Starting phenix.real_space_refine on Fri Nov 15 20:57:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/11_2024/8iw9_35764_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/11_2024/8iw9_35764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/11_2024/8iw9_35764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/11_2024/8iw9_35764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/11_2024/8iw9_35764_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iw9_35764/11_2024/8iw9_35764_neut.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6192 2.51 5 N 1663 2.21 5 O 1780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9693 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1843 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ARG:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2488 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 5, 'PHE:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 90 Chain: "C" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 363 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2328 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 12, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 164 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "S" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1741 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "N" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 930 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Time building chain proxies: 5.68, per 1000 atoms: 0.59 Number of scatterers: 9693 At special positions: 0 Unit cell: (106.92, 110.16, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1780 8.00 N 1663 7.00 C 6192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 186 " distance=2.02 Simple disulfide: pdb=" SG CYS R 125 " - pdb=" SG CYS R 152 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 16 sheets defined 33.9% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.869A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.521A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.506A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.674A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.969A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.155A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.523A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 12 through 24 removed outlier: 4.118A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 removed outlier: 3.594A pdb=" N ASP C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 48' Processing helix chain 'R' and resid 33 through 61 removed outlier: 3.520A pdb=" N ALA R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS R 61 " --> pdb=" O ILE R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 removed outlier: 3.858A pdb=" N VAL R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR R 84 " --> pdb=" O LEU R 80 " (cutoff:3.500A) Proline residue: R 87 - end of helix Processing helix chain 'R' and resid 102 through 136 removed outlier: 4.424A pdb=" N LYS R 106 " --> pdb=" O GLU R 102 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N PHE R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS R 116 " --> pdb=" O ASP R 112 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE R 117 " --> pdb=" O THR R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 168 removed outlier: 3.611A pdb=" N CYS R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE R 153 " --> pdb=" O SER R 149 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP R 157 " --> pdb=" O ILE R 153 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 175 removed outlier: 3.682A pdb=" N GLU R 174 " --> pdb=" O GLY R 171 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU R 175 " --> pdb=" O ALA R 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 171 through 175' Processing helix chain 'R' and resid 198 through 232 Proline residue: R 209 - end of helix Processing helix chain 'R' and resid 247 through 284 removed outlier: 3.960A pdb=" N LYS R 251 " --> pdb=" O GLU R 247 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG R 252 " --> pdb=" O ARG R 248 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS R 255 " --> pdb=" O LYS R 251 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA R 256 " --> pdb=" O ARG R 252 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE R 267 " --> pdb=" O ALA R 263 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 289 through 312 removed outlier: 3.675A pdb=" N TYR R 293 " --> pdb=" O PRO R 289 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE R 295 " --> pdb=" O TYR R 291 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER R 304 " --> pdb=" O VAL R 300 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 328 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.217A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.830A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.007A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.541A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.988A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.620A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.911A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.892A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.692A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.991A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.661A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.086A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.513A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.907A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.907A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.316A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 