Starting phenix.real_space_refine on Sat Jul 20 01:47:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/07_2024/8jip_36323_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/07_2024/8jip_36323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/07_2024/8jip_36323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/07_2024/8jip_36323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/07_2024/8jip_36323_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jip_36323/07_2024/8jip_36323_neut_trim.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5961 2.51 5 N 1609 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 76": "OE1" <-> "OE2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R GLU 138": "OE1" <-> "OE2" Residue "R GLU 139": "OE1" <-> "OE2" Residue "R GLU 292": "OE1" <-> "OE2" Residue "R GLU 294": "OE1" <-> "OE2" Residue "R GLU 373": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "P GLU 12": "OE1" <-> "OE2" Residue "P GLU 17": "OE1" <-> "OE2" Residue "P GLU 27": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9362 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3109 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 2016 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 231 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2590 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 6.04, per 1000 atoms: 0.65 Number of scatterers: 9362 At special positions: 0 Unit cell: (85.14, 100.62, 175.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1735 8.00 N 1609 7.00 C 5961 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.6 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 41.2% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'R' and resid 31 through 51 Processing helix chain 'R' and resid 89 through 94 removed outlier: 3.745A pdb=" N SER R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 169 removed outlier: 3.505A pdb=" N THR R 149 " --> pdb=" O TYR R 145 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 204 removed outlier: 3.561A pdb=" N SER R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 199 " --> pdb=" O PHE R 195 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 222 removed outlier: 3.781A pdb=" N LEU R 217 " --> pdb=" O GLN R 213 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU R 218 " --> pdb=" O TRP R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 232 removed outlier: 3.624A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 257 removed outlier: 3.973A pdb=" N CYS R 236 " --> pdb=" O LEU R 232 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU R 254 " --> pdb=" O TYR R 250 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU R 255 " --> pdb=" O LEU R 251 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE R 257 " --> pdb=" O THR R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 291 removed outlier: 3.735A pdb=" N TRP R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) Proline residue: R 277 - end of helix removed outlier: 3.821A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 294 through 298 removed outlier: 3.822A pdb=" N TRP R 297 " --> pdb=" O GLU R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 326 removed outlier: 3.890A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 327 through 336 Processing helix chain 'R' and resid 344 through 349 Processing helix chain 'R' and resid 355 through 361 removed outlier: 4.331A pdb=" N LEU R 359 " --> pdb=" O THR R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 366 Processing helix chain 'R' and resid 377 through 402 removed outlier: 3.505A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER R 389 " --> pdb=" O PHE R 385 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR R 402 " --> pdb=" O VAL R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 421 removed outlier: 3.650A pdb=" N GLU R 412 " --> pdb=" O GLU R 408 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE R 413 " --> pdb=" O VAL R 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 31 removed outlier: 3.519A pdb=" N