Starting phenix.real_space_refine on Thu Dec 26 13:37:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stb_25423/12_2024/7stb_25423_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stb_25423/12_2024/7stb_25423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7stb_25423/12_2024/7stb_25423.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stb_25423/12_2024/7stb_25423.map" model { file = "/net/cci-nas-00/data/ceres_data/7stb_25423/12_2024/7stb_25423_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stb_25423/12_2024/7stb_25423_trim.cif" } resolution = 2.72 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= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 49 5.49 5 Mg 4 5.21 5 S 119 5.16 5 C 14313 2.51 5 N 3904 2.21 5 O 4425 1.98 5 H 22555 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 45369 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 8378 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 19, 'TRANS': 495} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5027 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 5196 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5304 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Chain: "E" Number of atoms: 5525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 5525 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 4539 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 3, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 5428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5428 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4710 Classifications: {'peptide': 293} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain breaks: 6 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 804 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "I" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 303 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.10, per 1000 atoms: 0.47 Number of scatterers: 45369 At special positions: 0 Unit cell: (128.856, 122.248, 145.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 119 16.00 P 49 15.00 Mg 4 11.99 O 4425 8.00 N 3904 7.00 C 14313 6.00 H 22555 1.00 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: 13.12 Conformation dependent library (CDL) restraints added in 4.6 seconds 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5266 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 16 sheets defined 54.6% alpha, 17.3% beta 7 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 22.47 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.572A pdb=" N VAL A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.610A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 175 through 176 No H-bonds generated for 'chain 'A' and resid 175 through 176' Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 296 through 306 removed outlier: 3.757A pdb=" N VAL A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 367 through 373 removed outlier: 3.786A pdb=" N LYS A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.990A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 408 removed outlier: 3.678A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.603A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 472 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 483 through 509 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 566 through 590 Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 removed outlier: 4.132A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 134 removed outlier: 3.704A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.642A pdb=" N LEU B 191 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 301 Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.660A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 removed outlier: 3.687A pdb=" N ASN C 12 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 58 through 71 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 89 through 102 removed outlier: 3.967A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 123 through 137 removed outlier: 4.109A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.686A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.610A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 270 removed outlier: 4.069A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 292 through 313 removed outlier: 3.908A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 42 through 52 removed outlier: 4.499A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 70 through 91 removed outlier: 3.602A pdb=" N THR D 74 " --> pdb=" O GLY D 70 " (cutoff:3.500A) Proline residue: D 85 - end of helix removed outlier: 4.085A pdb=" N LYS D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.859A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.561A pdb=" N LEU D 126 " --> pdb=" O SER D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.622A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 209 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.678A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 292 Processing helix chain 'D' and resid 296 through 311 Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.595A pdb=" N TRP D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.516A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.331A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 97 through 103 removed outlier: 6.890A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.904A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.559A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR E 161 " --> pdb=" O THR E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 292 removed outlier: 3.650A pdb=" N ALA E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 308 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 338 through 354 Processing helix chain 'F' and