Starting phenix.real_space_refine on Fri Jun 27 07:15:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wff_32464/06_2025/7wff_32464.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wff_32464/06_2025/7wff_32464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wff_32464/06_2025/7wff_32464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wff_32464/06_2025/7wff_32464.map" model { file = "/net/cci-nas-00/data/ceres_data/7wff_32464/06_2025/7wff_32464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wff_32464/06_2025/7wff_32464.cif" } resolution = 3.59 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 ------------------------------------------------------------------------------- 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= 0.005 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 S 177 5.16 5 C 21076 2.51 5 N 5105 2.21 5 O 5762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32124 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2372 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 3780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3780 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 467} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 776 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 3950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3950 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 21, 'TRANS': 475} Chain: "E" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 695 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "F" Number of atoms: 5330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5330 Classifications: {'peptide': 677} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 22, 'TRANS': 654} Chain breaks: 3 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 7, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "G" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1281 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain breaks: 1 Chain: "a" Number of atoms: 2655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2655 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain: "b" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2367 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 18, 'TRANS': 288} Chain breaks: 2 Chain: "c" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1005 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 10, 'TRANS': 117} Chain: "d" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 762 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "e" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1206 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "f" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1277 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 146} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "g" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 965 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "h" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1170 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "i" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1098 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 11, 'TRANS': 133} Chain: "j" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1331 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'LHG': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23629 SG CYS c 120 79.780 48.124 65.698 1.00 66.02 S ATOM 23662 SG CYS c 126 77.013 49.434 63.573 1.00 64.75 S ATOM 23680 SG CYS c 129 75.335 43.501 64.010 1.00 67.34 S ATOM 23955 SG CYS c 162 78.165 43.477 66.375 1.00 73.63 S Time building chain proxies: 17.78, per 1000 atoms: 0.55 Number of scatterers: 32124 At special positions: 0 Unit cell: (124.8, 144.56, 215.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 177 16.00 P 2 15.00 O 5762 8.00 N 5105 7.00 C 21076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.84 Conformation dependent library (CDL) restraints added in 4.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES c 301 " pdb="FE2 FES c 301 " - pdb=" SG CYS c 129 " pdb="FE1 FES c 301 " - pdb=" SG CYS c 120 " pdb="FE1 FES c 301 " - pdb=" SG CYS c 126 " pdb="FE2 FES c 301 " - pdb=" SG CYS c 162 " Number of angles added : 6 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7504 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 15 sheets defined 58.0% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 26 through 60 Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 70 through 84 removed outlier: 3.758A pdb=" N ALA A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 111 Proline residue: A 102 - end of helix removed outlier: 3.864A pdb=" N ILE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 129 through 140 removed outlier: 3.964A pdb=" N LEU A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TRP A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 3.698A pdb=" N GLY A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 171 removed outlier: 3.606A pdb=" N LEU A 159 " --> pdb=" O LYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 187 Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.864A pdb=" N SER A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 250 through 275 removed outlier: 3.511A pdb=" N GLY A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 325 removed outlier: 3.768A pdb=" N THR A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.921A pdb=" N LEU A 334 " --> pdb=" O MET A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 removed outlier: 3.684A pdb=" N ILE A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'B' and resid 32 through 49 removed outlier: 4.225A pdb=" N LEU B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 78 removed outlier: 3.914A pdb=" N TYR B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 112 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 125 through 146 removed outlier: 3.921A pdb=" N PHE B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU B 131 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 145 " --> pdb=" O MET B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 168 Proline residue: B 156 - end of helix Processing helix chain 'B' and resid 174 through 205 Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.706A pdb=" N VAL B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 245 removed outlier: 3.558A pdb=" N SER B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 removed outlier: 4.029A pdb=" N HIS B 250 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.149A pdb=" N ASP B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 286 removed outlier: 