GLN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.511A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.587A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.492A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.694A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.762A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.568A pdb=" N ARG A 284 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.666A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'P' and resid 3 through 27 removed outlier: 3.515A pdb=" N GLN P 20 " --> pdb=" O SER P 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 22 removed outlier: 3.763A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 42 removed outlier: 4.056A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.698A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.787A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 79 through 81 removed outlier: 3.854A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.291A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ALA A 220 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.805A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 319 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.043A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.551A pdb=" N TYR B 124 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.873A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.106A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.955A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 276 through 277 Processing sheet with id=AB2, first strand: chain 'N' and resid 3 through 7 removed outlier: 4.182A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.841A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA N 97 " --> pdb=" O ASN N 35 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 71 through 73 368 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1531 1.30 - 1.43: 2611 1.43 - 1.55: 5351 1.55 - 1.68: 2 1.68 - 1.81: 77 Bond restraints: 9572 Sorted by residual: bond pdb=" C LEU R 218 " pdb=" O LEU R 218 " ideal model delta sigma weight residual 1.236 1.168 0.068 1.22e-02 6.72e+03 3.08e+01 bond pdb=" C LEU R 89 " pdb=" N PRO R 90 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.20e-02 6.94e+03 1.64e+01 bond pdb=" C SER P 11 " pdb=" O SER P 11 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.17e-02 7.31e+03 1.41e+01 bond pdb=" CA SER P 11 " pdb=" C SER P 11 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.30e-02 5.92e+03 1.37e+01 bond pdb=" C ASP R 53 " pdb=" N PRO R 54 " ideal model delta sigma weight residual 1.329 1.373 -0.044 1.18e-02 7.18e+03 1.37e+01 ... (remaining 9567 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.62: 230 106.62 - 114.40: 5520 114.40 - 122.19: 5485 122.19 - 129.97: 1659 129.97 - 137.75: 89 Bond angle restraints: 12983 Sorted by residual: angle pdb=" N ARG R 64 " pdb=" CA ARG R 64 " pdb=" C ARG R 64 " ideal model delta sigma weight residual 114.31 102.32 11.99 1.29e+00 6.01e-01 8.63e+01 angle pdb=" C THR A 292 " pdb=" N PRO A 293 " pdb=" CA PRO A 293 " ideal model delta sigma weight residual 120.66 111.89 8.77 1.09e+00 8.42e-01 6.47e+01 angle pdb=" N THR R 353 " pdb=" CA THR R 353 " pdb=" C THR R 353 " ideal model delta sigma weight residual 114.04 104.13 9.91 1.24e+00 6.50e-01 6.39e+01 angle pdb=" N LEU R 379 " pdb=" CA LEU R 379 " pdb=" C LEU R 379 " ideal model delta sigma weight residual 111.07 102.56 8.51 1.07e+00 8.73e-01 6.33e+01 angle pdb=" N PRO R 73 " pdb=" CA PRO R 73 " pdb=" C PRO R 73 " ideal model delta sigma weight residual 110.80 121.96 -11.16 1.51e+00 4.39e-01 5.46e+01 ... (remaining 12978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4808 17.82 - 35.64: 572 35.64 - 53.46: 204 53.46 - 71.28: 70 71.28 - 89.11: 17 Dihedral angle restraints: 5671 sinusoidal: 2226 harmonic: 3445 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 172.23 -79.23 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual -86.00 -151.66 65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -149.84 63.84 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 5668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1288 0.101 - 0.201: 134 0.201 - 