resid 17 through 26 removed outlier: 3.606A pdb=" N ILE F 21 " --> pdb=" O HIS F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 Proline residue: F 30 - end of helix No H-bonds generated for 'chain 'F' and resid 27 through 32' Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 88 through 93 removed outlier: 3.570A pdb=" N VAL F 93 " --> pdb=" O ILE F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 removed outlier: 4.304A pdb=" N LEU F 145 " --> pdb=" O THR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 173 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 245 through 251 removed outlier: 3.823A pdb=" N ILE F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 328 Processing helix chain 'G' and resid 9 through 27 Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 98 through 106 Processing helix chain 'G' and resid 127 through 131 Processing helix chain 'G' and resid 161 through 174 Processing helix chain 'G' and resid 188 through 205 Processing helix chain 'G' and resid 234 through 244 removed outlier: 3.755A pdb=" N ASN G 243 " --> pdb=" O ASN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 333 Processing helix chain 'G' and resid 334 through 339 Proline residue: G 337 - end of helix No H-bonds generated for 'chain 'G' and resid 334 through 339' Processing helix chain 'H' and resid 12 through 28 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 97 through 115 removed outlier: 3.939A pdb=" N SER H 115 " --> pdb=" O MET H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 220 removed outlier: 3.711A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 252 Processing helix chain 'H' and resid 253 through 256 removed outlier: 3.972A pdb=" N TYR H 256 " --> pdb=" O VAL H 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 253 through 256' Processing helix chain 'H' and resid 412 through 423 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.247A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 78 removed outlier: 3.540A pdb=" N LEU B 113 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N TYR B 163 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER B 48 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.145A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU C 50 " --> pdb=" O PHE C 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 189 removed outlier: 6.997A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.172A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.695A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU E 85 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.475A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 69 through 72 removed outlier: 3.660A pdb=" N SER F 127 " --> pdb=" O CYS H 295 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS H 291 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU H 281 " --> pdb=" O TRP H 296 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N ASN H 286 " --> pdb=" O HIS H 261 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N HIS H 261 " --> pdb=" O ASN H 286 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS H 406 " --> pdb=" O GLY H 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 79 through 85 removed outlier: 5.948A pdb=" N ASP F 36 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU F 51 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 305 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS F 216 " --> pdb=" O ILE F 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 232 through 238 removed outlier: 3.634A pdb=" N GLU F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU G 63 " --> pdb=" O THR G 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 78 through 82 removed outlier: 4.304A pdb=" N SER G 93 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 78 through 82 removed outlier: 7.222A pdb=" N ASP G 29 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N MET G 44 " --> pdb=" O ASP G 29 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLN G 365 " --> pdb=" O ASN G 348 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN G 348 " --> pdb=" O GLN G 365 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 320 through 325 removed outlier: 3.623A pdb=" N SER G 283 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS H 206 " --> pdb=" O SER G 283 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS H 122 " --> pdb=" O GLY H 157 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 123 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU H 3 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU H 79 " --> pdb=" O ILE H 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 320 through 325 removed outlier: 3.623A pdb=" N SER G 283 " --> pdb=" O LYS H 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS H 206 " --> pdb=" O SER G 283 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN H 96 " --> pdb=" O PRO H 208 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY H 462 " --> pdb=" O LEU H 444 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER H 443 " --> pdb=" O GLU H 427 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU H 427 " --> pdb=" O SER H 443 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 270 through 271 removed outlier: 6.363A pdb=" N VAL G 270 " --> pdb=" O LEU G 278 " (cutoff:3.500A) 1282 hydrogen bonds defined for protein. 3663 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 21.56 Time building geometry restraints manager: 15.