4.363A pdb=" N PHE B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 314 removed outlier: 4.155A pdb=" N GLY B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 320 through 341 removed outlier: 3.917A pdb=" N ILE B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 338 " --> pdb=" O TYR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 375 removed outlier: 3.927A pdb=" N GLY B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.518A pdb=" N ALA B 385 " --> pdb=" O ARG B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.796A pdb=" N LYS B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 407 Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 429 through 454 removed outlier: 3.615A pdb=" N ILE B 435 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 453 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 497 Proline residue: B 494 - end of helix Processing helix chain 'B' and resid 498 through 507 removed outlier: 3.975A pdb=" N ASP B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.678A pdb=" N SER B 511 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 512 " --> pdb=" O LEU B 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 508 through 512' Processing helix chain 'C' and resid 7 through 31 removed outlier: 3.823A pdb=" N ALA C 12 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 60 through 85 removed outlier: 4.379A pdb=" N VAL C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Proline residue: C 81 - end of helix Processing helix chain 'C' and resid 90 through 114 removed outlier: 3.801A pdb=" N PHE C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 18 removed outlier: 3.557A pdb=" N ILE D 15 " --> pdb=" O PRO D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 25 Processing helix chain 'D' and resid 34 through 59 removed outlier: 4.567A pdb=" N ASN D 38 " --> pdb=" O GLY D 34 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR D 59 " --> pdb=" O TYR D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 110 Processing helix chain 'D' and resid 116 through 137 removed outlier: 3.899A pdb=" N ILE D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 149 Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.729A pdb=" N MET D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 194 removed outlier: 4.213A pdb=" N PHE D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 212 through 231 removed outlier: 4.192A pdb=" N LEU D 218 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 244 removed outlier: 4.240A pdb=" N ASP D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 removed outlier: 4.103A pdb=" N LEU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 275 through 304 removed outlier: 3.688A pdb=" N MET D 281 " --> pdb=" O HIS D 277 " (cutoff:3.500A) Proline residue: D 284 - end of helix removed outlier: 3.614A pdb=" N VAL D 288 " --> pdb=" O PRO D 284 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 302 - end of helix Processing helix chain 'D' and resid 307 through 328 removed outlier: 3.592A pdb=" N ILE D 311 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE D 322 " --> pdb=" O HIS D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 363 Processing helix chain 'D' and resid 377 through 392 Processing helix chain 'D' and resid 397 through 412 removed outlier: 3.981A pdb=" N ILE D 401 " --> pdb=" O MET D 397 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 430 removed outlier: 4.020A pdb=" N PHE D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 447 Proline residue: D 436 - end of helix Processing helix chain 'D' and resid 464 through 484 Proline residue: D 477 - end of helix Processing helix chain 'D' and resid 485 through 488 Processing helix chain 'D' and resid 492 through 505 removed outlier: 4.549A pdb=" N ASN D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR D 503 " --> pdb=" O ILE D 499 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 23 removed outlier: 4.022A pdb=" N VAL E 8 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU E 18 " --> pdb=" O PHE E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 53 Processing helix chain 'E' and resid 57 through 88 Processing helix chain 'F' and resid 16 through 24 Processing helix chain 'F' and resid 29 through 36 removed outlier: 3.509A pdb=" N LEU F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 65 Processing helix chain 'F' and resid 90 through 115 removed outlier: 3.699A pdb=" N VAL F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN F 113 " --> pdb=" O ILE F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 140 removed outlier: 3.732A pdb=" N PHE F 125 " --> pdb=" O TYR F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 163 Processing helix chain 'F' and resid 168 through 200 removed outlier: 3.792A pdb=" N GLY F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 212 removed outlier: 3.755A pdb=" N LEU F 208 " --> pdb=" O GLU F 204 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU F 210 " --> pdb=" O GLN F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.912A pdb=" N GLY F 236 " --> pdb=" O LEU F 232 " (cutoff:3.500A) Proline residue: F 237 - end of helix Processing helix chain 'F' and resid 252 through 256 removed outlier: 3.790A pdb=" N GLU F 255 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY F 256 " --> pdb=" O ALA F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 256' Processing helix chain 'F' and resid 257 through 264 Processing helix chain 'F' and resid 267 through 281 removed outlier: 3.644A pdb=" N GLY F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE F 274 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 277 " --> pdb=" O GLY F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 284 No H-bonds generated for 'chain 'F' and resid 282 through 284' Processing helix chain 'F' and resid 289 through 302 Processing helix chain 'F' and resid 314 through 336 Processing helix chain 'F' and resid 338 through 372 removed outlier: 3.505A pdb=" N ALA F 342 " --> pdb=" O SER F 338 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU F 343 " --> pdb=" O TYR F 339 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA F 354 " --> pdb=" O ALA F 350 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU F 355 " --> pdb=" O TYR F 351 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA F 369 " --> pdb=" O HIS F 365 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE F 370 " --> pdb=" O SER F 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 379 removed outlier: 3.523A pdb=" N GLN F 379 " --> pdb=" O PRO F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 