0.302: 15 0.302 - 0.403: 4 0.403 - 0.504: 1 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CA ASN R 407 " pdb=" N ASN R 407 " pdb=" C ASN R 407 " pdb=" CB ASN R 407 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" CA ASN R 63 " pdb=" N ASN R 63 " pdb=" C ASN R 63 " pdb=" CB ASN R 63 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1439 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 D6M P 101 " -0.039 2.00e-02 2.50e+03 4.74e-02 2.81e+01 pdb=" C04 D6M P 101 " 0.056 2.00e-02 2.50e+03 pdb=" C12 D6M P 101 " 0.049 2.00e-02 2.50e+03 pdb=" N03 D6M P 101 " -0.064 2.00e-02 2.50e+03 pdb=" O01 D6M P 101 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 323 " 0.026 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" C ILE R 323 " -0.089 2.00e-02 2.50e+03 pdb=" O ILE R 323 " 0.033 2.00e-02 2.50e+03 pdb=" N PHE R 324 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 289 " 0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C TYR R 289 " -0.071 2.00e-02 2.50e+03 pdb=" O TYR R 289 " 0.026 2.00e-02 2.50e+03 pdb=" N LEU R 290 " 0.024 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 590 2.71 - 3.25: 9021 3.25 - 3.80: 14807 3.80 - 4.35: 18017 4.35 - 4.90: 30178 Nonbonded interactions: 72613 Sorted by model distance: nonbonded pdb=" N GLU A 276 " pdb=" OE1 GLU A 276 " model vdw 2.156 2.520 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.216 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.229 2.440 nonbonded pdb=" O LYS N 65 " pdb=" NH1 ARG N 67 " model vdw 2.252 2.520 nonbonded pdb=" O PHE R 385 " pdb=" OG SER R 389 " model vdw 2.255 2.440 ... (remaining 72608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 27.680 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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 : 0.006 0.068 9572 Z= 0.403 Angle : 1.049 12.753 12983 Z= 0.699 Chirality : 0.066 0.504 1442 Planarity : 0.005 0.056 1654 Dihedral : 18.747 89.106 3425 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.62 % Favored : 92.61 % Rotamer: Outliers : 14.94 % Allowed : 9.23 % Favored : 75.83 % Cbeta Deviations : 0.09 % 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: -2.27 (0.24), residues: 1164 helix: -1.39 (0.25), residues: 422 sheet: -0.30 (0.38), residues: 190 loop : -1.99 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 39 HIS 0.005 0.001 HIS R 99 PHE 0.016 0.002 PHE R 187 TYR 0.016 0.002 TYR A 56 ARG 0.004 0.000 ARG R 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 170 time to evaluate : 1.116 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: R 107 GLU cc_start: 0.5188 (OUTLIER) cc_final: 0.4396 (pm20) REVERT: R 112 GLN cc_start: 0.1989 (OUTLIER) cc_final: 0.1314 (mt0) REVERT: A 229 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.7669 (p0) REVERT: A 231 ASN cc_start: 0.9505 (t0) cc_final: 0.9303 (t0) REVERT: A 232 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8692 (mtp85) REVERT: A 359 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8422 (mp0) REVERT: P 1 HIS cc_start: 0.8532 (OUTLIER) cc_final: 0.7858 (p-80) REVERT: P 11 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.8205 (t) REVERT: P 13 TYR cc_start: 0.9042 (t80) cc_final: 0.8752 (t80) REVERT: P 21 ASP cc_start: 0.9180 (m-30) cc_final: 0.8972 (m-30) REVERT: B 44 GLN cc_start: 0.7341 (mp-120) cc_final: 0.6841 (mp-120) REVERT: B 172 GLU cc_start: 0.9190 (tp30) cc_final: 0.8825 (tp30) REVERT: B 175 GLN cc_start: 0.8456 (mp10) cc_final: 0.8089 (mp10) REVERT: B 217 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6565 (pmt) REVERT: B 220 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: B 259 GLN cc_start: 0.8264 (tp-100) cc_final: 0.8002 (tp40) REVERT: B 264 TYR cc_start: 0.7692 (OUTLIER) cc_final: 0.7397 (m-10) REVERT: B 303 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7259 (OUTLIER) REVERT: G 21 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7315 (pp-130) REVERT: N 43 LYS cc_start: 0.8857 (ptpp) cc_final: 0.8575 (pmtt) outliers start: 149 outliers final: 42 residues processed: 284 average time/residue: 1.1454 time to fit residues: 347.5850 Evaluate side-chains 165 