 0.002 TYR B 710 ARG 0.010 0.001 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 1065) hydrogen bonds : angle 5.79133 ( 3018) SS BOND : bond 0.00546 ( 24) SS BOND : angle 1.59719 ( 48) covalent geometry : bond 0.00606 (29427) covalent geometry : angle 0.75607 (40225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 313 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 PHE cc_start: 0.6052 (t80) cc_final: 0.5561 (t80) REVERT: A 155 MET cc_start: 0.7853 (ppp) cc_final: 0.7557 (ppp) REVERT: A 766 MET cc_start: 0.8934 (mmp) cc_final: 0.8659 (mmp) REVERT: B 135 MET cc_start: 0.8815 (ppp) cc_final: 0.8221 (ppp) REVERT: B 267 LEU cc_start: 0.8901 (mp) cc_final: 0.8414 (tp) REVERT: B 286 TYR cc_start: 0.7597 (t80) cc_final: 0.5831 (t80) REVERT: B 291 ARG cc_start: 0.8570 (mtt-85) cc_final: 0.7602 (mtt-85) REVERT: B 396 PHE cc_start: 0.5658 (m-80) cc_final: 0.5352 (m-80) REVERT: B 536 MET cc_start: 0.8285 (tmm) cc_final: 0.7955 (tmm) REVERT: C 91 LEU cc_start: 0.8985 (tp) cc_final: 0.8772 (tp) REVERT: C 155 MET cc_start: 0.8928 (ppp) cc_final: 0.8217 (ppp) REVERT: D 80 LYS cc_start: 0.9368 (tmtt) cc_final: 0.8986 (tppt) REVERT: D 133 MET cc_start: 0.8530 (mpp) cc_final: 0.8275 (mpp) REVERT: D 338 MET cc_start: 0.8901 (mmm) cc_final: 0.8658 (mmm) REVERT: K 83 MET cc_start: 0.0905 (mmp) cc_final: 0.0421 (mmp) REVERT: L 140 TYR cc_start: 0.5271 (t80) cc_final: 0.5011 (t80) outliers start: 5 outliers final: 1 residues processed: 318 average time/residue: 0.3962 time to fit residues: 202.8970 Evaluate side-chains 228 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 113 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 353 optimal weight: 50.0000 chunk 231 optimal weight: 0.3980 chunk 338 optimal weight: 4.9990 chunk 334 optimal weight: 30.0000 chunk 261 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 HIS ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 GLN L 39 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.123424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.089169 restraints weight = 113059.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.086798 restraints weight = 76935.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.087309 restraints weight = 72262.387| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29451 Z= 0.124 Angle : 0.627 8.787 40273 Z= 0.328 Chirality : 0.043 0.211 4717 Planarity : 0.005 0.069 5145 Dihedral : 4.836 25.073 4229 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.22 % Favored : 88.38 % Rotamer: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -1.47 (0.14), residues: 3966 helix: 1.20 (0.15), residues: 1212 sheet: -1.07 (0.21), residues: 683 loop : -2.39 (0.14), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 378 HIS 0.008 0.001 HIS A 449 PHE 0.029 0.001 PHE D 210 TYR 0.018 0.001 TYR D 321 ARG 0.016 0.001 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 1065) hydrogen bonds : angle 5.16140 ( 3018) SS BOND : bond 0.00413 ( 24) SS BOND : angle 1.31944 ( 48) covalent geometry : bond 0.00269 (29427) covalent geometry : angle 0.62588 (40225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 PHE cc_start: 0.6006 (t80) cc_final: 0.5552 (t80) REVERT: A 155 MET cc_start: 0.8039 (ppp) cc_final: 0.7798 (ppp) REVERT: A 687 MET cc_start: 0.8711 (ppp) cc_final: 0.8229 (ppp) REVERT: B 267 LEU cc_start: 0.8835 (mp) cc_final: 0.8326 (tp) REVERT: B 286 TYR cc_start: 0.7457 (t80) cc_final: 0.6939 (t80) REVERT: B 507 MET cc_start: 0.8806 (mmm) cc_final: 0.8593 (mtt) REVERT: B 536 MET cc_start: 0.8255 (tmm) cc_final: 0.7974 (tmm) REVERT: B 614 TRP cc_start: 0.7754 (t-100) cc_final: 