3 through 5 Processing sheet with id=AB6, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB7, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.353A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1272 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: 2.74 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3126 1.34 - 1.46: 2490 1.46 - 1.58: 4219 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 9915 Sorted by residual: bond pdb=" CA ASP B 186 " pdb=" C ASP B 186 " ideal model delta sigma weight residual 1.524 1.504 0.020 1.30e-02 5.92e+03 2.27e+00 bond pdb=" CB GLU R 247 " pdb=" CG GLU R 247 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.17e+00 bond pdb=" CA LEU C 37 " pdb=" C LEU C 37 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.24e-02 6.50e+03 1.92e+00 bond pdb=" N LEU R 184 " pdb=" CA LEU R 184 " ideal model delta sigma weight residual 1.458 1.481 -0.022 1.77e-02 3.19e+03 1.60e+00 bond pdb=" N GLU A 309 " pdb=" CA GLU A 309 " ideal model delta sigma weight residual 1.459 1.475 -0.016 1.28e-02 6.10e+03 1.57e+00 ... (remaining 9910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 13055 1.60 - 3.19: 355 3.19 - 4.79: 63 4.79 - 6.39: 23 6.39 - 7.98: 6 Bond angle restraints: 13502 Sorted by residual: angle pdb=" N VAL R 187 " pdb=" CA VAL R 187 " pdb=" C VAL R 187 " ideal model delta sigma weight residual 110.62 116.80 -6.18 1.02e+00 9.61e-01 3.67e+01 angle pdb=" N THR B 165 " pdb=" CA THR B 165 " pdb=" C THR B 165 " ideal model delta sigma weight residual 110.50 118.48 -7.98 1.41e+00 5.03e-01 3.21e+01 angle pdb=" N CYS B 233 " pdb=" CA CYS B 233 " pdb=" C CYS B 233 " ideal model delta sigma weight residual 112.59 119.46 -6.87 1.22e+00 6.72e-01 3.18e+01 angle pdb=" N ASN A 218 " pdb=" CA ASN A 218 " pdb=" C ASN A 218 " ideal model delta sigma weight residual 109.95 117.74 -7.79 1.59e+00 3.96e-01 2.40e+01 angle pdb=" N THR R 67 " pdb=" CA THR R 67 " pdb=" C THR R 67 " ideal model delta sigma weight residual 113.41 107.75 5.66 1.22e+00 6.72e-01 2.15e+01 ... (remaining 13497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 5151 17.12 - 34.25: 466 34.25 - 51.37: 143 51.37 - 68.49: 17 68.49 - 85.62: 9 Dihedral angle restraints: 5786 sinusoidal: 2037 harmonic: 3749 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -5.19 -80.81 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.07 34.93 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CB CYS R 22 " pdb=" SG CYS R 22 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual -86.00 -120.23 34.23 1 1.00e+01 1.00e-02 1.66e+01 ... (remaining 5783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1377 0.071 - 0.142: 158 0.142 - 0.213: 10 0.213 - 0.284: 2 0.284 - 0.354: 1 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CA LEU R 184 " pdb=" N LEU R 184 " pdb=" C LEU R 184 " pdb=" CB LEU R 184 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA CYS B 233 " pdb=" N CYS B 233 " pdb=" C CYS B 233 " pdb=" CB CYS B 233 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ARG R 332 " pdb=" N ARG R 332 " pdb=" C ARG R 332 " pdb=" CB ARG R 332 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1545 not shown) Planarity restraints: 1717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 217 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C VAL A 217 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL A 217 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN A 218 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 162 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.22e+00 pdb=" C GLY B 162 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY B 162 " 0.013 2.00e-02 2.50e+03 pdb=" N ASP B 163 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 81 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C VAL R 81 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL R 81 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY R 82 " 0.010 2.00e-02 2.50e+03 ... (remaining 1714 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 339 2.71 - 3.26: 9499 3.26 - 3.81: 15014 3.81 - 4.35: 17960 4.35 - 4.90: 32261 Nonbonded interactions: 75073 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.168 3.040 nonbonded pdb=" O SER R 26 " pdb=" OG SER R 96 " model vdw 2.169 3.040 nonbonded pdb=" N GLU C 58 " pdb=" OE1 GLU C 58 " model vdw 2.205 3.120 nonbonded pdb=" OD2 ASP R 112 " pdb=" OH TYR R 301 " model vdw 2.219 3.040 nonbonded pdb=" N GLU B 130 " pdb=" OE1 GLU B 130 " model vdw 2.249 3.120 ... (remaining 75068 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.240 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 : 0.003 0.044 9915 Z= 0.218 Angle : 0.663 7.984 13502 Z= 0.407 Chirality : 0.046 0.354 1548 Planarity : 0.004 0.042 1717 Dihedral : 14.652 85.618 3359 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.61 % Allowed : 17.73 % Favored : 81.66 % Cbeta Deviations : 0.08 % 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: 0.21 (0.24), residues: 1273 helix: 1.52 (0.28), residues: 388 sheet: 0.47 (0.29), residues: 317 loop : -1.03 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 PHE 0.009 0.001 PHE R 60 TYR 0.026 0.001 TYR S 235 ARG 0.012 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 229 ARG cc_start: 0.8124 (tpp80) cc_final: 0.7895 (tpp80) REVERT: N 77 ASN cc_start: 0.9105 (m-40) cc_final: 0.8871 (m-40) outliers start: 6 outliers final: 6 residues processed: 127 average time/residue: 0.2380 time to fit residues: 42.2048 Evaluate side-chains 119 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain R residue 186 CYS Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain S residue 48 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 119 ASN C 11 GLN ** R 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9915 Z= 0.273 Angle : 0.570 6.404 13502 Z= 0.310 Chirality : 0.043 0.225 1548 Planarity : 0.004 0.035 1717 Dihedral : 4.522 40.416 1406 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.77 % Allowed : 15.57 % Favored : 81.66 % 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: 0.67 (0.24), residues: 1273 helix: 2.09 (0.27), residues: 401 sheet: 0.71 (0.30), residues: 304 loop : -0.94 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.020 0.001 PHE R 60 TYR 0.028 0.001 TYR S 235 ARG 0.006 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 50 ASN cc_start: 0.8413 (m-40) cc_final: 0.8122 (m-40) REVERT: R 78 ASP cc_start: 0.7575 (t70) cc_final: 0.7232 (t70) REVERT: S 76 LYS cc_start: 0.9425 (mtpp) cc_final: 0.9178 (mtmm) outliers start: 27 outliers final: 14 residues processed: 137 average time/residue: 0.2334 time to fit residues: 44.4004 Evaluate side-chains 123 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 323 LYS Chi-restraints excluded: chain R residue 338 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 32 GLN B 340 ASN C 11 GLN ** R 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9915 Z= 0.262 Angle : 0.548 6.584 13502 Z= 0.296 Chirality : 0.043 0.230 1548 Planarity : 0.003 0.033 1717 Dihedral : 4.459 39.498 1404 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.97 % Allowed : 15.57 % Favored : 81.45 % 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: 0.84 (0.24), residues: 1273 helix: 2.39 (0.26), residues: 402 sheet: 0.71 (0.30), residues: 300 loop : -0.91 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE R 60 TYR 0.030 0.001 TYR S 235 ARG 0.006 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8511 (mm-40) REVERT: R 50 ASN cc_start: 0.8430 (m-40) cc_final: 0.8128 (m-40) REVERT: R 78 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7585 (t70) REVERT: R 229 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.7956 (tpp80) REVERT: S 76 LYS cc_start: 0.9454 (mtpp) cc_final: 0.9236 (mtmm) REVERT: S 81 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8179 (pt) REVERT: S 220 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8471 (mp0) outliers start: 29 outliers final: 20 residues processed: 141 average time/residue: 0.2260 time to fit residues: 44.5351 Evaluate side-chains 133 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 277 ASP Chi-restraints excluded: chain R residue 292 VAL Chi-restraints excluded: chain R residue 338 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 220 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 60 optimal weight: 0.0670 chunk 109 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 88 ASN B 340 ASN C 11 GLN R 196 GLN ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9915 Z= 0.169 Angle : 0.514 7.150 13502 Z= 0.276 Chirality : 0.041 0.204 1548 Planarity : 0.003 0.036 1717 Dihedral : 4.280 39.066 1404 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.87 % Allowed : 16.50 % Favored : 80.64 % 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: 1.00 (0.24), residues: 1273 helix: 2.59 (0.26), residues: 402 sheet: 0.77 (0.30), residues: 300 loop : -0.85 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 298 HIS 0.003 0.001 HIS A 357 PHE 0.011 0.001 PHE A 212 TYR 0.025 0.001 TYR S 235 ARG 0.005 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8781 (ptp-170) cc_final: 0.8561 (ptp90) REVERT: B 175 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8475 (mm-40) REVERT: R 50 ASN cc_start: 0.8401 (m-40) cc_final: 0.8111 (m-40) REVERT: R 78 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7588 (t70) REVERT: R 196 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7100 (tp40) REVERT: R 225 LYS cc_start: 0.8954 (ttmm) cc_final: 0.8642 (ttmm) REVERT: R 229 ARG cc_start: 0.8245 (ttm-80) cc_final: 0.7937 (tpp80) outliers start: 28 outliers final: 19 residues processed: 139 average time/residue: 0.2412 time to fit residues: 46.3897 Evaluate side-chains 129 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 196 GLN Chi-restraints excluded: chain R residue 258 LYS Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 277 ASP Chi-restraints excluded: chain R residue 338 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 220 GLU Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.3980 chunk 69 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.2980 chunk 109 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 32 GLN B 220 GLN B 340 ASN C 11 GLN R 196 GLN ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9915 Z= 0.140 Angle : 0.500 6.346 13502 Z= 0.267 Chirality : 0.041 0.186 1548 Planarity : 0.003 0.038 1717 Dihedral : 4.080 38.463 1403 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.28 % Allowed : 16.60 % Favored : 80.12 % 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: 1.09 (0.24), residues: 1273 helix: 2.66 (0.26), residues: 402 sheet: 0.81 (0.30), residues: 304 loop : -0.79 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 298 HIS 0.002 0.000 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.021 0.001 TYR S 235 ARG 0.006 0.000 ARG R 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8758 (ptp-170) cc_final: 0.8551 (ptp90) REVERT: B 59 TYR cc_start: 0.9443 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: B 175 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8451 (mm-40) REVERT: B 259 GLN cc_start: 0.8843 (pt0) cc_final: 0.8408 (pt0) REVERT: R 50 ASN cc_start: 0.8371 (m-40) cc_final: 0.8065 (m-40) REVERT: R 78 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7527 (t70) REVERT: R 225 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8628 (ttmm) REVERT: R 229 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7833 (tpp80) REVERT: S 76 LYS cc_start: 0.9481 (mtpp) cc_final: 0.9267 (mtmm) REVERT: N 38 ARG cc_start: 0.9150 (ptt180) cc_final: 0.8726 (ptt180) outliers start: 32 outliers final: 18 residues processed: 145 average time/residue: 0.2295 time to fit residues: 46.2334 Evaluate side-chains 129 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 258 LYS Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 338 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 220 GLN B 340 ASN C 11 GLN R 191 GLN ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9915 Z= 0.297 Angle : 0.561 6.856 13502 Z= 0.304 Chirality : 0.043 0.236 1548 Planarity : 0.003 0.041 1717 Dihedral : 4.334 37.562 1403 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.38 % Allowed : 15.88 % Favored : 80.74 % 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: 1.00 (0.24), residues: 1273 helix: 2.61 (0.26), residues: 401 sheet: 0.72 (0.30), residues: 302 loop : -0.83 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE R 60 TYR 0.031 0.001 TYR S 235 ARG 0.005 0.000 ARG R 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.8787 (ptp-170) cc_final: 0.8558 (ptp90) REVERT: B 59 TYR cc_start: 0.9482 (OUTLIER) cc_final: 0.8788 (m-80) REVERT: B 175 GLN cc_start: 0.8813 (mm-40) cc_final: 0.8523 (mm-40) REVERT: R 50 ASN cc_start: 0.8465 (m-40) cc_final: 0.8190 (m-40) REVERT: R 78 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7600 (t70) REVERT: R 225 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8560 (ttmm) REVERT: S 76 LYS cc_start: 0.9493 (mtpp) cc_final: 0.9291 (mtmm) REVERT: S 81 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8179 (pt) REVERT: N 106 ASP cc_start: 0.7568 (p0) cc_final: 0.7361 (p0) outliers start: 33 outliers final: 24 residues processed: 137 average time/residue: 0.2290 time to fit residues: 44.0982 Evaluate side-chains 134 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 277 ASP Chi-restraints excluded: chain R residue 284 MET Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 338 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN C 11 GLN ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9915 Z= 0.330 Angle : 0.583 7.684 13502 Z= 0.315 Chirality : 0.043 0.230 1548 Planarity : 0.004 0.042 1717 Dihedral : 4.459 37.440 1402 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.48 % Allowed : 16.91 % Favored : 79.61 % 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: 0.91 (0.24), residues: 1273 helix: 2.53 (0.26), residues: 401 sheet: 0.64 (0.30), residues: 308 loop : -0.88 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 36 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE R 60 TYR 0.028 0.001 TYR S 235 ARG 0.005 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.9488 (OUTLIER) cc_final: 0.8803 (m-80) REVERT: R 50 ASN cc_start: 0.8399 (m-40) cc_final: 0.8119 (m-40) REVERT: R 78 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7720 (t70) REVERT: R 225 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8639 (ttmm) REVERT: S 76 LYS cc_start: 0.9495 (mtpp) cc_final: 0.9290 (mtmm) REVERT: S 81 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8211 (pt) outliers start: 34 outliers final: 24 residues processed: 138 average time/residue: 0.2400 time to fit residues: 46.1000 Evaluate side-chains 136 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 277 ASP Chi-restraints excluded: chain R residue 338 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 chunk 82 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN C 11 GLN ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9915 Z= 0.165 Angle : 0.537 7.612 13502 Z= 0.288 Chirality : 0.041 0.184 1548 Planarity : 0.003 0.040 1717 Dihedral : 4.235 37.534 1402 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.87 % Allowed : 17.42 % Favored : 79.71 % 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: 1.05 (0.24), residues: 1273 helix: 2.68 (0.26), residues: 401 sheet: 0.75 (0.30), residues: 307 loop : -0.83 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 298 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.020 0.001 TYR S 235 ARG 0.006 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.9470 (OUTLIER) cc_final: 0.8702 (m-80) REVERT: C 62 ARG