Starting phenix.real_space_refine on Wed Nov 20 06:52:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/11_2024/8emw_28267.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/11_2024/8emw_28267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/11_2024/8emw_28267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/11_2024/8emw_28267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/11_2024/8emw_28267.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8emw_28267/11_2024/8emw_28267.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11633 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 79 5.16 5 C 7373 2.51 5 N 2034 2.21 5 O 2227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11714 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5926 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 47, 'TRANS': 695} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2512 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 420 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2516 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 339 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.72, per 1000 atoms: 0.57 Number of scatterers: 11714 At special positions: 0 Unit cell: (83.061, 132.562, 119.977, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 79 16.00 O 2227 8.00 N 2034 7.00 C 7373 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 2.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2832 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 30 sheets defined 21.6% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.545A pdb=" N ARG A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 24' Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.509A pdb=" N TRP A 131 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 145 Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 157 through 163 removed outlier: 3.873A pdb=" N GLN A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 179 removed outlier: 3.766A pdb=" N LYS A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.969A pdb=" N VAL A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.612A pdb=" N LYS A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.762A pdb=" N ASP A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.667A pdb=" N PHE A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 251 " --> pdb=" O MET A 247 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.009A pdb=" N LEU A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 347 through 357 removed outlier: 4.021A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 removed outlier: 3.578A pdb=" N GLU A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.714A pdb=" N GLN A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS A 429 " --> pdb=" O MET A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 437 removed outlier: 4.006A pdb=" N LEU A 437 " --> pdb=" O GLY A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 437' Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.542A pdb=" N THR A 592 " --> pdb=" O GLU A 589 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 593 " --> pdb=" O MET A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 593' Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.635A pdb=" N ALA A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 640 removed outlier: 3.665A pdb=" N PHE A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 removed outlier: 3.698A pdb=" N ASN A 666 " --> pdb=" O GLN A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 706 Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.698A pdb=" N ARG A 874 " --> pdb=" O ASP A 870 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLN A 875 " --> pdb=" O GLN A 871 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 877 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA A 878 " --> pdb=" O ARG A 874 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 removed outlier: 4.170A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.029A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.800A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.535A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET G 38 " --> pdb=" O ALA G 34 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 12 Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'D' and resid 9 through 21 removed outlier: 3.600A pdb=" N LEU D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.513A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 3.604A pdb=" N SER A 26 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N THR A 42 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR A 55 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TRP A 