407 Processing helix chain 'F' and resid 414 through 425 Processing helix chain 'F' and resid 429 through 454 removed outlier: 3.886A pdb=" N ILE F 433 " --> pdb=" O PRO F 429 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE F 434 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA F 435 " --> pdb=" O PHE F 431 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR F 453 " --> pdb=" O ILE F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 474 Processing helix chain 'F' and resid 544 through 561 Proline residue: F 550 - end of helix Processing helix chain 'F' and resid 562 through 564 No H-bonds generated for 'chain 'F' and resid 562 through 564' Processing helix chain 'F' and resid 571 through 576 Processing helix chain 'F' and resid 602 through 625 removed outlier: 3.801A pdb=" N LEU F 623 " --> pdb=" O ILE F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 633 through 644 removed outlier: 3.742A pdb=" N SER F 639 " --> pdb=" O THR F 635 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN F 641 " --> pdb=" O LEU F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 664 removed outlier: 4.198A pdb=" N ASN F 655 " --> pdb=" O GLU F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 675 Processing helix chain 'F' and resid 675 through 694 removed outlier: 3.539A pdb=" N ILE F 693 " --> pdb=" O PHE F 689 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE F 694 " --> pdb=" O ASP F 690 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 714 removed outlier: 3.789A pdb=" N THR F 698 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY F 702 " --> pdb=" O THR F 698 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 28 Processing helix chain 'G' and resid 31 through 53 Processing helix chain 'G' and resid 55 through 67 removed outlier: 4.027A pdb=" N VAL G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 80 Processing helix chain 'G' and resid 99 through 116 Processing helix chain 'G' and resid 119 through 125 Processing helix chain 'G' and resid 139 through 150 removed outlier: 3.550A pdb=" N THR G 150 " --> pdb=" O ILE G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 175 removed outlier: 4.090A pdb=" N SER G 160 " --> pdb=" O PHE G 156 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE G 161 " --> pdb=" O GLU G 157 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG G 175 " --> pdb=" O ILE G 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 131 removed outlier: 3.651A pdb=" N ASN a 129 " --> pdb=" O GLY a 125 " (cutoff:3.500A) Processing helix chain 'a' and resid 132 through 143 Processing helix chain 'a' and resid 157 through 162 Processing helix chain 'a' and resid 173 through 177 removed outlier: 3.858A pdb=" N HIS a 177 " --> pdb=" O PRO a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 180 through 194 Processing helix chain 'a' and resid 208 through 216 removed outlier: 3.762A pdb=" N THR a 216 " --> pdb=" O PHE a 212 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 237 Processing helix chain 'a' and resid 248 through 253 Processing helix chain 'a' and resid 257 through 264 Processing helix chain 'a' and resid 284 through 298 Processing helix chain 'a' and resid 315 through 319 removed outlier: 3.957A pdb=" N SER a 318 " --> pdb=" O SER a 315 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET a 319 " --> pdb=" O LYS a 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 315 through 319' Processing helix chain 'a' and resid 331 through 341 Processing helix chain 'a' and resid 352 through 354 No H-bonds generated for 'chain 'a' and resid 352 through 354' Processing helix chain 'a' and resid 355 through 363 Processing helix chain 'a' and resid 374 through 385 removed outlier: 3.590A pdb=" N ASP a 384 " --> pdb=" O ALA a 380 " (cutoff:3.500A) Processing helix chain 'a' and resid 393 through 401 removed outlier: 4.316A pdb=" N GLN a 397 " --> pdb=" O THR a 393 " (cutoff:3.500A) Processing helix chain 'a' and resid 402 through 404 No H-bonds generated for 'chain 'a' and resid 402 through 404' Processing helix chain 'a' and resid 412 through 420 Processing helix chain 'a' and resid 422 through 427 removed outlier: 3.922A pdb=" N LYS a 426 " --> pdb=" O TYR a 422 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER a 427 " --> pdb=" O ALA a 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 422 through 427' Processing helix chain 'a' and resid 444 through 454 Processing helix chain 'b' and resid 29 through 38 Processing helix chain 'b' and resid 261 through 266 Processing helix chain 'b' and resid 304 through 311 removed outlier: 3.829A pdb=" N TRP b 308 " --> pdb=" O GLY b 305 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP b 309 " --> pdb=" O SER b 306 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 105 Processing helix chain 'c' and resid 111 through 119 removed outlier: 4.231A pdb=" N LYS c 115 " --> pdb=" O PRO c 112 " (cutoff:3.500A) Proline residue: c 116 - end of helix removed outlier: 4.078A pdb=" N ASN c 119 " --> pdb=" O PRO c 116 " (cutoff:3.500A) Processing helix chain 'c' and resid 146 through 151 removed outlier: 3.815A pdb=" N LEU c 151 " --> pdb=" O GLU c 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 109 Processing helix chain 'd' and resid 110 through 112 No H-bonds generated for 'chain 'd' and resid 110 through 112' Processing helix chain 'd' and resid 115 through 119 removed outlier: 4.018A pdb=" N ASP d 118 " --> pdb=" O PRO d 115 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER d 119 " --> pdb=" O PHE d 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 115 through 119' Processing helix chain 'd' and resid 121 through 126 removed outlier: 4.118A pdb=" N ASP d 125 " --> pdb=" O GLU d 121 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY d 126 " --> pdb=" O TYR d 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 121 through 126' Processing helix chain 'd' and resid 132 through 155 Proline residue: d 142 - end of helix removed outlier: 3.515A pdb=" N GLU d 155 " --> pdb=" O GLU d 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 109 Processing helix chain 'e' and resid 114 through 129 removed outlier: 6.090A pdb=" N SER e 120 " --> pdb=" O GLN e 116 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU e 124 " --> pdb=" O SER e 120 " (cutoff:3.500A) Proline residue: e 125 - end of helix Processing helix chain 'e' and resid 137 through 155 removed outlier: 3.974A pdb=" N PHE e 141 " --> pdb=" O GLY e 137 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 165 Processing helix chain 'e' and resid 166 through 170 Processing helix