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 22500 1.06 - 1.28: 3801 1.28 - 1.50: 9706 1.50 - 1.73: 9639 1.73 - 1.95: 179 Bond restraints: 45825 Sorted by residual: bond pdb=" CB PRO E 63 " pdb=" CG PRO E 63 " ideal model delta sigma weight residual 1.492 1.650 -0.158 5.00e-02 4.00e+02 9.98e+00 bond pdb=" CG PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 1.503 1.403 0.100 3.40e-02 8.65e+02 8.73e+00 bond pdb=" N PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 1.473 1.500 -0.027 1.40e-02 5.10e+03 3.77e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N MET G 1 " pdb=" H MET G 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 45820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 82903 3.01 - 6.03: 83 6.03 - 9.04: 2 9.04 - 12.05: 1 12.05 - 15.06: 1 Bond angle restraints: 82990 Sorted by residual: angle pdb=" CA PRO E 63 " pdb=" N PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 112.00 96.94 15.06 1.40e+00 5.10e-01 1.16e+02 angle pdb=" N PRO E 63 " pdb=" CD PRO E 63 " pdb=" CG PRO E 63 " ideal model delta sigma weight residual 103.20 94.36 8.84 1.50e+00 4.44e-01 3.48e+01 angle pdb=" CA PRO E 63 " pdb=" CB PRO E 63 " pdb=" CG PRO E 63 " ideal model delta sigma weight residual 104.50 98.74 5.76 1.90e+00 2.77e-01 9.18e+00 angle pdb=" O3' DA I 0 " pdb=" P DC I 1 " pdb=" O5' DC I 1 " ideal model delta sigma weight residual 104.00 99.72 4.28 1.50e+00 4.44e-01 8.12e+00 angle pdb=" C GLY E 62 " pdb=" N PRO E 63 " pdb=" CD PRO E 63 " ideal model delta sigma weight residual 125.00 136.68 -11.68 4.10e+00 5.95e-02 8.12e+00 ... (remaining 82985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 20561 31.32 - 62.63: 642 62.63 - 93.95: 29 93.95 - 125.26: 2 125.26 - 156.58: 3 Dihedral angle restraints: 21237 sinusoidal: 11945 harmonic: 9292 Sorted by residual: dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.41 120.59 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" O1A AGS D 402 " pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sinusoidal sigma weight residual -67.73 77.93 -145.66 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" O1A AGS C 402 " pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sinusoidal sigma weight residual -67.73 74.68 -142.41 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 21234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2542 0.032 - 0.063: 708 0.063 - 0.095: 225 0.095 - 0.126: 151 0.126 - 0.158: 18 Chirality restraints: 3644 Sorted by residual: chirality pdb=" CA ILE F 41 " pdb=" N ILE F 41 " pdb=" C ILE F 41 " pdb=" CB ILE F 41 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA PRO E 63 " pdb=" N PRO E 63 " pdb=" C PRO E 63 " pdb=" CB PRO E 63 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE F 269 " pdb=" N ILE F 269 " pdb=" C ILE F 269 " pdb=" CB ILE F 269 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 3641 not shown) Planarity restraints: 6533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 62 " 0.054 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO E 63 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 63 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 63 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 32 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO D 33 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 33 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 33 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 162 " -0.124 9.50e-02 1.11e+02 4.15e-02 2.06e+00 pdb=" NE ARG B 162 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 162 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 162 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B 162 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG B 162 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B 162 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG B 162 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 162 " -0.000 2.00e-02 2.50e+03 ... (remaining 6530 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 2204 2.19 - 2.80: 93519 2.80 - 3.40: 124855 3.40 - 4.00: 167163 4.00 - 4.60: 259721 Nonbonded interactions: 647462 Sorted by model distance: nonbonded pdb=" O PHE A 387 " pdb=" HD1 HIS A 438 " model vdw 1.593 2.450 nonbonded pdb=" OD1 ASP A 402 " pdb="HH12 ARG E 331 " model vdw 1.594 2.450 nonbonded pdb=" O ARG H 20 " pdb="HD21 ASN H 24 " model vdw 1.595 2.450 nonbonded pdb=" HG1 THR A 224 " pdb=" O3G AGS A 901 " model vdw 1.596 2.450 nonbonded pdb=" H LYS D 34 " pdb=" OE2 GLU D 38 " model vdw 1.598 2.450 ... (remaining 647457 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: 20.800 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 114.370 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.160 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:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.002 0.158 23270 Z= 0.158 Angle : 0.448 15.063 31605 Z= 0.246 Chirality : 0.039 0.158 3644 Planarity : 0.003 0.073 3878 Dihedral : 14.255 156.576 8866 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 2.20 (0.17), residues: 2707 helix: 2.46 (0.15), residues: 1297 sheet: 0.99 (0.22), residues: 562 loop : 0.25 (0.24), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 42 HIS 0.006 0.001 HIS D 340 PHE 0.015 0.001 PHE F 236 TYR 0.008 0.001 TYR E 287 ARG 0.007 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 3 residues processed: 410 average time/residue: 3.2435 time to fit residues: 1518.2271 Evaluate side-chains 187 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 143 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 411 ASN B 146 GLN B 208 ASN B 250 GLN C 30 GLN C 291 GLN E 19 ASN E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 23270 Z= 0.270 Angle : 0.547 6.206 31605 Z= 0.298 Chirality : 0.041 0.176 3644 Planarity : 0.004 0.045 3878 Dihedral : 12.866 153.703 3408 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 1.33 % Allowed : 9.53 % Favored : 89.14 % 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: 1.77 (0.17), residues: 2707 helix: 2.09 (0.15), residues: 1311 sheet: 0.80 (0.22), residues: 569 loop : 0.04 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 294 HIS 0.007 0.001 HIS E 341 PHE 0.017 0.001 PHE G 152 TYR 0.015 0.001 TYR B 186 ARG 0.009 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 4.