0.7530 (t-100) REVERT: C 155 MET cc_start: 0.8908 (ppp) cc_final: 0.8147 (ppp) REVERT: D 133 MET cc_start: 0.8570 (mpp) cc_final: 0.8226 (mpp) REVERT: D 338 MET cc_start: 0.8919 (mmm) cc_final: 0.8449 (mmm) REVERT: G 73 ASP cc_start: 0.8729 (t70) cc_final: 0.8489 (t0) REVERT: K 83 MET cc_start: 0.1702 (mmp) cc_final: 0.0825 (mmp) REVERT: K 157 GLU cc_start: 0.6409 (mt-10) cc_final: 0.6165 (mm-30) REVERT: L 140 TYR cc_start: 0.5006 (t80) cc_final: 0.4735 (t80) outliers start: 1 outliers final: 1 residues processed: 316 average time/residue: 0.3592 time to fit residues: 188.4623 Evaluate side-chains 244 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 141 optimal weight: 8.9990 chunk 319 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 chunk 166 optimal weight: 3.9990 chunk 252 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 135 optimal weight: 0.6980 chunk 217 optimal weight: 0.0870 chunk 25 optimal weight: 5.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 405 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 146 HIS ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 GLN K 208 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.124971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.089463 restraints weight = 112840.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.087885 restraints weight = 71918.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.088341 restraints weight = 68733.369| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29451 Z= 0.113 Angle : 0.608 12.696 40273 Z= 0.315 Chirality : 0.043 0.216 4717 Planarity : 0.004 0.068 5145 Dihedral : 4.608 23.881 4229 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.50 % Favored : 88.12 % Rotamer: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -1.42 (0.14), residues: 3966 helix: 1.20 (0.15), residues: 1235 sheet: -1.08 (0.21), residues: 691 loop : -2.36 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 104 HIS 0.006 0.001 HIS B 119 PHE 0.027 0.001 PHE D 210 TYR 0.038 0.001 TYR D 656 ARG 0.006 0.000 ARG K 100 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 1065) hydrogen bonds : angle 4.85451 ( 3018) SS BOND : bond 0.00273 ( 24) SS BOND : angle 1.20230 ( 48) covalent geometry : bond 0.00243 (29427) covalent geometry : angle 0.60674 (40225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 3.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9115 (tmm) cc_final: 0.8863 (tmm) REVERT: A 152 PHE cc_start: 0.5936 (t80) cc_final: 0.5587 (t80) REVERT: A 687 MET cc_start: 0.8655 (ppp) cc_final: 0.8191 (ppp) REVERT: B 112 MET cc_start: 0.9016 (mtm) cc_final: 0.8505 (mpp) REVERT: B 267 LEU cc_start: 0.8809 (mp) cc_final: 0.8334 (tp) REVERT: B 396 PHE cc_start: 0.4264 (m-80) cc_final: 0.3737 (m-80) REVERT: B 536 MET cc_start: 0.8313 (tmm) cc_final: 0.7928 (tmm) REVERT: B 614 TRP cc_start: 0.7856 (t-100) cc_final: 0.7567 (t-100) REVERT: C 155 MET cc_start: 0.8933 (ppp) cc_final: 0.8078 (ppp) REVERT: D 80 LYS cc_start: 0.9388 (tmtt) cc_final: 0.8943 (tppt) REVERT: K 83 MET cc_start: 0.2018 (mmp) cc_final: 0.1060 (mmp) REVERT: K 157 GLU cc_start: 0.6395 (mt-10) cc_final: 0.6194 (mm-30) REVERT: L 140 TYR cc_start: 0.5378 (t80) cc_final: 0.5116 (t80) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.3869 time to fit residues: 204.2759 Evaluate side-chains 250 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 184 optimal weight: 0.0020 chunk 326 optimal weight: 50.0000 chunk 212 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 314 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 389 optimal weight: 50.0000 chunk 166 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 overall best weight: 2.