chain 'f' and resid 145 through 155 removed outlier: 4.090A pdb=" N TYR f 151 " --> pdb=" O GLU f 147 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP f 152 " --> pdb=" O GLU f 148 " (cutoff:3.500A) Processing helix chain 'f' and resid 217 through 219 No H-bonds generated for 'chain 'f' and resid 217 through 219' Processing helix chain 'f' and resid 222 through 231 removed outlier: 3.794A pdb=" N LEU f 226 " --> pdb=" O VAL f 222 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 79 Processing helix chain 'g' and resid 85 through 102 removed outlier: 3.841A pdb=" N LYS g 94 " --> pdb=" O ALA g 90 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP g 102 " --> pdb=" O GLU g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 108 removed outlier: 3.544A pdb=" N ASP g 108 " --> pdb=" O ARG g 104 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 134 removed outlier: 3.794A pdb=" N GLN g 128 " --> pdb=" O ALA g 124 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR g 131 " --> pdb=" O SER g 127 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN g 132 " --> pdb=" O GLN g 128 " (cutoff:3.500A) Processing helix chain 'g' and resid 135 through 137 No H-bonds generated for 'chain 'g' and resid 135 through 137' Processing helix chain 'g' and resid 138 through 165 removed outlier: 4.144A pdb=" N ASN g 143 " --> pdb=" O GLU g 139 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASP g 144 " --> pdb=" O SER g 140 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 183 Processing helix chain 'h' and resid 115 through 132 removed outlier: 3.669A pdb=" N LYS h 124 " --> pdb=" O MET h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 133 through 135 No H-bonds generated for 'chain 'h' and resid 133 through 135' Processing helix chain 'h' and resid 141 through 166 Processing helix chain 'h' and resid 171 through 195 removed outlier: 3.930A pdb=" N ASN h 185 " --> pdb=" O ARG h 181 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR h 195 " --> pdb=" O ASP h 191 " (cutoff:3.500A) Processing helix chain 'h' and resid 197 through 220 removed outlier: 4.320A pdb=" N ASP h 207 " --> pdb=" O SER h 203 " (cutoff:3.500A) Processing helix chain 'i' and resid 149 through 157 Processing helix chain 'j' and resid 114 through 124 Processing helix chain 'j' and resid 220 through 229 Processing sheet with id=AA1, first strand: chain 'D' and resid 69 through 72 removed outlier: 6.023A pdb=" N LEU D 70 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE D 88 " --> pdb=" O LEU D 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 69 through 70 removed outlier: 3.505A pdb=" N HIS F 69 " --> pdb=" O ILE F 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 117 through 118 Processing sheet with id=AA4, first strand: chain 'a' and resid 151 through 152 Processing sheet with id=AA5, first strand: chain 'a' and resid 348 through 350 removed outlier: 5.675A pdb=" N PHE a 348 " --> pdb=" O VAL a 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'b' and resid 42 through 47 removed outlier: 3.505A pdb=" N SER b 47 " --> pdb=" O ILE b 50 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N SER b 66 " --> pdb=" O VAL b 72 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N VAL b 72 " --> pdb=" O SER b 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 125 through 126 Processing sheet with id=AA8, first strand: chain 'c' and resid 158 through 160 Processing sheet with id=AA9, first strand: chain 'f' and resid 91 through 92 Processing sheet with id=AB1, first strand: chain 'f' and resid 128 through 129 Processing sheet with id=AB2, first strand: chain 'f' and resid 164 through 174 removed outlier: 5.631A pdb=" N ALA f 165 " --> pdb=" O ARG f 188 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ARG f 188 " --> pdb=" O ALA f 165 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE f 167 " --> pdb=" O GLY f 186 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY f 186 " --> pdb=" O ILE f 167 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP f 169 " --> pdb=" O GLU f 184 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ASN f 179 " --> pdb=" O VAL f 202 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL f 202 " --> pdb=" O ASN f 179 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR f 181 " --> pdb=" O VAL f 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'i' and resid 97 through 102 removed outlier: 3.689A pdb=" N LEU i 101 " --> pdb=" O LYS i 170 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS i 170 " --> pdb=" O LEU i 101 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN i 116 " --> pdb=" O VAL i 208 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE i 210 " --> pdb=" O LEU i 114 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU i 114 " --> pdb=" O ILE i 210 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP i 130 " --> pdb=" O ALA i 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'i' and resid 97 through 102 removed outlier: 3.689A pdb=" N LEU i 101 " --> pdb=" O LYS i 170 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS i 170 " --> pdb=" O LEU i 101 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ASN i 116 " --> pdb=" O VAL i 208 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE i 210 " --> pdb=" O LEU i 114 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU i 114 " --> pdb=" O ILE i 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'j' and resid 216 through 219 removed outlier: 6.947A pdb=" N VAL j 106 " --> pdb=" O ILE j 218 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N TYR j 89 " --> pdb=" O CYS j 247 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N CYS j 247 " --> pdb=" O TYR j 89 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP j 91 " --> pdb=" O ALA j 245 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 140 through 141 removed outlier: 3.511A pdb=" N ARG j 140 " --> pdb=" O GLN j 148 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLN j 196 " --> pdb=" O ALA j 186 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER j 184 " --> pdb=" O PHE j 198 " (cutoff:3.500A) 1698 hydrogen bonds defined for protein. 4944 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.03 Time building geometry restraints manager: 9.