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 312 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7974 (mtpp) outliers start: 33 outliers final: 11 residues processed: 215 average time/residue: 3.2192 time to fit residues: 795.7279 Evaluate side-chains 176 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 584 TYR Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 270 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN G 69 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23270 Z= 0.296 Angle : 0.540 6.083 31605 Z= 0.292 Chirality : 0.041 0.184 3644 Planarity : 0.004 0.050 3878 Dihedral : 12.716 153.682 3404 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 1.33 % Allowed : 10.54 % Favored : 88.13 % 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: 1.43 (0.17), residues: 2707 helix: 1.86 (0.15), residues: 1311 sheet: 0.63 (0.22), residues: 568 loop : -0.20 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 294 HIS 0.007 0.001 HIS E 341 PHE 0.020 0.001 PHE G 152 TYR 0.012 0.001 TYR G 148 ARG 0.011 0.001 ARG H 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 3.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 MET cc_start: 0.6897 (ttt) cc_final: 0.6355 (ttt) REVERT: C 312 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7941 (mtpp) outliers start: 33 outliers final: 13 residues processed: 192 average time/residue: 2.9335 time to fit residues: 652.7656 Evaluate side-chains 171 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain H residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 251 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23270 Z= 0.294 Angle : 0.535 7.949 31605 Z= 0.290 Chirality : 0.041 0.183 3644 Planarity : 0.004 0.050 3878 Dihedral : 12.854 154.196 3402 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 1.74 % Allowed : 11.31 % Favored : 86.95 % 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: 1.29 (0.17), residues: 2707 helix: 1.78 (0.15), residues: 1321 sheet: 0.47 (0.21), residues: 570 loop : -0.29 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 16 HIS 0.008 0.001 HIS D 340 PHE 0.020 0.002 PHE G 152 TYR 0.012 0.001 TYR A 501 ARG 0.006 0.000 ARG D 165 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 4.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 312 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7935 (mtpp) REVERT: F 318 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5360 (mm-30) outliers start: 43 outliers final: 14 residues processed: 195 average time/residue: 2.9997 time to fit residues: 680.4097 Evaluate side-chains 168 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 3.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 226 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 411 ASN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN F 17 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23270 Z= 0.249 Angle : 0.515 6.055 31605 Z= 0.278 Chirality : 0.041 0.169 3644 Planarity : 0.004 0.046 3878 Dihedral : 12.877 153.843 3402 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 1.49 % Allowed : 12.36 % Favored : 86.15 % 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: 1.32 (0.17), residues: 2707 helix: 1.84 (0.15), residues: 1317 sheet: 0.45 (0.21), residues: 569 loop : -0.31 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 42 HIS 0.009 0.001 HIS F 17 PHE 0.016 0.001 PHE G 152 TYR 0.011 0.001 TYR G 148 ARG 0.004 0.000 ARG D 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 3.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.6296 (OUTLIER) cc_final: 0.5992 (m-80) REVERT: C 312 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7899 (mtpp) REVERT: F 318 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.5167 (mm-30) outliers start: 37 outliers final: 21 residues processed: 185 average time/residue: 2.8034 time to fit residues: 605.9007 Evaluate side-chains 178 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 3.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 284 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 5.9990 chunk 239 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 266 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23270 Z= 0.182 Angle : 0.495 6.045 31605 Z= 0.267 Chirality : 0.040 0.164 3644 Planarity : 0.004 0.046 3878 Dihedral : 12.849 153.938 3402 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 1.21 % Allowed : 13.17 % Favored : 85.62 % 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: 1.43 (0.17), residues: 2707 helix: 1.93 (0.15), residues: 1320 sheet: 0.48 (0.22), residues: 567 loop : -0.23 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 42 HIS 0.004 0.001 HIS D 340 PHE 0.017 0.001 PHE A 523 TYR 0.011 0.001 TYR A 501 ARG 0.005 0.000 ARG F 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.6272 (OUTLIER) cc_final: 0.5959 (m-80) REVERT: C 312 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7802 (mtpp) REVERT: F 318 GLU cc_start: 0.5439 (OUTLIER) cc_final: 0.5178 (mm-30) outliers start: 30 outliers final: 13 residues processed: 178 average time/residue: 2.8470 time to fit residues: 590.6419 Evaluate side-chains 170 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 143 ASN Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23270 Z= 0.252 Angle : 0.514 6.454 31605 Z= 0.277 Chirality : 0.040 0.164 3644 Planarity : 0.004 0.052 3878 Dihedral : 12.915 153.989 3402 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.42 % Rotamer: Outliers : 1.21 % Allowed : 13.17 % Favored : 85.62 % 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: 1.34 (0.17), residues: 2707 helix: 1.88 (0.15), residues: 1320 sheet: 0.42 (0.21), residues: 567 loop : -0.31 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 16 HIS 0.006 0.001 HIS D 340 PHE 0.020 