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** 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 = 0.4081 r_free = 0.4081 target = 0.120160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.087599 restraints weight = 115301.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084631 restraints weight = 91034.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084735 restraints weight = 76193.296| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29451 Z= 0.181 Angle : 0.651 9.786 40273 Z= 0.339 Chirality : 0.044 0.214 4717 Planarity : 0.005 0.065 5145 Dihedral : 4.817 24.254 4229 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.63 % Favored : 87.04 % Rotamer: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -1.46 (0.14), residues: 3966 helix: 1.22 (0.15), residues: 1239 sheet: -1.14 (0.20), residues: 700 loop : -2.42 (0.14), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 372 HIS 0.006 0.001 HIS C 761 PHE 0.028 0.002 PHE D 210 TYR 0.024 0.001 TYR A 158 ARG 0.006 0.000 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1065) hydrogen bonds : angle 4.88938 ( 3018) SS BOND : bond 0.00469 ( 24) SS BOND : angle 1.13710 ( 48) covalent geometry : bond 0.00418 (29427) covalent geometry : angle 0.64992 (40225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 3.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9116 (tmm) cc_final: 0.8804 (tmm) REVERT: A 155 MET cc_start: 0.7962 (ppp) cc_final: 0.7761 (ppp) REVERT: A 687 MET cc_start: 0.8633 (ppp) cc_final: 0.8164 (ppp) REVERT: B 267 LEU cc_start: 0.8765 (mp) cc_final: 0.8390 (tp) REVERT: B 286 TYR cc_start: 0.7580 (t80) cc_final: 0.6903 (t80) REVERT: B 396 PHE cc_start: 0.4852 (m-80) cc_final: 0.4354 (m-80) REVERT: B 536 MET cc_start: 0.8108 (tmm) cc_final: 0.7776 (tmm) REVERT: B 614 TRP cc_start: 0.7799 (t-100) cc_final: 0.7518 (t-100) REVERT: C 155 MET cc_start: 0.8925 (ppp) cc_final: 0.8173 (ppp) REVERT: D 80 LYS cc_start: 0.9342 (tmtt) cc_final: 0.8959 (tppt) REVERT: D 83 ILE cc_start: 0.9189 (mm) cc_final: 0.8984 (mm) REVERT: D 338 MET cc_start: 0.8857 (mmm) cc_final: 0.8411 (mmm) REVERT: K 34 MET cc_start: -0.0862 (mmt) cc_final: -0.1110 (mmm) REVERT: K 83 MET cc_start: 0.1899 (mmp) cc_final: 0.0957 (mmp) REVERT: K 157 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6227 (mm-30) REVERT: L 62 ARG cc_start: 0.9192 (ttm-80) cc_final: 0.8916 (ttp80) REVERT: L 140 TYR cc_start: 0.5466 (t80) cc_final: 0.5237 (t80) outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.3735 time to fit residues: 183.6222 Evaluate side-chains 242 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 386 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 353 optimal weight: 50.0000 chunk 384 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 391 optimal weight: 30.0000 chunk 379 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 GLN ** I 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.118081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.082594 restraints weight = 115520.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081258 restraints weight = 79576.