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 112 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 43 ARG Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 47 GLN Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 107 GLU Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 118 LEU Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 317 ILE Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 412 GLU Chi-restraints excluded: chain R residue 421 ARG Chi-restraints excluded: chain R residue 423 GLU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain P residue 1 HIS Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 21 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.0270 chunk 66 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 63 ASN R 112 GLN R 182 ASN R 221 GLN R 234 GLN R 302 ASN R 304 ASN R 338 ASN R 394 GLN R 406 ASN A 238 ASN N 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9572 Z= 0.204 Angle : 0.653 9.063 12983 Z= 0.337 Chirality : 0.041 0.146 1442 Planarity : 0.004 0.043 1654 Dihedral : 10.477 75.455 1432 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.87 % Favored : 95.96 % Rotamer: Outliers : 5.92 % Allowed : 19.36 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.24), residues: 1164 helix: 0.25 (0.26), residues: 441 sheet: 0.07 (0.40), residues: 191 loop : -1.90 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 39 HIS 0.002 0.001 HIS R 374 PHE 0.036 0.002 PHE R 80 TYR 0.023 0.001 TYR R 148 ARG 0.006 0.001 ARG R 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 125 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2631 (OUTLIER) cc_final: 0.2168 (mt0) REVERT: A 231 ASN cc_start: 0.9490 (t0) cc_final: 0.9241 (t0) REVERT: B 172 GLU cc_start: 0.9207 (tp30) cc_final: 0.8842 (tp30) REVERT: B 175 GLN cc_start: 0.8488 (mp10) cc_final: 0.8080 (mp10) REVERT: B 220 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7279 (mp10) REVERT: B 260 GLU cc_start: 0.7520 (pp20) cc_final: 0.7301 (pp20) REVERT: B 301 LYS cc_start: 0.7424 (mppt) cc_final: 0.7061 (mmtm) REVERT: B 303 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.6837 (m-30) REVERT: G 21 MET cc_start: 0.7442 (ppp) cc_final: 0.7137 (pp-130) REVERT: N 43 LYS cc_start: 0.8946 (ptpp) cc_final: 0.8592 (pmtt) outliers start: 59 outliers final: 29 residues processed: 171 average time/residue: 1.0905 time to fit residues: 200.6408 Evaluate side-chains 141 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 109 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 348 ARG Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 86 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 83 optimal weight: 0.0570 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN R 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9572 Z= 0.185 Angle : 0.584 8.428 12983 Z= 0.298 Chirality : 0.040 0.143 1442 Planarity : 0.004 0.040 1654 Dihedral : 8.246 67.673 1359 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 4.61 % Allowed : 21.97 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1164 helix: 1.04 (0.26), residues: 440 sheet: 0.36 (0.42), residues: 179 loop : -1.84 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 39 HIS 0.003 0.001 HIS P 1 PHE 0.024 0.001 PHE R 80 TYR 0.016 0.001 TYR R 148 ARG 0.013 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 116 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2855 (OUTLIER) cc_final: 0.2213 (mt0) REVERT: A 20 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8270 (tm-30) REVERT: A 52 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 231 ASN cc_start: 0.9462 (t0) cc_final: 0.9102 (m110) REVERT: B 172 GLU cc_start: 0.9220 (tp30) cc_final: 0.8857 (tp30) REVERT: B 175 GLN cc_start: 0.8508 (mp10) cc_final: 0.8112 (mp10) REVERT: B 260 GLU cc_start: 0.7725 (pp20) cc_final: 0.7507 (pp20) REVERT: G 21 MET cc_start: 0.7435 (ppp) cc_final: 0.7150 (pp-130) REVERT: N 65 LYS cc_start: 0.9138 (ttpt) cc_final: 0.8913 (ttpt) outliers start: 46 outliers final: 25 residues processed: 151 average time/residue: 1.1067 time to fit residues: 179.4755 Evaluate side-chains 133 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 