54 " --> pdb=" O ASP A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 69 through 74 removed outlier: 3.989A pdb=" N ASP A 71 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 104 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 241 Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 328 Processing sheet with id=AA6, first strand: chain 'A' and resid 330 through 331 removed outlier: 7.430A pdb=" N SER A 330 " --> pdb=" O LEU A 674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA8, first strand: chain 'A' and resid 408 through 411 removed outlier: 6.601A pdb=" N VAL A 408 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LYS A 466 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 410 " --> pdb=" O LYS A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 620 through 621 removed outlier: 6.441A pdb=" N PHE A 620 " --> pdb=" O TYR A 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 781 through 786 removed outlier: 4.376A pdb=" N LYS A 785 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN A 726 " --> pdb=" O LYS A 785 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU A 839 " --> pdb=" O ILE A 733 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 781 through 786 removed outlier: 4.376A pdb=" N LYS A 785 " --> pdb=" O ASN A 726 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN A 726 " --> pdb=" O LYS A 785 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 745 through 752 removed outlier: 5.097A pdb=" N GLU A 800 " --> pdb=" O PHE A 805 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 805 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 824 through 826 removed outlier: 5.553A pdb=" N LEU A 825 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.018A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 58 through 61 removed outlier: 6.846A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 100 through 103 removed outlier: 7.272A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.733A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.569A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.623A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.663A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.732A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.572A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.572A pdb=" N ILE C 80 " --> pdb=" O SER C 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 111 through 112 removed outlier: 3.589A pdb=" N VAL C 112 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AC8, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.902A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 167 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 161 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.630A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 232 through 234 Processing sheet with id=AD2, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.683A pdb=" N SER C 277 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 315 through 320 removed outlier: 3.534A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 768 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: 3.82 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3660 1.33 - 1.45: 2007 1.45 - 1.57: 6153 1.57 - 1.70: 0 1.70 - 1.82: 119 Bond restraints: 11939 Sorted by residual: bond pdb=" CA SER A 37 " pdb=" CB SER A 37 " ideal model delta sigma weight residual 1.532 1.485 0.047 1.58e-02 4.01e+03 8.68e+00 bond pdb=" N ASP C 291 " pdb=" CA ASP C 291 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.26e-02 6.30e+03 6.27e+00 bond pdb=" N ASP C 290 " pdb=" CA ASP C 290 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.22e-02 6.72e+03 6.11e+00 bond pdb=" N ASP A 125 " pdb=" CA ASP A 125 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.31e-02 5.83e+03 5.98e+00 bond pdb=" N SER A 37 " pdb=" CA SER A 37 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.63e+00 ... (remaining 11934 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 15473 1.98 - 3.95: 621 3.95 - 5.93: 61 5.93 - 7.90: 15 7.90 - 9.88: 8 Bond angle restraints: 16178 Sorted by residual: angle pdb=" N THR A 127 " pdb=" CA THR A 127 " pdb=" C THR A 127 " ideal model delta sigma weight residual 113.89 105.90 7.99 1.58e+00 4.01e-01 2.56e+01 angle pdb=" C ASN A 39 " pdb=" CA ASN A 39 " pdb=" CB ASN A 39 " ideal model delta sigma weight residual 113.45 103.94 9.51 1.98e+00 2.55e-01 2.31e+01 angle pdb=" C ASP C 163 " pdb=" N THR C 164 " pdb=" CA THR C 164 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" N ASP C 291 " pdb=" CA ASP C 291 " pdb=" C ASP C 291 " ideal model delta sigma weight residual 112.92 108.08 4.84 1.23e+00 6.61e-01 1.55e+01 