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.081030 restraints weight = 84270.713| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 29451 Z= 0.270 Angle : 0.740 10.183 40273 Z= 0.389 Chirality : 0.047 0.226 4717 Planarity : 0.005 0.063 5145 Dihedral : 5.339 28.556 4229 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.40 % Allowed : 14.12 % Favored : 85.48 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -1.80 (0.14), residues: 3966 helix: 0.88 (0.15), residues: 1245 sheet: -1.44 (0.20), residues: 729 loop : -2.56 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 378 HIS 0.012 0.002 HIS C 761 PHE 0.041 0.002 PHE C 472 TYR 0.023 0.002 TYR D 180 ARG 0.011 0.001 ARG D 291 Details of bonding type rmsd hydrogen bonds : bond 0.04385 ( 1065) hydrogen bonds : angle 5.15565 ( 3018) SS BOND : bond 0.00316 ( 24) SS BOND : angle 1.71681 ( 48) covalent geometry : bond 0.00627 (29427) covalent geometry : angle 0.73799 (40225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9209 (tmm) cc_final: 0.8846 (tmm) REVERT: A 687 MET cc_start: 0.8613 (ppp) cc_final: 0.8098 (ppp) REVERT: B 267 LEU cc_start: 0.8836 (mp) cc_final: 0.8497 (tp) REVERT: B 286 TYR cc_start: 0.7712 (t80) cc_final: 0.7015 (t80) REVERT: B 396 PHE cc_start: 0.5253 (m-80) cc_final: 0.4863 (m-80) REVERT: B 536 MET cc_start: 0.8269 (tmm) cc_final: 0.7953 (tmm) REVERT: C 155 MET cc_start: 0.9005 (ppp) cc_final: 0.8190 (ppp) REVERT: C 766 MET cc_start: 0.9346 (mmm) cc_final: 0.8778 (mpp) REVERT: D 80 LYS cc_start: 0.9403 (tmtt) cc_final: 0.8936 (tppt) REVERT: K 83 MET cc_start: 0.2353 (mmp) cc_final: 0.1413 (mmp) REVERT: K 109 MET cc_start: 0.6886 (mmm) cc_final: 0.6624 (mmm) REVERT: L 62 ARG cc_start: 0.9253 (ttm-80) cc_final: 0.8953 (ttp-170) REVERT: L 140 TYR cc_start: 0.5512 (t80) cc_final: 0.5258 (t80) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.3642 time to fit residues: 168.4192 Evaluate side-chains 232 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 202 optimal weight: 0.9980 chunk 347 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 337 optimal weight: 8.9990 chunk 285 optimal weight: 0.9980 chunk 295 optimal weight: 9.9990 chunk 106 optimal weight: 50.0000 chunk 67 optimal weight: 5.9990 chunk 324 optimal weight: 40.0000 chunk 154 optimal weight: 30.0000 chunk 92 optimal weight: 4.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 GLN ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN L 39 GLN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.117806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.082259 restraints weight = 113965.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080133 restraints weight = 73711.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080693 restraints weight = 77730.884| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 29451 Z= 0.257 Angle : 0.728 10.376 40273 Z= 0.382 Chirality : 0.046 0.231 4717 Planarity : 0.005 0.063 5145 Dihedral : 5.416 29.173 4229 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.07 % Favored : 85.58 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -1.88 (0.14), residues: 3966 helix: 0.82 (0.15), residues: 1245 sheet: -1.46 (0.20), residues: 709 loop : -2.63 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 160 HIS 0.009 0.001 HIS A 449 PHE 0.035 0.002 PHE D 210 TYR 0.027 0.002 TYR D 286 ARG 0.008 0.001 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 1065) hydrogen bonds : angle 5.14712 ( 3018) SS BOND : bond 0.00408 ( 24) SS BOND : angle 1.65425 ( 48) covalent geometry : bond 0.00596 (29427) covalent geometry : angle 0.72656 (40225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9201 (tmm) cc_final: 0.8822 (tmm) REVERT: A 155 MET cc_start: 0.8008 (ppp) cc_final: 0.7779 (ppp) REVERT: A 687 MET cc_start: 0.8568 (ppp) cc_final: 0.8078 (ppp) REVERT: B 112 MET cc_start: 0.8824 (mtm) cc_final: 0.8564 (pmm) REVERT: B 267 LEU cc_start: 0.8813 (mp) cc_final: 0.8454 (tp) REVERT: B 286 TYR cc_start: 0.7713 (t80) cc_final: 0.7051 (t80) REVERT: B 396 PHE cc_start: 0.5197 (m-80) cc_final: 0.4861 (m-80) REVERT: B 536 MET cc_start: 0.8252 (tmm) cc_final: 0.7957 (tmm) REVERT: B 588 LEU cc_start: 0.9124 (mm) cc_final: 0.8819 (tp) REVERT: C 155 MET cc_start: 0.8940 (ppp) cc_final: 0.8187 (ppp) REVERT: C 766 MET cc_start: 0.9176 (mmm) cc_final: 0.8793 (mpp) REVERT: D 80 LYS cc_start: 0.9371 (tmtt) cc_final: 0.8900 (tppt) REVERT: K 34 MET cc_start: -0.3078 (mmm) cc_final: -0.3474 (mmm) REVERT: K 83 MET cc_start: 0.2590 (mmp) cc_final: 0.1599 (mmp) REVERT: K 157 GLU cc_start: 0.6378 (mt-10) cc_final: 0.6158 (mm-30) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.3491 time to fit residues: 158.9280 Evaluate side-chains 228 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 326 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 290 optimal weight: 0.0030 chunk 237 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 162 HIS ** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 GLN K 39 GLN L 39 GLN L 197 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.120219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.085383 restraints weight = 113603.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083762 restraints weight = 79742.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083476 restraints weight = 72507.169| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29451 Z= 0.128 Angle : 0.644 9.235 40273 Z= 0.333 Chirality : 0.044 0.238 4717 Planarity : 0.004 0.066 5145 Dihedral : 4.990 28.434 4229 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.33 % Allowed : 12.03 % Favored : 87.64 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -1.57 (0.14), residues: 3966 helix: 1.12 (0.15), residues: 1236 sheet: -1.21 (0.21), residues: 696 loop : -2.48 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 160 HIS 0.008 0.001 HIS A 293 PHE 0.031 0.001 PHE D 210 TYR 0.018 0.001 TYR D 286 ARG 0.007 0.000 ARG B 721 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 1065) hydrogen bonds : angle 4.80927 ( 3018) SS BOND : bond 0.00358 ( 24) SS BOND : angle 1.27613 ( 48) covalent geometry : bond 0.00290 (29427) covalent geometry : angle 0.64287 (40225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9166 (tmm) cc_final: 0.8770 (tmm) REVERT: A 150 VAL cc_start: 0.8977 (t) cc_final: 0.8765 (t) REVERT: A 152 PHE cc_start: 0.6458 (t80) cc_final: 0.6111 (t80) REVERT: A 321 PHE cc_start: 0.7704 (t80) cc_final: 0.7487 (t80) REVERT: A 687 MET cc_start: 0.8381 (ppp) cc_final: 0.7940 (ppp) REVERT: B 267 LEU cc_start: 0.9031 (mp) cc_final: 0.8681 (tp) REVERT: B 286 TYR cc_start: 0.7657 (t80) cc_final: 0.7063 (t80) REVERT: B 396 PHE cc_start: 0.5117 (m-80) cc_final: 0.4847 (m-80) REVERT: B 415 PRO cc_start: 0.8386 (Cg_endo) cc_final: 0.8064 (Cg_exo) REVERT: B 536 MET cc_start: 0.8129 (tmm) cc_final: 0.7863 (tmm) REVERT: B 588 LEU cc_start: 0.9075 (mm) cc_final: 0.8820 (tp) REVERT: C 155 MET cc_start: 0.8915 (ppp) cc_final: 0.8185 (ppp) REVERT: C 766 MET cc_start: 0.9251 (mmm) cc_final: 0.8935 (mpp) REVERT: D 80 LYS cc_start: 0.9392 (tmtt) cc_final: 0.8943 (tppt) REVERT: D 166 ASP cc_start: 0.8311 (t70) cc_final: 0.8088 (t70) REVERT: D 338 MET cc_start: 0.8818 (mmm) cc_final: 0.8362 (mmm) REVERT: K 34 MET cc_start: -0.3180 (mmm) cc_final: -0.3470 (mmm) REVERT: K 83 MET cc_start: 0.2763 (mmp) cc_final: 0.1488 (mmp) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3930 time to fit residues: 197.3813 Evaluate side-chains 239 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 329 optimal weight: 30.0000 chunk 303 optimal weight: 6.9990 chunk 359 optimal weight: 30.0000 chunk 348 optimal weight: 10.0000 chunk 284 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 281 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 295 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.117546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.081847 restraints weight = 114397.