9.9990 chunk 77 optimal weight: 0.0870 chunk 53 optimal weight: 0.0060 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 overall best weight: 0.9576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 ASN R 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9572 Z= 0.192 Angle : 0.595 14.306 12983 Z= 0.294 Chirality : 0.041 0.183 1442 Planarity : 0.003 0.039 1654 Dihedral : 7.072 72.030 1341 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 4.01 % Allowed : 23.47 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1164 helix: 1.38 (0.26), residues: 442 sheet: 0.38 (0.42), residues: 179 loop : -1.84 (0.24), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 39 HIS 0.003 0.001 HIS A 324 PHE 0.016 0.001 PHE R 80 TYR 0.020 0.001 TYR R 148 ARG 0.009 0.001 ARG P 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 110 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2862 (OUTLIER) cc_final: 0.2264 (mt0) REVERT: A 231 ASN cc_start: 0.9432 (t0) cc_final: 0.9120 (m110) REVERT: B 172 GLU cc_start: 0.9231 (tp30) cc_final: 0.8922 (tp30) REVERT: B 175 GLN cc_start: 0.8511 (mp10) cc_final: 0.8109 (mp10) REVERT: B 260 GLU cc_start: 0.7848 (pp20) cc_final: 0.7636 (pp20) REVERT: G 21 MET cc_start: 0.7459 (ppp) cc_final: 0.7191 (pp-130) outliers start: 40 outliers final: 26 residues processed: 138 average time/residue: 1.0834 time to fit residues: 161.5043 Evaluate side-chains 132 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 125 GLU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 0.0270 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 0.4980 chunk 98 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 99 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9572 Z= 0.242 Angle : 0.602 10.724 12983 Z= 0.305 Chirality : 0.041 0.141 1442 Planarity : 0.003 0.037 1654 Dihedral : 6.474 74.732 1332 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 4.81 % Allowed : 23.07 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.25), residues: 1164 helix: 1.44 (0.26), residues: 449 sheet: 0.31 (0.41), residues: 179 loop : -1.80 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 39 HIS 0.003 0.001 HIS A 324 PHE 0.016 0.001 PHE N 108 TYR 0.019 0.001 TYR R 148 ARG 0.007 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 109 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2641 (OUTLIER) cc_final: 0.0782 (pm20) REVERT: A 20 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8212 (tm-30) REVERT: A 53 MET cc_start: 0.9559 (mpt) cc_final: 0.9213 (mmp) REVERT: A 231 ASN cc_start: 0.9449 (t0) cc_final: 0.9149 (m110) REVERT: B 172 GLU cc_start: 0.9244 (tp30) cc_final: 0.8917 (tp30) REVERT: B 175 GLN cc_start: 0.8519 (mp10) cc_final: 0.8101 (mp10) REVERT: B 260 GLU cc_start: 0.8083 (pp20) cc_final: 0.7628 (pp20) REVERT: G 21 MET cc_start: 0.7433 (ppp) cc_final: 0.7135 (pp-130) REVERT: N 5 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7920 (tp40) outliers start: 48 outliers final: 28 residues processed: 147 average time/residue: 1.1070 time to fit residues: 175.0529 Evaluate side-chains 129 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 140 GLN Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 9572 Z= 0.230 Angle : 0.600 10.836 12983 Z= 0.302 Chirality : 0.041 0.141 1442 Planarity : 0.003 0.071 1654 Dihedral : 6.091 75.171 1325 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 4.11 % Allowed : 25.78 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1164 helix: 1.56 (0.26), residues: 447 sheet: 0.35 (0.42), residues: 169 loop : -1.77 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 39 HIS 0.003 0.001 HIS A 324 PHE 0.015 0.001 PHE R 156 TYR 0.019 0.001 TYR R 148 ARG 0.011 0.000 ARG P 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 106 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2662 (OUTLIER) cc_final: 0.0833 (pm20) REVERT: A 53 MET cc_start: 0.9446 (mpt) cc_final: 0.9153 (mmp) REVERT: A 231 ASN cc_start: 0.9431 (t0) cc_final: 0.9137 (m110) REVERT: B 172 GLU cc_start: 0.9245 (tp30) cc_final: 0.8907 (tp30) REVERT: B 175 GLN cc_start: 0.8521 (mp10) cc_final: 0.8104 (mp10) REVERT: B 298 ASP cc_start: 0.8816 (m-30) cc_final: 0.8090 (p0) REVERT: G 21 MET cc_start: 0.7420 (ppp) cc_final: 0.7135 (pp-130) outliers start: 41 outliers final: 24 residues processed: 136 average time/residue: 1.1127 time to fit residues: 163.3563 Evaluate side-chains 127 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 405 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 37 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 20.