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 13514 1.40 - 1.60: 19095 1.60 - 1.79: 150 1.79 - 1.99: 147 1.99 - 2.19: 4 Bond restraints: 32910 Sorted by residual: bond pdb=" C1 SQD F 802 " pdb=" O5 SQD F 802 " ideal model delta sigma weight residual 1.500 1.404 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C5 SQD F 802 " pdb=" O5 SQD F 802 " ideal model delta sigma weight residual 1.483 1.408 0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C3 SQD F 802 " pdb=" O3 SQD F 802 " ideal model delta sigma weight residual 1.451 1.378 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C23 SQD F 802 " pdb=" C24 SQD F 802 " ideal model delta sigma weight residual 1.592 1.520 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" O9 SQD F 802 " pdb=" S SQD F 802 " ideal model delta sigma weight residual 1.511 1.442 0.069 2.00e-02 2.50e+03 1.17e+01 ... (remaining 32905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 43984 3.14 - 6.28: 585 6.28 - 9.43: 49 9.43 - 12.57: 7 12.57 - 15.71: 4 Bond angle restraints: 44629 Sorted by residual: angle pdb=" S1 FES c 301 " pdb="FE2 FES c 301 " pdb=" S2 FES c 301 " ideal model delta sigma weight residual 104.33 88.72 15.61 1.14e+00 7.69e-01 1.87e+02 angle pdb=" S1 FES c 301 " pdb="FE1 FES c 301 " pdb=" S2 FES c 301 " ideal model delta sigma weight residual 104.33 88.62 15.71 1.20e+00 6.94e-01 1.71e+02 angle pdb="FE1 FES c 301 " pdb=" S2 FES c 301 " pdb="FE2 FES c 301 " ideal model delta sigma weight residual 75.66 89.90 -14.24 1.14e+00 7.69e-01 1.56e+02 angle pdb="FE1 FES c 301 " pdb=" S1 FES c 301 " pdb="FE2 FES c 301 " ideal model delta sigma weight residual 75.66 89.74 -14.08 1.20e+00 6.94e-01 1.38e+02 angle pdb=" N PRO F 409 " pdb=" CA PRO F 409 " pdb=" C PRO F 409 " ideal model delta sigma weight residual 110.70 120.94 -10.24 1.22e+00 6.72e-01 7.05e+01 ... (remaining 44624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 17196 17.55 - 35.10: 1723 35.10 - 52.64: 287 52.64 - 70.19: 41 70.19 - 87.74: 19 Dihedral angle restraints: 19266 sinusoidal: 7536 harmonic: 11730 Sorted by residual: dihedral pdb=" CA LEU B 246 " pdb=" C LEU B 246 " pdb=" N ALA B 247 " pdb=" CA ALA B 247 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA TYR a 160 " pdb=" C TYR a 160 " pdb=" N GLU a 161 " pdb=" CA GLU a 161 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ALA f 117 " pdb=" C ALA f 117 " pdb=" N PHE f 118 " pdb=" CA PHE f 118 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 19263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.901: 5061 0.901 - 1.802: 0 1.802 - 2.703: 0 2.703 - 3.604: 0 3.604 - 4.505: 1 Chirality restraints: 5062 Sorted by residual: chirality pdb=" C1 SQD F 802 " pdb=" C2 SQD F 802 " pdb=" O5 SQD F 802 " pdb=" O6 SQD F 802 " both_signs ideal model delta sigma weight residual False -2.39 2.12 -4.51 2.00e-01 2.50e+01 5.07e+02 chirality pdb=" CA PRO F 409 " pdb=" N PRO F 409 " pdb=" C PRO F 409 " pdb=" CB PRO F 409 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA LYS a 164 " pdb=" N LYS a 164 " pdb=" C LYS a 164 " pdb=" CB LYS a 164 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 5059 not shown) Planarity restraints: 5538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C23 LHG D 601 " 0.161 2.00e-02 2.50e+03 9.29e-02 8.62e+01 pdb=" C24 LHG D 601 " -0.048 2.00e-02 2.50e+03 pdb=" O10 LHG D 601 " -0.059 2.00e-02 2.50e+03 pdb=" O8 LHG D 601 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG F 801 " -0.099 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C24 LHG F 801 " 0.029 2.00e-02 2.50e+03 pdb=" O10 LHG F 801 " 0.037 2.00e-02 2.50e+03 pdb=" O8 LHG F 801 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG F 801 " 0.095 2.00e-02 2.50e+03 5.48e-02 3.00e+01 pdb=" C8 LHG F 801 " -0.027 2.00e-02 2.50e+03 pdb=" O7 LHG F 801 " -0.029 2.00e-02 2.50e+03 pdb=" O9 LHG F 801 " -0.038 2.00e-02 2.50e+03 ... (remaining 5535 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3543 2.74 - 3.28: 34264 3.28 - 3.82: 55493 3.82 - 4.36: 69096 4.36 - 4.90: 115160 Nonbonded interactions: 277556 Sorted by model distance: nonbonded pdb=" OG SER i 132 " pdb=" O ARG i 137 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR A 176 " pdb=" OH TYR C 80 " model vdw 2.204 3.040 nonbonded pdb=" O SER D 473 " pdb=" OH TYR d 98 " model vdw 2.216 3.040 nonbonded pdb=" O ILE D 132 " pdb=" OG SER D 136 " model vdw 2.217 3.040 nonbonded pdb=" O LEU b 251 " pdb=" OH TYR b 316 " model vdw 2.218 3.040 ... (remaining 277551 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 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: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 75.790 Find NCS groups from input model: 0.780 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: 0.020 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 0.096 32914 Z= 0.305 Angle : 0.942 15.712 44635 Z= 0.520 Chirality : 0.081 4.505 5062 Planarity : 0.006 0.093 5538 Dihedral : 14.275 87.738 11762 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.03 % Favored : 90.88 % Rotamer: Outliers : 0.26 % Allowed : 4.34 % Favored : 95.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.11), residues: 4011 helix: -2.00 (0.09), residues: 2146 sheet: -3.36 (0.24), residues: 305 loop : -3.35 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP h 80 HIS 0.013 0.002 HIS F 265 PHE 0.027 0.002 PHE F 149 TYR 0.038 0.002 TYR G 66 ARG 0.007 0.001 ARG G 175 Details of bonding type rmsd hydrogen bonds : bond 0.13822 ( 1681) hydrogen bonds : angle 6.66130 ( 4944) metal coordination : bond 0.06431 ( 4) metal coordination : angle 3.66977 ( 6) covalent geometry : bond 0.00637 (32910) covalent geometry : angle 0.94103 (44629) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1067 time to evaluate : 3.420 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: A 187 ASN cc_start: 0.8583 (m-40) cc_final: 0.8320 (m-40) REVERT: A 210 ARG cc_start: 0.7449 (mmm-85) cc_final: 0.6621 (mmp-170) REVERT: A 261 TYR cc_start: 0.8168 (m-80) cc_final: 0.7957 (m-80) REVERT: B 182 LYS cc_start: 0.8750 (mttt) cc_final: 0.8220 (mtpp) REVERT: B 300 GLU cc_start: 0.7134 (tt0) cc_final: 0.6822 (tt0) REVERT: B 351 MET cc_start: 0.8145 (tmm) cc_final: 0.7850 (ttt) REVERT: C 6 GLU cc_start: 0.6836 (tt0) cc_final: 0.6598 (tt0) REVERT: C 82 TRP cc_start: 0.7338 (t60) cc_final: 0.7066 (t60) REVERT: C 86 PHE cc_start: 0.8628 (t80) cc_final: 0.8384 (t80) REVERT: C 87 ASP cc_start: 0.7030 (t70) cc_final: 0.6573 (t0) REVERT: C 98 PHE cc_start: 0.8053 (t80) cc_final: 0.7763 (t80) REVERT: D 76 TRP cc_start: 0.8429 (t60) cc_final: 0.8066 (t-100) REVERT: D 124 MET cc_start: 0.8750 (mmt) cc_final: 0.8366 (tpt) REVERT: D 505 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.5354 (m-80) REVERT: E 23 THR cc_start: 0.7534 (p) cc_final: 0.7231 (p) REVERT: E 42 ASN cc_start: 0.7721 (t0) cc_final: 0.6687 (t0) REVERT: E 50 ASP cc_start: 0.6935 (t0) cc_final: 0.6647 (t0) REVERT: E 56 GLN cc_start: 0.7146 (mp10) cc_final: 0.6642 (mp10) REVERT: E 78 LEU cc_start: 0.9070 (mt) cc_final: 0.8320 (mm) REVERT: F 21 LEU cc_start: 0.8641 (mm) cc_final: 0.8242 (mm) REVERT: F 240 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8428 (mmtm) REVERT: F 340 ARG cc_start: 0.8390 (tpt170) cc_final: 0.7970 (ptm-80) REVERT: F 344 PHE cc_start: 0.8750 (t80) cc_final: 0.8494 (t80) REVERT: F 381 MET cc_start: 0.8204 (ttp) cc_final: 0.7716 (ttp) REVERT: G 41 PHE cc_start: 0.8030 (t80) cc_final: 0.7495 (t80) REVERT: G 45 CYS cc_start: 0.8400 (m) cc_final: 0.8014 (m) REVERT: G 50 TYR cc_start: 0.8368 (m-10) cc_final: 0.8095 (m-10) REVERT: G 55 SER cc_start: 0.8108 (p) cc_final: 0.7831 (t) REVERT: G 121 TYR cc_start: 0.8588 (m-80) cc_final: 0.8388 (m-80) REVERT: G 152 PHE cc_start: 0.8326 (m-80) cc_final: 0.7944 (m-10) REVERT: a 195 TYR cc_start: 0.8807 (m-80) cc_final: 0.8591 (m-80) REVERT: b 91 TYR cc_start: 0.7777 (t80) cc_final: 0.7562 (t80) REVERT: b 206 ASN cc_start: 0.8799 (t0) cc_final: 0.8442 (t0) REVERT: b 299 MET cc_start: 0.7375 (mtp) cc_final: 0.7098 (mtp) REVERT: b 344 GLU cc_start: 0.7408 (pt0) cc_final: 0.7207 (pt0) REVERT: c 82 ASP cc_start: 0.8609 (t0) cc_final: 0.8333 (t0) REVERT: c 115 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8288 (mmtm) REVERT: d 78 ILE cc_start: 0.9025 (mm) cc_final: 0.8641 (mm) REVERT: e 160 ASP cc_start: 0.8073 (t0) cc_final: 0.7692 (t70) REVERT: f 148 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8225 (tt0) REVERT: f 197 PHE cc_start: 0.8190 (t80) cc_final: 0.7943 (t80) REVERT: g 81 MET cc_start: 0.7799 (mtt) cc_final: 0.7492 (mtm) REVERT: g 154 GLU cc_start: 0.7569 (pp20) cc_final: 0.6719 (tm-30) REVERT: g 160 ASP cc_start: 0.8318 (t70) cc_final: 0.7938 (t0) REVERT: g 172 TYR cc_start: 0.8489 (t80) cc_final: 0.8239 (t80) REVERT: g 176 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7712 (mm-30) REVERT: h 97 GLU cc_start: 0.6686 (tt0) cc_final: 0.6323 (tt0) REVERT: h 120 MET cc_start: 0.7727 (ttp) cc_final: 0.7448 (ttt) REVERT: h 158 TYR cc_start: 0.8256 (m-80) cc_final: 0.8029 (m-80) REVERT: j 142 ILE cc_start: 0.8109 (mm) cc_final: 0.7827 (mm) REVERT: j 151 ASP cc_start: 0.7273 (p0) cc_final: 0.6952 (p0) REVERT: j 156 ASN cc_start: 0.8683 (p0) cc_final: 0.8300 (p0) outliers start: 9 outliers final: 2 residues processed: 1073 average time/residue: 0.4333 time to fit residues: 745.4144 Evaluate side-chains 765 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 762 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 505 TYR Chi-restraints excluded: chain a residue 186 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 336 optimal weight: 0.8980 chunk 301 optimal weight: 9.9990 chunk 167 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 311 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 361 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN B 478 ASN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 ASN F 62 GLN F 78 ASN F 119 GLN ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS F 459 ASN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 170 ASN a 177 HIS b 169 ASN b 347 ASN c 106 ASN c 157 ASN c 189 ASN ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN e 54 GLN e 111 GLN e 116 GLN ** e 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 126 GLN f 215 ASN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 126 ASN h 162 ASN i 194 ASN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.124441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103657 restraints weight = 66998.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.106261 restraints weight = 32065.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107908 restraints weight = 19834.812| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32914 Z= 0.156 Angle : 0.713 27.608 44635 Z= 0.356 Chirality : 0.045 0.244 5062 Planarity : 0.005 0.076 5538 Dihedral : 6.741 58.007 4445 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.98 % Favored : 91.97 % Rotamer: Outliers : 2.40 % Allowed : 13.47 % Favored : 84.13 % 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: -2.57 (0.12), residues: 4011 helix: -0.59 (0.10), residues: 2173 sheet: -3.11 (0.25), residues: 322 loop : -2.98 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP h 80 HIS 0.012 0.001 HIS a 309 PHE 0.033 0.002 PHE f 118 TYR 0.023 0.002 TYR b 271 ARG 0.008 0.001 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 1681) hydrogen bonds : angle 4.98409 ( 4944) metal coordination : bond 0.01242 ( 4) metal coordination : angle 16.18984 ( 6) covalent geometry : bond 0.00352 (32910) covalent geometry : angle 0.68740 (44629) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 879 time to evaluate : 3.727 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: A 49 TRP cc_start: 0.6285 (t60) cc_final: 0.5930 (t60) REVERT: A 172 GLU cc_start: 0.8738 (tt0) cc_final: 0.8306 (tt0) REVERT: A 182 ILE cc_start: 0.8699 (mm) cc_final: 0.8488 (mm) REVERT: A 210 ARG cc_start: 0.7334 (mmm-85) cc_final: 0.6513 (mmt180) REVERT: A 270 PHE cc_start: 0.8717 (m-80) cc_final: 0.8308 (m-80) REVERT: A 338 TRP cc_start: 0.8333 (m100) cc_final: 0.7947 (m100) REVERT: B 128 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: B 182 LYS cc_start: 0.8797 (mttt) cc_final: 0.8149 (mtpp) REVERT: B 218 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8697 (mm) REVERT: B 351 MET cc_start: 0.8214 (tmm) cc_final: 0.7848 (ttt) REVERT: C 84 MET cc_start: 0.7751 (tpt) cc_final: 0.7138 (tpt) REVERT: C 99 ILE cc_start: 0.8362 (mt) cc_final: 0.8146 (mm) REVERT: D 76 TRP cc_start: 0.8378 (t60) cc_final: 0.7967 (t-100) REVERT: D 124 MET cc_start: 0.8838 (mmt) cc_final: 0.8269 (tpt) REVERT: D 128 TYR cc_start: 0.9120 (t80) cc_final: 0.8667 (t80) REVERT: D 150 GLU cc_start: 0.7246 (pp20) cc_final: 0.6653 (pp20) REVERT: D 503 TYR cc_start: 0.8710 (m-80) cc_final: 0.8474 (m-80) REVERT: E 1 MET cc_start: 0.7558 (tpt) cc_final: 0.7270 (tpt) REVERT: E 31 LEU cc_start: 0.9118 (tp) cc_final: 0.8807 (tp) REVERT: E 35 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7714 (mm-30) REVERT: E 56 GLN cc_start: 0.7020 (mp10) cc_final: 0.6756 (mp10) REVERT: E 78 LEU cc_start: 0.9097 (mt) cc_final: 0.8874 (mm) REVERT: F 21 LEU cc_start: 0.8776 (mm) cc_final: 0.8272 (mm) REVERT: F 46 PHE cc_start: 0.8524 (t80) cc_final: 0.8249 (t80) REVERT: F 321 TYR cc_start: 0.8917 (m-80) cc_final: 0.8534 (m-10) REVERT: F 329 TYR cc_start: 0.8002 (m-80) cc_final: 0.7782 (m-80) REVERT: F 340 ARG cc_start: 0.8216 (tpt170) cc_final: 0.7764 (ptm-80) REVERT: F 466 SER cc_start: 0.8928 (t) cc_final: 0.8435 (t) REVERT: F 619 ILE cc_start: 