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.080185 restraints weight = 78436.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.080065 restraints weight = 78933.084| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 29451 Z= 0.266 Angle : 0.751 11.096 40273 Z= 0.393 Chirality : 0.047 0.240 4717 Planarity : 0.005 0.060 5145 Dihedral : 5.427 37.914 4229 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 14.40 % Favored : 85.22 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.83 (0.14), residues: 3966 helix: 0.91 (0.15), residues: 1238 sheet: -1.45 (0.21), residues: 690 loop : -2.61 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP C 160 HIS 0.021 0.002 HIS C 761 PHE 0.034 0.002 PHE C 472 TYR 0.024 0.002 TYR D 286 ARG 0.006 0.001 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 1065) hydrogen bonds : angle 5.14081 ( 3018) SS BOND : bond 0.00433 ( 24) SS BOND : angle 1.54259 ( 48) covalent geometry : bond 0.00615 (29427) covalent geometry : angle 0.74961 (40225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 3.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9229 (tmm) cc_final: 0.8831 (tmm) REVERT: A 150 VAL cc_start: 0.9017 (t) cc_final: 0.8813 (t) REVERT: A 155 MET cc_start: 0.7983 (ppp) cc_final: 0.7762 (ppp) REVERT: A 222 SER cc_start: 0.8667 (t) cc_final: 0.8343 (p) REVERT: A 501 MET cc_start: 0.8245 (ttm) cc_final: 0.7974 (ttm) REVERT: A 687 MET cc_start: 0.8459 (ppp) cc_final: 0.8015 (ppp) REVERT: B 267 LEU cc_start: 0.8948 (mp) cc_final: 0.8601 (tp) REVERT: B 286 TYR cc_start: 0.7703 (t80) cc_final: 0.7009 (t80) REVERT: B 396 PHE cc_start: 0.5351 (m-80) cc_final: 0.5146 (m-80) REVERT: B 450 MET cc_start: 0.7211 (mpp) cc_final: 0.6873 (mpp) REVERT: B 536 MET cc_start: 0.8246 (tmm) cc_final: 0.7912 (tmm) REVERT: C 155 MET cc_start: 0.8966 (ppp) cc_final: 0.8184 (ppp) REVERT: D 80 LYS cc_start: 0.9428 (tmtt) cc_final: 0.8948 (tppt) REVERT: D 338 MET cc_start: 0.8801 (mmm) cc_final: 0.8369 (mmm) REVERT: K 34 MET cc_start: -0.3210 (mmm) cc_final: -0.3498 (mmm) REVERT: K 83 MET cc_start: 0.2792 (mmp) cc_final: 0.1451 (mmp) REVERT: L 62 ARG cc_start: 0.9237 (ttm-80) cc_final: 0.8958 (ttt180) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3664 time to fit residues: 163.3797 Evaluate side-chains 227 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 3.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 234 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 180 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 228 optimal weight: 0.9990 chunk 385 optimal weight: 10.0000 chunk 395 optimal weight: 50.0000 chunk 264 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 380 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.117501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.081630 restraints weight = 114448.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080597 restraints weight = 80328.