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 63 ASN R 177 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 9572 Z= 0.190 Angle : 0.593 11.274 12983 Z= 0.299 Chirality : 0.040 0.234 1442 Planarity : 0.003 0.044 1654 Dihedral : 5.712 76.086 1323 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.35 % Favored : 96.56 % Rotamer: Outliers : 3.01 % Allowed : 27.18 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1164 helix: 1.75 (0.26), residues: 448 sheet: 0.64 (0.43), residues: 165 loop : -1.72 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP N 47 HIS 0.002 0.000 HIS A 324 PHE 0.017 0.001 PHE A 185 TYR 0.017 0.001 TYR R 148 ARG 0.007 0.000 ARG P 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2806 (pt0) cc_final: 0.0848 (pm20) REVERT: R 140 GLN cc_start: 0.7558 (mp10) cc_final: 0.7087 (pt0) REVERT: A 53 MET cc_start: 0.9442 (mpt) cc_final: 0.9164 (mmp) REVERT: A 231 ASN cc_start: 0.9417 (t0) cc_final: 0.9144 (m110) REVERT: A 289 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8854 (mp0) REVERT: B 172 GLU cc_start: 0.9232 (tp30) cc_final: 0.8896 (tp30) REVERT: B 175 GLN cc_start: 0.8518 (mp10) cc_final: 0.8090 (mp10) REVERT: B 260 GLU cc_start: 0.7994 (pp20) cc_final: 0.7556 (pp20) REVERT: G 21 MET cc_start: 0.7378 (ppp) cc_final: 0.7085 (pp-130) REVERT: G 47 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7699 (mm-30) REVERT: N 46 GLU cc_start: 0.7215 (pm20) cc_final: 0.6986 (pm20) outliers start: 30 outliers final: 20 residues processed: 131 average time/residue: 1.1203 time to fit residues: 157.8902 Evaluate side-chains 127 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 63 ASN Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 63 ASN R 177 ASN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 9572 Z= 0.271 Angle : 0.623 12.223 12983 Z= 0.318 Chirality : 0.042 0.250 1442 Planarity : 0.003 0.034 1654 Dihedral : 5.289 59.332 1320 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.41 % Allowed : 26.98 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1164 helix: 1.79 (0.26), residues: 449 sheet: 0.28 (0.41), residues: 179 loop : -1.69 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 47 HIS 0.003 0.001 HIS A 324 PHE 0.017 0.002 PHE N 108 TYR 0.019 0.001 TYR R 148 ARG 0.006 0.000 ARG P 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2843 (pt0) cc_final: 0.0959 (pm20) REVERT: A 53 MET cc_start: 0.9416 (mpt) cc_final: 0.9138 (mmp) REVERT: A 231 ASN cc_start: 0.9421 (t0) cc_final: 0.9134 (m110) REVERT: A 284 ARG cc_start: 0.8340 (mpp80) cc_final: 0.7987 (mpt-90) REVERT: A 289 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8852 (mp0) REVERT: P 21 ASP cc_start: 0.9382 (m-30) cc_final: 0.9006 (t0) REVERT: B 9 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7771 (mp10) REVERT: B 172 GLU cc_start: 0.9245 (tp30) cc_final: 0.8909 (tp30) REVERT: B 175 GLN cc_start: 0.8548 (mp10) cc_final: 0.8089 (mp10) REVERT: B 298 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8114 (p0) REVERT: G 21 MET cc_start: 0.7418 (ppp) cc_final: 0.7125 (pp-130) outliers start: 34 outliers final: 21 residues processed: 129 average time/residue: 1.1355 time to fit residues: 157.6799 Evaluate side-chains 122 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 108 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 9572 Z= 0.247 Angle : 0.641 12.548 12983 Z= 0.327 Chirality : 0.042 0.224 1442 Planarity : 0.004 0.069 1654 Dihedral : 5.273 58.660 1320 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.31 % Allowed : 27.28 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.25), residues: 1164 helix: 1.80 (0.26), residues: 448 sheet: 0.50 (0.42), residues: 