cc_start: 0.8205 (ptp90) cc_final: 0.7670 (ptp90) REVERT: R 50 ASN cc_start: 0.8350 (m-40) cc_final: 0.8074 (m-40) REVERT: R 78 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7632 (t70) REVERT: R 225 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8686 (ttmm) outliers start: 28 outliers final: 22 residues processed: 139 average time/residue: 0.2301 time to fit residues: 45.3993 Evaluate side-chains 136 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 267 PHE Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 338 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 220 GLN B 340 ASN C 11 GLN ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9915 Z= 0.248 Angle : 0.562 7.188 13502 Z= 0.302 Chirality : 0.042 0.202 1548 Planarity : 0.003 0.039 1717 Dihedral : 4.276 37.022 1402 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.77 % Allowed : 17.62 % Favored : 79.61 % 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: 1.03 (0.24), residues: 1273 helix: 2.65 (0.26), residues: 401 sheet: 0.72 (0.31), residues: 303 loop : -0.81 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE R 60 TYR 0.024 0.001 TYR S 235 ARG 0.006 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.9480 (OUTLIER) cc_final: 0.8749 (m-80) REVERT: C 62 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7689 (ptp90) REVERT: R 50 ASN cc_start: 0.8400 (m-40) cc_final: 0.8143 (m-40) REVERT: R 78 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7645 (t70) REVERT: R 225 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8658 (ttmm) REVERT: S 73 ASP cc_start: 0.8401 (t0) cc_final: 0.7723 (t0) REVERT: S 76 LYS cc_start: 0.9443 (mtmm) cc_final: 0.9131 (mtmm) REVERT: S 81 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8178 (pt) outliers start: 27 outliers final: 24 residues processed: 134 average time/residue: 0.2224 time to fit residues: 42.0422 Evaluate side-chains 140 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 11 GLN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 267 PHE Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 338 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 30.0000 chunk 61 optimal weight: 40.0000 chunk 79 optimal weight: 0.9980 chunk 106 optimal weight: 0.0050 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN C 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9915 Z= 0.154 Angle : 0.534 7.386 13502 Z= 0.285 Chirality : 0.041 0.187 1548 Planarity : 0.003 0.039 1717 Dihedral : 4.131 37.233 1402 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.77 % Allowed : 17.52 % Favored : 79.71 % 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: 1.15 (0.24), residues: 1273 helix: 2.76 (0.26), residues: 400 sheet: 0.79 (0.31), residues: 306 loop : -0.76 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 298 HIS 0.003 0.000 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.018 0.001 TYR S 235 ARG 0.006 0.000 ARG S 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2546 Ramachandran restraints generated. 1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.9464 (OUTLIER) cc_final: 0.8699 (m-80) REVERT: B 220 GLN cc_start: 0.8713 (mt0) cc_final: 0.8511 (mt0) REVERT: C 62 ARG cc_start: 0.8256 (ptp90) cc_final: 0.7736 (ptp90) REVERT: R 50 ASN cc_start: 0.8271 (m-40) cc_final: 0.7956 (m-40) REVERT: R 78 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7599 (t70) REVERT: R 225 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8679 (ttmm) REVERT: S 73 ASP cc_start: 0.8418 (t0) cc_final: 0.7661 (t0) REVERT: S 76 LYS cc_start: 0.9451 (mtmm) cc_final: 0.9208 (mtmm) REVERT: N 38 ARG cc_start: 0.9148 (ptt180) cc_final: 0.8899 (ptt180) REVERT: N 106 ASP cc_start: 0.8029 (p0) cc_final: 0.7745 (p0) outliers start: 27 outliers final: 24 residues processed: 142 average time/residue: 0.2328 time to fit residues: 46.1162 Evaluate side-chains 142 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 11 GLN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 99 TYR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 258 LYS Chi-restraints excluded: chain R residue 267 PHE Chi-restraints excluded: chain R residue 269 VAL Chi-restraints excluded: chain R residue 302 TYR Chi-restraints excluded: chain R residue 338 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 102 optimal weight: 0.0010 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 0.0040 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN C 11 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.057074 restraints weight = 22211.975| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.67 r_work: 0.2606 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2483 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9915 Z= 0.174 Angle : 0.531 7.254 13502 Z= 0.285 Chirality : 0.041 0.175 1548 Planarity : 0.003 0.039 1717 Dihedral : 4.082 37.031 1402 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.66 % Allowed : 17.93 % Favored : 79.41 % 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: 1.16 (0.24), residues: 1273 helix: 2.76 (0.26), residues: 401 sheet: 0.77 (0.30), residues: 306 loop : -0.73 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE A 212 TYR 0.020 0.001 TYR S 235 ARG 0.006 0.000 ARG S 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2268.43 seconds wall clock time: 42 minutes 8.86 seconds (2528.86 seconds total)