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.080084 restraints weight = 77739.767| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 29451 Z= 0.252 Angle : 0.743 10.672 40273 Z= 0.388 Chirality : 0.047 0.247 4717 Planarity : 0.005 0.061 5145 Dihedral : 5.568 42.750 4229 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.64 % Favored : 86.01 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.92 (0.14), residues: 3966 helix: 0.78 (0.15), residues: 1235 sheet: -1.44 (0.21), residues: 683 loop : -2.64 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP C 160 HIS 0.012 0.001 HIS C 761 PHE 0.032 0.002 PHE C 472 TYR 0.058 0.002 TYR C 158 ARG 0.006 0.001 ARG A 468 Details of bonding type rmsd hydrogen bonds : bond 0.04214 ( 1065) hydrogen bonds : angle 5.19691 ( 3018) SS BOND : bond 0.00488 ( 24) SS BOND : angle 1.55808 ( 48) covalent geometry : bond 0.00587 (29427) covalent geometry : angle 0.74151 (40225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7932 Ramachandran restraints generated. 3966 Oldfield, 0 Emsley, 3966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.9221 (tmm) cc_final: 0.8794 (tmm) REVERT: A 125 MET cc_start: 0.8430 (ptt) cc_final: 0.8151 (ptt) REVERT: A 150 VAL cc_start: 0.9096 (t) cc_final: 0.8889 (t) REVERT: A 222 SER cc_start: 0.8793 (t) cc_final: 0.8485 (p) REVERT: A 501 MET cc_start: 0.7946 (ttm) cc_final: 0.7556 (ttp) REVERT: A 687 MET cc_start: 0.8448 (ppp) cc_final: 0.8020 (ppp) REVERT: B 112 MET cc_start: 0.8590 (pmm) cc_final: 0.8294 (pmm) REVERT: B 286 TYR cc_start: 0.7704 (t80) cc_final: 0.6961 (t80) REVERT: B 450 MET cc_start: 0.7179 (mpp) cc_final: 0.6817 (mpp) REVERT: B 536 MET cc_start: 0.8253 (tmm) cc_final: 0.7959 (tmm) REVERT: B 588 LEU cc_start: 0.9130 (mm) cc_final: 0.8870 (tp) REVERT: C 155 MET cc_start: 0.9027 (ppp) cc_final: 0.8244 (ppp) REVERT: C 766 MET cc_start: 0.9307 (mmm) cc_final: 0.8687 (mpp) REVERT: C 785 MET cc_start: 0.4609 (pmm) cc_final: 0.4406 (pmm) REVERT: K 34 MET cc_start: -0.3165 (mmm) cc_final: -0.3396 (mmm) REVERT: K 83 MET cc_start: 0.3045 (mmp) cc_final: 0.1799 (mmp) REVERT: L 62 ARG cc_start: 0.9279 (ttm-80) cc_final: 0.8960 (ttt180) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.3730 time to fit residues: 168.3783 Evaluate side-chains 222 residues out of total 3458 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 209 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 388 optimal weight: 40.0000 chunk 327 optimal weight: 6.9990 chunk 226 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 260 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 381 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS ** B 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 173 HIS ** 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 = 0.4037 r_free = 0.4037 target = 0.117151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.081006 restraints weight = 114769.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.078584 restraints weight = 92388.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.079144 restraints weight = 82966.658| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 29451 Z= 0.248 Angle : 0.743 12.233 40273 Z= 0.388 Chirality : 0.047 0.249 4717 Planarity : 0.005 0.060 5145 Dihedral : 5.562 43.893 4229 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.38 % Allowed : 14.47 % Favored : 85.15 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.96 (0.14), residues: 3966 helix: 0.81 (0.15), residues: 1231 sheet: -1.50 (0.21), residues: 680 loop : -2.67 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 160 HIS 0.017 0.001 HIS C 761 PHE 0.031 0.002 PHE D 210 TYR 0.023 0.002 TYR B 281 ARG 0.007 0.001 ARG B 469 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 1065) hydrogen bonds : angle 5.16274 ( 3018) SS BOND : bond 0.00376 ( 24) SS BOND : angle 1.53196 ( 48) covalent geometry : bond 0.00578 (29427) covalent geometry : angle 0.74177 (40225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10051.47 seconds wall clock time: 176 minutes 9.31 seconds (10569.31 seconds total)