angle pdb=" C TYR C 289 " pdb=" CA TYR C 289 " pdb=" CB TYR C 289 " ideal model delta sigma weight residual 114.10 105.86 8.24 2.11e+00 2.25e-01 1.53e+01 ... (remaining 16173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 6314 17.36 - 34.73: 738 34.73 - 52.09: 135 52.09 - 69.46: 14 69.46 - 86.82: 15 Dihedral angle restraints: 7216 sinusoidal: 2845 harmonic: 4371 Sorted by residual: dihedral pdb=" CA TYR A 406 " pdb=" C TYR A 406 " pdb=" N PRO A 407 " pdb=" CA PRO A 407 " ideal model delta harmonic sigma weight residual -180.00 -152.11 -27.89 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA PRO A 702 " pdb=" C PRO A 702 " pdb=" N GLU A 703 " pdb=" CA GLU A 703 " ideal model delta harmonic sigma weight residual -180.00 -156.18 -23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASN C 313 " pdb=" C ASN C 313 " pdb=" N ARG C 314 " pdb=" CA ARG C 314 " ideal model delta harmonic sigma weight residual -180.00 -158.04 -21.96 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 7213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1512 0.071 - 0.142: 283 0.142 - 0.212: 24 0.212 - 0.283: 6 0.283 - 0.354: 1 Chirality restraints: 1826 Sorted by residual: chirality pdb=" CA ASP A 126 " pdb=" N ASP A 126 " pdb=" C ASP A 126 " pdb=" CB ASP A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA ASN A 39 " pdb=" N ASN A 39 " pdb=" C ASN A 39 " pdb=" CB ASN A 39 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB VAL A 347 " pdb=" CA VAL A 347 " pdb=" CG1 VAL A 347 " pdb=" CG2 VAL A 347 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1823 not shown) Planarity restraints: 2098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 370 " -0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 371 " 0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 369 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO A 370 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 455 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 456 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " 0.038 5.00e-02 4.00e+02 ... (remaining 2095 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2838 2.78 - 3.31: 9861 3.31 - 3.84: 18694 3.84 - 4.37: 21694 4.37 - 4.90: 37965 Nonbonded interactions: 91052 Sorted by model distance: nonbonded pdb=" OH TYR A 240 " pdb=" OD2 ASP C 186 " model vdw 2.248 3.040 nonbonded pdb=" O SER A 68 " pdb=" OG SER A 68 " model vdw 2.262 3.040 nonbonded pdb=" O VAL A 361 " pdb=" OG SER A 411 " model vdw 2.275 3.040 nonbonded pdb=" OG SER C 161 " pdb=" O THR C 165 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.288 3.040 ... (remaining 91047 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 'B' and (resid 4 through 34 or (resid 35 through 36 and (name N or name C \ A or name C or name O or name CB )) or resid 37 through 41 or (resid 42 and (nam \ e N or name CA or name C or name O or name CB )) or resid 43 through 51 or (resi \ d 52 and (name N or name CA or name C or name O or name CB )) or resid 53 throug \ h 152 or (resid 153 and (name N or name CA or name C or name O or name CB )) or \ resid 154 through 174 or (resid 175 and (name N or name CA or name C or name O o \ r name CB )) or resid 176 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB )) or resid 198 through 291 or (resid 292 and (name N \ or name CA or name C or name O or name CB )) or resid 293 through 340)) selection = (chain 'C' and (resid 4 through 136 or (resid 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 213 or (resid 214 through 215 an \ d (name N or name CA or name C or name O or name CB )) or resid 216 through 258 \ or (resid 259 and (name N or name CA or name C or name O or name CB )) or resid \ 260 through 282 or (resid 283 and (name N or name CA or name C or name O or name \ CB )) or resid 284 through 340)) } 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.240 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 : 0.008 0.104 11939 Z= 0.536 Angle : 0.908 9.878 16178 Z= 0.503 Chirality : 0.056 0.354 1826 Planarity : 0.007 0.102 2098 Dihedral : 15.242 86.819 4384 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.17), residues: 1486 helix: -4.92 (0.10), residues: 308 sheet: -3.25 (0.24), residues: 374 loop : -2.74 (0.18), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.011 0.002 HIS A 332 PHE 0.033 0.003 PHE B 199 TYR 0.021 0.003 TYR A 692 ARG 0.006 0.001 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.8030 (p0) cc_final: 0.7789 (p0) REVERT: A 173 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8117 (tppt) REVERT: A 215 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7707 (ttp80) REVERT: A 236 LYS cc_start: 0.7854 (tptt) cc_final: 0.7580 (mttp) REVERT: A 247 MET cc_start: 0.7560 (ttp) cc_final: 0.7159 (ttp) REVERT: A 290 GLN cc_start: 0.7581 (mt0) cc_final: 0.7325 (mt0) REVERT: A 341 LEU cc_start: 0.8880 (mp) cc_final: 0.8677 (mp) REVERT: A 374 GLU cc_start: 0.8306 (pm20) cc_final: 0.7672 (pm20) REVERT: A 460 MET cc_start: 0.8644 (ttp) cc_final: 0.8215 (ttp) REVERT: A 577 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7189 (mm-30) REVERT: A 583 GLU cc_start: 0.7749 (tt0) cc_final: 0.7542 (mt-10) REVERT: A 870 ASP cc_start: 0.7837 (t0) cc_final: 0.7603 (t0) REVERT: B 12 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7664 (tm-30) REVERT: B 325 MET cc_start: 0.7238 (mmp) cc_final: 0.6568 (mtp) REVERT: B 340 ASN cc_start: 0.8139 (t0) cc_final: 0.7894 (t0) REVERT: C 78 LYS cc_start: 0.8212 (tttm) cc_final: 0.7940 (mtpp) REVERT: C 188 MET cc_start: 0.7864 (mmm) cc_final: 0.7557 (mmm) REVERT: C 312 ASP cc_start: 0.7021 (p0) cc_final: 0.6798 (p0) REVERT: D 44 HIS cc_start: 0.7815 (m-70) cc_final: 0.7613 (m-70) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2964 time to fit residues: 99.0597 Evaluate side-chains 176 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 124 GLN A 163 GLN A 379 HIS ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 GLN B 35 ASN B 91 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN C 16 ASN C 230 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11939 Z= 0.241 Angle : 0.598 7.404 16178 Z= 0.317 Chirality : 0.044 0.145 1826 Planarity : 0.005 0.058 2098 Dihedral : 5.440 23.047 1630 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.13 % Allowed : 15.86 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.18), residues: 1486 helix: -3.52 (0.20), residues: 327 sheet: -2.89 (0.24), residues: 367 loop : -2.29 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS A 332 PHE 0.017 0.002 PHE B 199 TYR 0.016 0.001 TYR A 822 ARG 0.003 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 210 time to evaluate : 1.492 Fit side-chains REVERT: A 46 ASP cc_start: 0.8045 (p0) cc_final: 0.7743 (p0) REVERT: A 60 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7661 (mt-10) REVERT: A 173 LYS cc_start: 0.8403 (ttpt) cc_final: 0.7929 (tppt) REVERT: A 215 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7401 (ttp-170) REVERT: A 236 LYS cc_start: 0.7945 (tptt) cc_final: 0.7620 (mttp) REVERT: A 283 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7854 (tm-30) REVERT: A 290 GLN cc_start: 0.7588 (mt0) cc_final: 0.7312 (mt0) REVERT: A 374 GLU cc_start: 0.8177 (pm20) cc_final: 0.7806 (pm20) REVERT: A 439 ILE cc_start: 0.8617 (pt) cc_final: 0.8359 (mt) REVERT: A 869 MET cc_start: 0.7904 (mmp) cc_final: 0.7622 (mmp) REVERT: A 870 ASP cc_start: 0.8111 (t0) cc_final: 0.7716 (t0) REVERT: B 12 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7497 (tm-30) REVERT: B 45 MET cc_start: 0.7844 (mtm) cc_final: 0.7499 (mtm) REVERT: B 325 MET cc_start: 0.7184 (mmp) cc_final: 0.6613 (mtp) REVERT: C 78 LYS cc_start: 0.8191 (tttm) cc_final: 0.7873 (mtpp) REVERT: C 82 TRP cc_start: 0.8609 (m100) cc_final: 0.8315 (m100) REVERT: C 156 GLN cc_start: 0.7305 (mm-40) cc_final: 0.6988 (mm-40) REVERT: C 234 PHE cc_start: 0.7828 (m-80) cc_final: 0.7606 (m-80) REVERT: C 312 ASP cc_start: 0.7113 (p0) cc_final: 0.6896 (p0) REVERT: D 44 HIS cc_start: 0.7874 (m-70) cc_final: 0.7634 (m-70) outliers start: 27 outliers final: 19 residues processed: 228 average time/residue: 0.2552 time to fit residues: 82.6701 Evaluate side-chains 204 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN A 736 GLN A 821 HIS A 871 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 340 ASN ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 11939 Z= 0.397 Angle : 0.636 9.044 16178 Z= 0.332 Chirality : 0.046 0.145 1826 Planarity : 0.004 0.047 2098 Dihedral : 5.362 25.477 1630 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.95 % Allowed : 18.86 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.19), residues: 1486 helix: -2.72 (0.23), residues: 323 sheet: -2.79 (0.25), residues: 370 loop : -2.06 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 169 HIS 0.005 0.001 HIS A 808 PHE 0.026 0.002 PHE A 636 TYR 0.019 0.002 TYR A 692 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 1.461 Fit side-chains REVERT: A 46 ASP cc_start: 0.8137 (p0) cc_final: 0.7839 (p0) REVERT: A 166 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: A 173 LYS cc_start: 0.8427 (ttpt) cc_final: 0.7971 (tppt) REVERT: A 215 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7498 (ttp-170) REVERT: A 236 LYS cc_start: 0.8196 (tptt) cc_final: 0.7663 (mttp) REVERT: A 341 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8537 (mp) REVERT: A 374 GLU cc_start: 0.8098 (pm20) cc_final: 0.7706 (pm20) REVERT: A 422 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8311 (mt0) REVERT: A 736 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: A 870 ASP cc_start: 0.8200 (t0) cc_final: 0.7778 (t0) REVERT: B 45 MET cc_start: 0.7949 (mtm) cc_final: 0.7511 (mtm) REVERT: C 82 TRP cc_start: 0.8682 (m100) cc_final: 0.8359 (m100) REVERT: C 156 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6990 (mm-40) REVERT: C 234 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: C 253 PHE cc_start: 0.8279 (m-10) cc_final: 0.7985 (m-10) REVERT: C 331 SER cc_start: 0.8971 (m) cc_final: 0.8624 (t) outliers start: 50 outliers final: 38 residues processed: 227 average time/residue: 0.2491 time to fit residues: 80.9240 Evaluate side-chains 225 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 128 optimal weight: 0.0000 chunk 38 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A 871 GLN B 340 ASN G 44 HIS D 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11939 Z= 0.164 Angle : 0.533 8.140 16178 Z= 0.276 Chirality : 0.042 0.143 1826 Planarity : 0.004 0.065 2098 Dihedral : 4.682 25.102 1630 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.84 % Allowed : 20.76 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.20), residues: 1486 helix: -2.09 (0.26), residues: 324 sheet: -2.55 (0.25), residues: 360 loop : -1.82 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.002 0.001 HIS B 54 PHE 0.015 0.001 PHE B 199 TYR 0.011 0.001 TYR A 822 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 1.073 Fit side-chains REVERT: A 46 ASP cc_start: 0.7857 (p0) cc_final: 0.7576 (p0) REVERT: A 125 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7846 (t0) REVERT: A 173 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7883 (tppt) REVERT: A 215 ARG cc_start: 0.7679 (ttp80) cc_final: 0.7385 (ttp-170) REVERT: A 236 LYS cc_start: 0.8032 (tptt) cc_final: 0.7652 (mttp) REVERT: A 252 GLN cc_start: 0.8147 (mt0) cc_final: 0.7516 (mt0) REVERT: A 374 GLU cc_start: 0.7937 (pm20) cc_final: 0.7081 (pm20) REVERT: A 422 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8222 (mt0) REVERT: A 460 MET cc_start: 0.8126 (ttp) cc_final: 0.7827 (ttm) REVERT: A 736 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: A 869 MET cc_start: 0.7688 (mmp) cc_final: 0.7010 (mmp) REVERT: A 870 ASP cc_start: 0.8092 (t0) cc_final: 0.7633 (t0) REVERT: B 45 MET cc_start: 0.7762 (mtm) cc_final: 0.7297 (mtm) REVERT: B 325 MET cc_start: 0.7216 (mmp) cc_final: 0.6556 (mtp) REVERT: C 13 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: C 82 TRP cc_start: 0.8653 (m100) cc_final: 0.8277 (m-10) REVERT: C 156 GLN cc_start: 0.7177 (mm-40) cc_final: 0.6913 (mm-40) REVERT: C 298 ASP cc_start: 0.8079 (t0) cc_final: 0.6614 (p0) REVERT: C 317 CYS cc_start: 0.8290 (p) cc_final: 0.7991 (p) REVERT: C 318 LEU cc_start: 0.8995 (tt) cc_final: 0.8785 (tt) REVERT: C 331 SER cc_start: 0.8860 (m) cc_final: 0.8480 (t) REVERT: D 14 LYS cc_start: 0.8447 (tmtt) cc_final: 0.7977 (ttmt) REVERT: D 44 HIS cc_start: 0.7611 (m90) cc_final: 0.7062 (m90) outliers start: 36 outliers final: 25 residues processed: 232 average time/residue: 0.2546 time to fit residues: 83.8126 Evaluate side-chains 225 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 GLN A 871 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 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 : 0.006 0.079 11939 Z= 0.375 Angle : 0.623 9.469 16178 Z= 0.318 Chirality : 0.046 0.139 1826 Planarity : 0.004 0.067 2098 Dihedral : 5.047 44.586 1630 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 4.03 % Allowed : 21.55 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.20), residues: 1486 helix: -1.81 (0.27), residues: 319 sheet: -2.67 (0.24), residues: 366 loop : -1.77 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.005 0.001 HIS A 808 PHE 0.020 0.002 PHE A 636 TYR 0.017 0.002 TYR A 692 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 1.388 Fit side-chains REVERT: A 46 ASP cc_start: 0.8065 (p0) cc_final: 0.7760 (p0) REVERT: A 121 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7514 (ttt) REVERT: A 173 LYS cc_start: 0.8395 (ttpt) cc_final: 0.7941 (tppt) REVERT: A 176 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8536 (mt) REVERT: A 215 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7446 (ttp-170) REVERT: A 252 GLN cc_start: 0.8148 (mt0) cc_final: 0.7525 (mt0) REVERT: A 364 ASP cc_start: 0.8001 (m-30) cc_final: 0.7730 (m-30) REVERT: A 374 GLU cc_start: 0.8099 (pm20) cc_final: 0.7681 (pm20) REVERT: A 422 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8213 (mt0) REVERT: A 869 MET cc_start: 0.7723 (mmp) cc_final: 0.7049 (mmp) REVERT: A 871 GLN cc_start: 0.7972 (tp40) cc_final: 0.7718 (tp-100) REVERT: A 874 ARG cc_start: 0.8501 (ptp-170) cc_final: 0.7784 (ptp-170) REVERT: B 45 MET cc_start: 0.7791 (mtm) cc_final: 0.7250 (mtm) REVERT: B 325 MET cc_start: 0.7297 (mmp) cc_final: 0.6807 (mtp) REVERT: C 82 TRP cc_start: 0.8714 (m100) cc_final: 0.8297 (m-10) REVERT: C 220 GLN cc_start: 0.7778 (mp-120) cc_final: 0.7493 (mp10) REVERT: C 331 SER cc_start: 0.8930 (m) cc_final: 0.8549 (t) REVERT: D 44 HIS cc_start: 0.7667 (m90) cc_final: 0.7144 (m90) outliers start: 51 outliers final: 42 residues processed: 228 average time/residue: 0.2469 time to fit residues: 80.5362 Evaluate side-chains 226 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 193 CYS Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 GLN B 239 ASN B 340 ASN C 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11939 Z= 0.162 Angle : 0.533 8.682 16178 Z= 0.271 Chirality : 0.043 0.140 1826 Planarity : 0.004 0.064 2098 Dihedral : 4.448 26.816 1630 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.39 % Allowed : 22.65 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.21), residues: 1486 helix: -1.41 (0.28), residues: 319 sheet: -2.50 (0.25), residues: 350 loop : -1.52 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.003 0.001 HIS B 54 PHE 0.015 0.001 PHE B 199 TYR 0.015 0.001 TYR G 40 ARG 0.007 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 1.316 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7773 (p0) cc_final: 0.7480 (p0) REVERT: A 76 ARG cc_start: 0.8444 (ptt90) cc_final: 0.7886 (ptt90) REVERT: A 173 LYS cc_start: 0.8280 (ttpt) cc_final: 0.7841 (tppt) REVERT: A 215 ARG cc_start: 0.7639 (ttp80) cc_final: 0.7421 (ttp-170) REVERT: A 252 GLN cc_start: 0.8143 (mt0) cc_final: 0.7678 (mt0) REVERT: A 273 ARG cc_start: 0.7112 (ttm110) cc_final: 0.6714 (ttm110) REVERT: A 374 GLU cc_start: 0.7944 (pm20) cc_final: 0.7361 (pm20) REVERT: A 736 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: A 828 GLU cc_start: 0.8597 (mp0) cc_final: 0.8306 (mp0) REVERT: A 869 MET cc_start: 0.7633 (mmp) cc_final: 0.6931 (mmp) REVERT: B 45 MET cc_start: 0.7743 (mtm) cc_final: 0.7333 (mtm) REVERT: B 297 TRP cc_start: 0.8774 (m100) cc_final: 0.8298 (m100) REVERT: B 325 MET cc_start: 0.7352 (mmp) cc_final: 0.6807 (mtp) REVERT: C 13 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8462 (pt0) REVERT: C 82 TRP cc_start: 0.8676 (m100) cc_final: 0.8215 (m-10) REVERT: C 317 CYS cc_start: 0.8335 (p) cc_final: 0.8034 (p) REVERT: C 318 LEU cc_start: 0.9015 (tt) cc_final: 0.8781 (tt) REVERT: C 331 SER cc_start: 0.8798 (m) cc_final: 0.8434 (t) REVERT: D 14 LYS cc_start: 0.8433 (tmtt) cc_final: 0.8001 (ttmt) REVERT: D 44 HIS cc_start: 0.7643 (m90) cc_final: 0.7101 (m90) outliers start: 43 outliers final: 28 residues processed: 226 average time/residue: 0.2514 time to fit residues: 80.6861 Evaluate side-chains 221 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11939 Z= 0.280 Angle : 0.574 9.091 16178 Z= 0.292 Chirality : 0.045 0.264 1826 Planarity : 0.004 0.064 2098 Dihedral : 4.574 24.859 1630 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.10 % Allowed : 22.34 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.21), residues: 1486 helix: -1.30 (0.28), residues: 325 sheet: -2.53 (0.25), residues: 368 loop : -1.54 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.004 0.001 HIS B 54 PHE 0.018 0.002 PHE B 199 TYR 0.015 0.001 TYR A 596 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 1.357 Fit side-chains REVERT: A 46 ASP cc_start: 0.7917 (p0) cc_final: 0.7600 (p0) REVERT: A 76 ARG cc_start: 0.8471 (ptt90) cc_final: 0.7926 (ptt90) REVERT: A 121 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7409 (ttt) REVERT: A 125 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7875 (t0) REVERT: A 173 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7884 (tppt) REVERT: A 215 ARG cc_start: 0.7730 (ttp80) cc_final: 0.7484 (ttp-170) REVERT: A 252 GLN cc_start: 0.8146 (mt0) cc_final: 0.7682 (mt0) REVERT: A 374 GLU cc_start: 0.8011 (pm20) cc_final: 0.7405 (pm20) REVERT: A 736 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: A 828 GLU cc_start: 0.8635 (mp0) cc_final: 0.8335 (mp0) REVERT: A 869 MET cc_start: 0.7642 (mmp) cc_final: 0.7019 (mmp) REVERT: A 874 ARG cc_start: 0.8481 (ptp-170) cc_final: 0.7758 (ptp-170) REVERT: B 13 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8535 (pp30) REVERT: B 45 MET cc_start: 0.7734 (mtm) cc_final: 0.7479 (mtm) REVERT: B 325 MET cc_start: 0.7334 (mmp) cc_final: 0.6714 (mtp) REVERT: C 13 GLN cc_start: 0.8740 (tt0) cc_final: 0.8478 (pt0) REVERT: C 49 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7467 (mpt-90) REVERT: C 82 TRP cc_start: 0.8718 (m100) cc_final: 0.8254 (m-10) REVERT: C 220 GLN cc_start: 0.7597 (mp10) cc_final: 0.7273 (mp10) REVERT: C 318 LEU cc_start: 0.9036 (tt) cc_final: 0.8760 (tt) REVERT: C 331 SER cc_start: 0.8897 (m) cc_final: 0.8542 (t) REVERT: D 14 LYS cc_start: 0.8467 (tmtt) cc_final: 0.8005 (ttmt) REVERT: D 44 HIS cc_start: 0.7606 (m90) cc_final: 0.7087 (m90) outliers start: 52 outliers final: 40 residues processed: 232 average time/residue: 0.2538 time to fit residues: 84.0209 Evaluate side-chains 236 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 808 HIS Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 48 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 71 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN A 871 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11939 Z= 0.198 Angle : 0.553 11.218 16178 Z= 0.281 Chirality : 0.044 0.279 1826 Planarity : 0.004 0.061 2098 Dihedral : 4.424 27.856 1630 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.63 % Allowed : 22.97 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.21), residues: 1486 helix: -1.06 (0.29), residues: 326 sheet: -2.35 (0.26), residues: 345 loop : -1.44 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.004 0.001 HIS B 54 PHE 0.016 0.001 PHE B 199 TYR 0.013 0.001 TYR A 596 ARG 0.008 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7827 (p0) cc_final: 0.7525 (p0) REVERT: A 76 ARG cc_start: 0.8439 (ptt90) cc_final: 0.7883 (ptt90) REVERT: A 173 LYS cc_start: 0.8269 (ttpt) cc_final: 0.7842 (tppt) REVERT: A 215 ARG cc_start: 0.7661 (ttp80) cc_final: 0.7448 (ttp-170) REVERT: A 252 GLN cc_start: 0.8124 (mt0) cc_final: 0.7695 (mt0) REVERT: A 273 ARG cc_start: 0.7122 (ttm110) cc_final: 0.6727 (ttm110) REVERT: A 374 GLU cc_start: 0.7946 (pm20) cc_final: 0.7357 (pm20) REVERT: A 641 LYS cc_start: 0.8446 (ttmt) cc_final: 0.7852 (mttp) REVERT: A 736 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: A 828 GLU cc_start: 0.8641 (mp0) cc_final: 0.8360 (mp0) REVERT: A 869 MET cc_start: 0.7613 (mmp) cc_final: 0.6912 (mmp) REVERT: B 13 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8482 (pp30) REVERT: B 45 MET cc_start: 0.7650 (mtm) cc_final: 0.7337 (mtm) REVERT: B 297 TRP cc_start: 0.8770 (m100) cc_final: 0.8289 (m100) REVERT: B 325 MET cc_start: 0.7350 (mmp) cc_final: 0.6738 (mtp) REVERT: C 13 GLN cc_start: 0.8758 (tt0) cc_final: 0.8439 (pt0) REVERT: C 17 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7952 (mt0) REVERT: C 49 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7513 (mpt-90) REVERT: C 82 TRP cc_start: 0.8722 (m100) cc_final: 0.8226 (m-10) REVERT: C 188 MET cc_start: 0.8433 (mmm) cc_final: 0.8071 (mmt) REVERT: C 220 GLN cc_start: 0.7540 (mp10) cc_final: 0.7187 (mp10) REVERT: C 259 GLN cc_start: 0.7266 (tt0) cc_final: 0.6840 (tm-30) REVERT: C 318 LEU cc_start: 0.8998 (tt) cc_final: 0.8749 (tt) REVERT: C 331 SER cc_start: 0.8830 (m) cc_final: 0.8462 (t) REVERT: D 14 LYS cc_start: 0.8459 (tmtt) cc_final: 0.8006 (ttmt) REVERT: D 44 HIS cc_start: 0.7613 (m90) cc_final: 0.7151 (m90) outliers start: 46 outliers final: 38 residues processed: 225 average time/residue: 0.2530 time to fit residues: 81.6139 Evaluate side-chains 228 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 736 GLN Chi-restraints excluded: chain A residue 757 ASP Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 chunk 126 optimal weight: 0.0050 chunk 87 optimal weight: 0.0770 overall best weight: 0.5754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11939 Z= 0.155 Angle : 0.538 12.587 16178 Z= 0.271 Chirality : 0.043 0.230 1826 Planarity : 0.004 0.059 2098 Dihedral : 4.268 28.686 1630 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.08 % Allowed : 23.99 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.21), residues: 1486 helix: -0.85 (0.29), residues: 327 sheet: -2.19 (0.27), residues: 339 loop : -1.35 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS B 54 PHE 0.014 0.001 PHE B 199 TYR 0.013 0.001 TYR G 40 ARG 0.007 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7763 (p0) cc_final: 0.7465 (p0) REVERT: A 76 ARG cc_start: 0.8416 (ptt90) cc_final: 0.7839 (ptt90) REVERT: A 100 GLU cc_start: 0.7193 (pt0) cc_final: 0.6635 (pm20) REVERT: A 173 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7746 (tppt) REVERT: A 252 GLN cc_start: 0.8087 (mt0) cc_final: 0.7694 (mt0) REVERT: A 273 ARG cc_start: 0.7155 (ttm110) cc_final: 0.6778 (ttm110) REVERT: A 290 GLN cc_start: 0.7181 (mt0) cc_final: 0.6649 (mt0) REVERT: A 374 GLU cc_start: 0.7884 (pm20) cc_final: 0.7308 (pm20) REVERT: A 641 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8179 (ttmm) REVERT: A 828 GLU cc_start: 0.8594 (mp0) cc_final: 0.8336 (mp0) REVERT: A 869 MET cc_start: 0.7637 (mmp) cc_final: 0.6996 (mmp) REVERT: B 13 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8505 (pp30) REVERT: B 297 TRP cc_start: 0.8765 (m100) cc_final: 0.8264 (m100) REVERT: B 325 MET cc_start: 0.7281 (mmp) cc_final: 0.6673 (mtp) REVERT: C 13 GLN cc_start: 0.8776 (tt0) cc_final: 0.8549 (pt0) REVERT: C 82 TRP cc_start: 0.8709 (m100) cc_final: 0.8194 (m-10) REVERT: C 220 GLN cc_start: 0.7563 (mp10) cc_final: 0.7172 (mp10) REVERT: C 259 GLN cc_start: 0.7227 (tt0) cc_final: 0.6517 (tm-30) REVERT: C 318 LEU cc_start: 0.8932 (tt) cc_final: 0.8704 (tt) REVERT: C 331 SER cc_start: 0.8773 (m) cc_final: 0.8400 (t) REVERT: D 14 LYS cc_start: 0.8443 (tmtt) cc_final: 0.8028 (ttmt) REVERT: D 44 HIS cc_start: 0.7709 (m90) cc_final: 0.7103 (m90) outliers start: 39 outliers final: 35 residues processed: 222 average time/residue: 0.2545 time to fit residues: 81.3135 Evaluate side-chains 219 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 640 ASN A 871 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11939 Z= 0.361 Angle : 0.629 11.019 16178 Z= 0.318 Chirality : 0.047 0.263 1826 Planarity : 0.004 0.061 2098 Dihedral : 4.690 26.200 1630 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.63 % Allowed : 24.07 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.21), residues: 1486 helix: -0.89 (0.29), residues: 326 sheet: -2.42 (0.24), residues: 386 loop : -1.40 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.005 0.001 HIS A 808 PHE 0.018 0.002 PHE B 199 TYR 0.017 0.002 TYR A 692 ARG 0.006 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 1.350 Fit side-chains REVERT: A 46 ASP cc_start: 0.7996 (p0) cc_final: 0.7679 (p0) REVERT: A 60 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7359 (mp0) REVERT: A 76 ARG cc_start: 0.8477 (ptt90) cc_final: 0.7962 (ptt90) REVERT: A 173 LYS cc_start: 0.8213 (ttpt) cc_final: 0.7821 (tppt) REVERT: A 252 GLN cc_start: 0.8135 (mt0) cc_final: 0.7705 (mt0) REVERT: A 273 ARG cc_start: 0.7172 (ttm110) cc_final: 0.6788 (ttm110) REVERT: A 290 GLN cc_start: 0.7245 (mt0) cc_final: 0.6813 (mt0) REVERT: A 374 GLU cc_start: 0.8066 (pm20) cc_final: 0.7427 (pm20) REVERT: A 641 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8244 (ttmm) REVERT: A 828 GLU cc_start: 0.8599 (mp0) cc_final: 0.8307 (mp0) REVERT: A 869 MET cc_start: 0.7594 (mmp) cc_final: 0.6937 (mmp) REVERT: A 871 GLN cc_start: 0.8010 (tp40) cc_final: 0.7748 (tt0) REVERT: A 874 ARG cc_start: 0.8480 (ptp-170) cc_final: 0.7802 (ptp-170) REVERT: B 45 MET cc_start: 0.7732 (mtm) cc_final: 0.7344 (mtm) REVERT: B 46 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7451 (mtt90) REVERT: B 325 MET cc_start: 0.7310 (mmp) cc_final: 0.6641 (mtp) REVERT: C 13 GLN cc_start: 0.8765 (tt0) cc_final: 0.8462 (pt0) REVERT: C 17 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7917 (mt0) REVERT: C 66 ASP cc_start: 0.7556 (p0) cc_final: 0.7102 (p0) REVERT: C 82 TRP cc_start: 0.8765 (m100) cc_final: 0.8208 (m-10) REVERT: C 220 GLN cc_start: 0.7656 (mp10) cc_final: 0.7384 (mp10) REVERT: C 318 LEU cc_start: 0.8971 (tt) cc_final: 0.8655 (tt) REVERT: C 331 SER cc_start: 0.8945 (m) cc_final: 0.8556 (t) REVERT: D 44 HIS cc_start: 0.7578 (m90) cc_final: 0.7263 (m90) outliers start: 46 outliers final: 41 residues processed: 225 average time/residue: 0.2370 time to fit residues: 76.5444 Evaluate side-chains 228 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 757 ASP Chi-restraints excluded: chain A residue 764 THR Chi-restraints excluded: chain A residue 824 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 6.9990 chunk 36 optimal weight: 0.0170 chunk 108 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.143778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108916 restraints weight = 17101.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.113015 restraints weight = 9207.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115704 restraints weight = 6229.889| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11939 Z= 0.213 Angle : 0.574 11.694 16178 Z= 0.288 Chirality : 0.044 0.225 1826 Planarity : 0.004 0.058 2098 Dihedral : 4.487 29.457 1630 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.31 % Allowed : 24.55 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.21), residues: 1486 helix: -0.74 (0.29), residues: 329 sheet: -2.23 (0.26), residues: 358 loop : -1.32 (0.21), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.004 0.001 HIS B 54 PHE 0.019 0.001 PHE C 222 TYR 0.013 0.001 TYR G 40 ARG 0.006 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.52 seconds wall clock time: 47 minutes 42.57 seconds (2862.57 seconds total)