172 loop : -1.71 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP R 39 HIS 0.003 0.001 HIS A 324 PHE 0.015 0.001 PHE N 108 TYR 0.019 0.001 TYR R 148 ARG 0.010 0.000 ARG R 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 112 GLN cc_start: 0.2702 (pt0) cc_final: 0.0857 (pm20) REVERT: A 53 MET cc_start: 0.9403 (mpt) cc_final: 0.9115 (mmp) REVERT: A 231 ASN cc_start: 0.9421 (t0) cc_final: 0.9131 (m110) REVERT: A 289 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8866 (mp0) REVERT: P 21 ASP cc_start: 0.9401 (m-30) cc_final: 0.9051 (t0) REVERT: B 9 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7794 (mp10) REVERT: B 172 GLU cc_start: 0.9238 (tp30) cc_final: 0.8904 (tp30) REVERT: B 175 GLN cc_start: 0.8544 (mp10) cc_final: 0.8108 (mp10) REVERT: B 260 GLU cc_start: 0.8065 (pp20) cc_final: 0.7692 (pp20) REVERT: B 283 ARG cc_start: 0.7169 (tpt-90) cc_final: 0.6958 (tpp80) REVERT: B 298 ASP cc_start: 0.8852 (OUTLIER) cc_final: 0.8170 (p0) REVERT: G 21 MET cc_start: 0.7417 (ppp) cc_final: 0.7126 (pp-130) outliers start: 33 outliers final: 25 residues processed: 130 average time/residue: 1.1641 time to fit residues: 162.5112 Evaluate side-chains 130 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 110 TRP Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 311 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 372 ASP Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 298 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 0.0070 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 0.0010 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN A 43 ASN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.148 9572 Z= 0.213 Angle : 0.626 11.838 12983 Z= 0.315 Chirality : 0.040 0.203 1442 Planarity : 0.003 0.034 1654 Dihedral : 5.051 56.937 1320 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.81 % Allowed : 29.19 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1164 helix: 1.99 (0.26), residues: 447 sheet: 0.59 (0.43), residues: 167 loop : -1.67 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP N 47 HIS 0.002 0.000 HIS A 324 PHE 0.014 0.001 PHE G 61 TYR 0.017 0.001 TYR R 148 ARG 0.009 0.000 ARG R 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.9413 (mpt) cc_final: 0.9148 (mmp) REVERT: A 231 ASN cc_start: 0.9400 (t0) cc_final: 0.9156 (m-40) REVERT: A 289 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8867 (mp0) REVERT: P 21 ASP cc_start: 0.9393 (m-30) cc_final: 0.9047 (t0) REVERT: B 172 GLU cc_start: 0.9225 (tp30) cc_final: 0.8896 (tp30) REVERT: B 175 GLN cc_start: 0.8524 (mp10) cc_final: 0.8090 (mp10) REVERT: B 259 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7684 (tm-30) REVERT: G 21 MET cc_start: 0.7323 (ppp) cc_final: 0.7071 (pp-130) outliers start: 18 outliers final: 14 residues processed: 119 average time/residue: 1.2442 time to fit residues: 158.6962 Evaluate side-chains 116 residues out of total 1024 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 102 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 36 VAL Chi-restraints excluded: chain R residue 62 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 90 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 65 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.133708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.084145 restraints weight = 17508.736| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.96 r_work: 0.2980 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 9572 Z= 0.219 Angle : 0.639 12.747 12983 Z= 0.321 Chirality : 0.041 0.181 1442 Planarity : 0.003 0.068 1654 Dihedral : 4.852 58.893 1316 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.91 % Allowed : 28.89 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1164 helix: 2.01 (0.26), residues: 447 sheet: 0.58 (0.43), residues: 165 loop : -1.70 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP N 47 HIS 0.003 0.000 HIS A 324 PHE 0.013 0.001 PHE G 61 TYR 0.018 0.001 TYR R 148 ARG 0.009 0.000 ARG P 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3765.56 seconds wall clock time: 66 minutes 46.96 seconds (4006.96 seconds total)