0.001 PHE A 523 TYR 0.011 0.001 TYR G 148 ARG 0.005 0.000 ARG F 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.6026 (m-80) REVERT: C 312 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7893 (mtpp) REVERT: F 318 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.5101 (mm-30) outliers start: 30 outliers final: 18 residues processed: 175 average time/residue: 2.8962 time to fit residues: 590.0752 Evaluate side-chains 171 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 131 optimal weight: 0.0970 chunk 24 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23270 Z= 0.191 Angle : 0.500 7.333 31605 Z= 0.268 Chirality : 0.040 0.156 3644 Planarity : 0.004 0.051 3878 Dihedral : 12.904 154.096 3402 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.45 % Rotamer: Outliers : 1.01 % Allowed : 13.69 % Favored : 85.30 % 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: 1.45 (0.17), residues: 2707 helix: 1.96 (0.15), residues: 1325 sheet: 0.42 (0.21), residues: 567 loop : -0.21 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 42 HIS 0.004 0.001 HIS D 340 PHE 0.017 0.001 PHE A 523 TYR 0.013 0.001 TYR A 501 ARG 0.007 0.000 ARG F 149 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 3.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.6294 (OUTLIER) cc_final: 0.5994 (m-80) REVERT: C 312 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7788 (mtpp) REVERT: F 318 GLU cc_start: 0.5384 (OUTLIER) cc_final: 0.5098 (mm-30) outliers start: 25 outliers final: 13 residues processed: 172 average time/residue: 2.7977 time to fit residues: 562.6656 Evaluate side-chains 166 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 0.0970 chunk 253 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23270 Z= 0.245 Angle : 0.521 9.711 31605 Z= 0.277 Chirality : 0.040 0.159 3644 Planarity : 0.004 0.049 3878 Dihedral : 12.948 154.324 3402 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 1.25 % Allowed : 13.57 % Favored : 85.18 % 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: 1.37 (0.17), residues: 2707 helix: 1.89 (0.15), residues: 1325 sheet: 0.39 (0.21), residues: 567 loop : -0.27 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 294 HIS 0.005 0.001 HIS E 341 PHE 0.019 0.001 PHE A 523 TYR 0.011 0.001 TYR G 148 ARG 0.006 0.000 ARG F 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 3.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.6352 (OUTLIER) cc_final: 0.6035 (m-80) REVERT: C 142 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7867 (tpp-160) REVERT: C 312 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7853 (mtpp) outliers start: 31 outliers final: 19 residues processed: 173 average time/residue: 3.0315 time to fit residues: 609.5250 Evaluate side-chains 170 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 167 GLN Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 273 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23270 Z= 0.215 Angle : 0.523 11.170 31605 Z= 0.277 Chirality : 0.040 0.153 3644 Planarity : 0.004 0.048 3878 Dihedral : 12.947 154.467 3402 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.58 % Favored : 96.38 % Rotamer: Outliers : 1.05 % Allowed : 13.85 % Favored : 85.10 % 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: 1.39 (0.17), residues: 2707 helix: 1.90 (0.15), residues: 1326 sheet: 0.39 (0.21), residues: 567 loop : -0.23 (0.23), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 294 HIS 0.005 0.001 HIS D 340 PHE 0.018 0.001 PHE A 523 TYR 0.013 0.001 TYR A 501 ARG 0.006 0.000 ARG F 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5414 Ramachandran restraints generated. 2707 Oldfield, 0 Emsley, 2707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue MET 520 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue MET 590 is missing expected H atoms. Skipping. Residue THR 600 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue THR 72 is missing expected H atoms. Skipping. Residue SER 2 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 51 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.6032 (m-80) REVERT: C 142 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7864 (tpp-160) REVERT: C 197 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7986 (tt) REVERT: C 312 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7808 (mtpp) outliers start: 26 outliers final: 17 residues processed: 167 average time/residue: 2.8335 time to fit residues: 551.3659 Evaluate side-chains 167 residues out of total 2495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain C residue 142 ARG Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 312 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 106 CYS Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 306 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 198 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 224 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.100327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.077297 restraints weight = 143765.675| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.93 r_work: 0.3294 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23270 Z= 0.180 Angle : 0.507 9.998 31605 Z= 0.269 Chirality : 0.040 0.157 3644 Planarity : 0.004 0.043 3878 Dihedral : 12.915 154.855 3402 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 0.97 % Allowed : 14.01 % Favored : 85.02 % 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: 1.47 (0.17), residues: 2707 helix: 1.99 (0.15), residues: 1326 sheet: 0.39 (0.22), residues: 561 loop : -0.20 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 294 HIS 0.004 0.001 HIS D 340 PHE 0.011 0.001 PHE G 152 TYR 0.009 0.001 TYR F 179 ARG 0.006 0.000 ARG B 272 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12931.29 seconds wall clock time: 231 minutes 54.48 seconds (13914.48 seconds total)