0.9308 (mm) cc_final: 0.8968 (mm) REVERT: G 41 PHE cc_start: 0.8009 (t80) cc_final: 0.7513 (t80) REVERT: G 50 TYR cc_start: 0.8517 (m-10) cc_final: 0.8244 (m-10) REVERT: G 56 HIS cc_start: 0.7898 (m-70) cc_final: 0.7386 (m-70) REVERT: G 152 PHE cc_start: 0.8338 (m-80) cc_final: 0.7917 (m-10) REVERT: a 200 LEU cc_start: 0.9286 (mt) cc_final: 0.8967 (mt) REVERT: a 237 MET cc_start: 0.7873 (mtt) cc_final: 0.7544 (mtt) REVERT: b 206 ASN cc_start: 0.8891 (t0) cc_final: 0.8514 (t0) REVERT: c 91 ARG cc_start: 0.7780 (ttt90) cc_final: 0.7470 (ttm-80) REVERT: c 115 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8393 (mmtm) REVERT: d 71 ILE cc_start: 0.8490 (mt) cc_final: 0.8192 (mt) REVERT: e 160 ASP cc_start: 0.8034 (t0) cc_final: 0.7302 (t0) REVERT: f 148 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8144 (tt0) REVERT: f 197 PHE cc_start: 0.7919 (t80) cc_final: 0.7574 (t80) REVERT: g 81 MET cc_start: 0.7841 (mtt) cc_final: 0.7515 (mtm) REVERT: g 160 ASP cc_start: 0.8281 (t70) cc_final: 0.7760 (t0) REVERT: g 172 TYR cc_start: 0.8489 (t80) cc_final: 0.8273 (t80) REVERT: g 176 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7550 (mm-30) REVERT: h 97 GLU cc_start: 0.6584 (tt0) cc_final: 0.6159 (tt0) REVERT: h 120 MET cc_start: 0.7574 (ttp) cc_final: 0.7213 (ttt) REVERT: h 134 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7569 (mm-30) REVERT: i 84 ASP cc_start: 0.7365 (m-30) cc_final: 0.7119 (m-30) REVERT: j 116 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8294 (mm-40) REVERT: j 151 ASP cc_start: 0.7405 (p0) cc_final: 0.7061 (p0) REVERT: j 156 ASN cc_start: 0.8721 (p0) cc_final: 0.8327 (p0) outliers start: 83 outliers final: 48 residues processed: 923 average time/residue: 0.4219 time to fit residues: 637.0691 Evaluate side-chains 800 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 750 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 265 TYR Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 9 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain a residue 162 LEU Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 204 CYS Chi-restraints excluded: chain b residue 347 ASN Chi-restraints excluded: chain c residue 93 ASN Chi-restraints excluded: chain d residue 125 ASP Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 157 HIS Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 146 LEU Chi-restraints excluded: chain h residue 79 PHE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 117 ILE Chi-restraints excluded: chain i residue 189 PHE Chi-restraints excluded: chain i residue 194 ASN Chi-restraints excluded: chain j residue 101 LEU Chi-restraints excluded: chain j residue 106 VAL Chi-restraints excluded: chain j residue 137 THR Chi-restraints excluded: chain j residue 226 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 21 optimal weight: 10.0000 chunk 159 optimal weight: 0.5980 chunk 84 optimal weight: 0.1980 chunk 76 optimal weight: 6.9990 chunk 119 optimal weight: 0.4980 chunk 271 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 364 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 349 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN E 44 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN F 182 ASN ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 ASN ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 170 ASN b 347 ASN c 106 ASN c 157 ASN d 82 HIS e 54 GLN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.125121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.104151 restraints weight = 67187.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106828 restraints weight = 31443.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.108548 restraints weight = 19134.299| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32914 Z= 0.139 Angle : 0.682 25.140 44635 Z= 0.339 Chirality : 0.045 0.258 5062 Planarity : 0.005 0.070 5538 Dihedral : 6.362 59.118 4441 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.90 % Favored : 92.07 % Rotamer: Outliers : 2.98 % Allowed : 16.33 % Favored : 80.69 % 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: -1.96 (0.13), residues: 4011 helix: -0.04 (0.11), residues: 2189 sheet: -2.94 (0.26), residues: 320 loop : -2.81 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP h 80 HIS 0.008 0.001 HIS B 250 PHE 0.028 0.001 PHE E 45 TYR 0.026 0.002 TYR a 160 ARG 0.007 0.001 ARG b 257 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 1681) hydrogen bonds : angle 4.70843 ( 4944) metal coordination : bond 0.01364 ( 4) metal coordination : angle 14.36337 ( 6) covalent geometry : bond 0.00315 (32910) covalent geometry : angle 0.66107 (44629) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 851 time to evaluate : 3.836 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: A 49 TRP cc_start: 0.6212 (t60) cc_final: 0.5857 (t60) REVERT: A 156 TYR cc_start: 0.7488 (t80) cc_final: 0.6738 (t80) REVERT: A 172 GLU cc_start: 0.8728 (tt0) cc_final: 0.8438 (tt0) REVERT: A 210 ARG cc_start: 0.7528 (mmm-85) cc_final: 0.6797 (mmt180) REVERT: A 223 LEU cc_start: 0.6902 (mp) cc_final: 0.6576 (mp) REVERT: A 338 TRP cc_start: 0.8328 (m100) cc_final: 0.8003 (m100) REVERT: B 128 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: B 182 LYS cc_start: 0.8820 (mttt) cc_final: 0.8137 (mtpp) REVERT: C 84 MET cc_start: 0.7719 (tpt) cc_final: 0.7126 (tpt) REVERT: D 76 TRP cc_start: 0.8335 (t60) cc_final: 0.7960 (t-100) REVERT: D 124 MET cc_start: 0.8824 (mmt) cc_final: 0.8262 (tpt) REVERT: D 150 GLU cc_start: 0.7124 (pp20) cc_final: 0.6871 (pp20) REVERT: D 364 LEU cc_start: 0.8185 (mt) cc_final: 0.7982 (mt) REVERT: D 503 TYR cc_start: 0.8638 (m-80) cc_final: 0.8427 (m-80) REVERT: E 1 MET cc_start: 0.7402 (tpt) cc_final: 0.7030 (tpt) REVERT: E 31 LEU cc_start: 0.9088 (tp) cc_final: 0.8785 (tp) REVERT: F 21 LEU cc_start: 0.8795 (mm) cc_final: 0.8274 (mm) REVERT: F 39 MET cc_start: 0.7585 (tpt) cc_final: 0.6918 (tpp) REVERT: F 46 PHE cc_start: 0.8512 (t80) cc_final: 0.8292 (t80) REVERT: F 299 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8495 (tp) REVERT: F 340 ARG cc_start: 0.8186 (tpt170) cc_final: 0.7781 (ptm-80) REVERT: F 619 ILE cc_start: 0.9378 (mm) cc_final: 0.9163 (mm) REVERT: G 41 PHE cc_start: 0.8067 (t80) cc_final: 0.7792 (t80) REVERT: G 56 HIS cc_start: 0.7905 (m-70) cc_final: 0.7364 (m-70) REVERT: G 66 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.6731 (t80) REVERT: G 81 MET cc_start: 0.7827 (ppp) cc_final: 0.7580 (ppp) REVERT: G 152 PHE cc_start: 0.8302 (m-80) cc_final: 0.7860 (m-10) REVERT: a 147 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7829 (mm-40) REVERT: b 206 ASN cc_start: 0.8850 (t0) cc_final: 0.8500 (t0) REVERT: c 115 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8262 (mmtm) REVERT: c 178 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8547 (tm-30) REVERT: d 71 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8267 (mt) REVERT: e 160 ASP cc_start: 0.7855 (t0) cc_final: 0.7257 (t0) REVERT: f 148 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8136 (tt0) REVERT: f 197 PHE cc_start: 0.7834 (t80) cc_final: 0.7572 (t80) REVERT: g 154 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7386 (tm-30) REVERT: g 160 ASP cc_start: 0.8297 (t70) cc_final: 0.7675 (t0) REVERT: g 172 TYR cc_start: 0.8532 (t80) cc_final: 0.8303 (t80) REVERT: g 176 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7570 (mm-30) REVERT: h 97 GLU cc_start: 0.6616 (tt0) cc_final: 0.6317 (tt0) REVERT: h 120 MET cc_start: 0.7615 (ttp) cc_final: 0.7365 (ttt) REVERT: h 158 TYR cc_start: 0.8322 (m-80) cc_final: 0.8065 (m-80) REVERT: i 178 LYS cc_start: 0.8845 (ttpp) cc_final: 0.8558 (ttpp) REVERT: j 87 LYS cc_start: 0.8215 (mttt) cc_final: 0.7806 (mttt) REVERT: j 151 ASP cc_start: 0.7422 (p0) cc_final: 0.7155 (p0) REVERT: j 156 ASN cc_start: 0.8708 (p0) cc_final: 0.8330 (p0) outliers start: 103 outliers final: 54 residues processed: 906 average time/residue: 0.4112 time to fit residues: 610.6590 Evaluate side-chains 802 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 744 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 162 LEU Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 285 ARG Chi-restraints excluded: chain c residue 93 ASN Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 103 CYS Chi-restraints excluded: chain d residue 125 ASP Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 157 HIS Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain g residue 111 SER Chi-restraints excluded: chain h residue 79 PHE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 189 PHE Chi-restraints excluded: chain j residue 101 LEU Chi-restraints excluded: chain j residue 106 VAL Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 196 GLN Chi-restraints excluded: chain j residue 226 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 207 optimal weight: 8.9990 chunk 318 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 321 optimal weight: 0.7980 chunk 306 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 380 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 323 optimal weight: 8.9990 chunk 257 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 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 280 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 465 HIS ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 663 ASN ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 170 ASN c 157 ASN e 54 GLN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 194 ASN ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.123776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.102720 restraints weight = 67191.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105350 restraints weight = 31597.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107003 restraints weight = 19296.729| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32914 Z= 0.155 Angle : 0.686 26.076 44635 Z= 0.340 Chirality : 0.045 0.262 5062 Planarity : 0.005 0.070 5538 Dihedral : 6.197 58.770 4439 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.98 % Favored : 92.00 % Rotamer: Outliers : 3.64 % Allowed : 18.94 % Favored : 77.42 % 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: -1.62 (0.13), residues: 4011 helix: 0.26 (0.11), residues: 2189 sheet: -2.85 (0.26), residues: 325 loop : -2.69 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP h 80 HIS 0.007 0.001 HIS D 344 PHE 0.035 0.001 PHE f 118 TYR 0.024 0.002 TYR F 148 ARG 0.005 0.000 ARG b 172 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 1681) hydrogen bonds : angle 4.61127 ( 4944) metal coordination : bond 0.01508 ( 4) metal coordination : angle 14.69805 ( 6) covalent geometry : bond 0.00357 (32910) covalent geometry : angle 0.66489 (44629) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 813 time to evaluate : 3.981 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: A 49 TRP cc_start: 0.6256 (t60) cc_final: 0.5828 (t60) REVERT: A 156 TYR cc_start: 0.7464 (t80) cc_final: 0.6819 (t80) REVERT: A 172 GLU cc_start: 0.8765 (tt0) cc_final: 0.8500 (tt0) REVERT: A 210 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.6845 (mmt180) REVERT: A 275 TYR cc_start: 0.7158 (m-80) cc_final: 0.6928 (m-80) REVERT: A 305 PHE cc_start: 0.8251 (m-10) cc_final: 0.7985 (m-10) REVERT: B 128 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7340 (pm20) REVERT: B 182 LYS cc_start: 0.8863 (mttt) cc_final: 0.8173 (mtpp) REVERT: B 321 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8458 (mtpt) REVERT: C 84 MET cc_start: 0.7649 (tpt) cc_final: 0.7110 (tpt) REVERT: D 76 TRP cc_start: 0.8323 (t60) cc_final: 0.7977 (t-100) REVERT: D 124 MET cc_start: 0.8842 (mmt) cc_final: 0.8378 (tpt) REVERT: D 128 TYR cc_start: 0.9093 (t80) cc_final: 0.8882 (t80) REVERT: D 364 LEU cc_start: 0.8216 (mt) cc_final: 0.7993 (mt) REVERT: D 503 TYR cc_start: 0.8623 (m-80) cc_final: 0.8419 (m-80) REVERT: E 1 MET cc_start: 0.7337 (tpt) cc_final: 0.6924 (tpt) REVERT: E 35 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7731 (mm-30) REVERT: F 21 LEU cc_start: 0.8848 (mm) cc_final: 0.8314 (mm) REVERT: F 27 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8269 (tt) REVERT: F 39 MET cc_start: 0.7602 (tpt) cc_final: 0.7013 (tpp) REVERT: F 340 ARG cc_start: 0.8165 (tpt170) cc_final: 0.7762 (ptm-80) REVERT: F 619 ILE cc_start: 0.9368 (mm) cc_final: 0.9162 (mm) REVERT: G 41 PHE cc_start: 0.8145 (t80) cc_final: 0.7689 (t80) REVERT: G 50 TYR cc_start: 0.8512 (m-10) cc_final: 0.8269 (m-10) REVERT: G 56 HIS cc_start: 0.7908 (m-70) cc_final: 0.7492 (m-70) REVERT: G 66 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.6942 (t80) REVERT: G 152 PHE cc_start: 0.8362 (m-80) cc_final: 0.7950 (m-10) REVERT: a 147 GLN cc_start: 0.8145 (mm-40) cc_final: 0.7885 (mm-40) REVERT: a 246 ASN cc_start: 0.7662 (m-40) cc_final: 0.7197 (t0) REVERT: c 115 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8307 (mmtm) REVERT: c 178 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8630 (tm-30) REVERT: d 71 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8367 (mt) REVERT: d 107 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8551 (mm) REVERT: e 160 ASP cc_start: 0.7825 (t0) cc_final: 0.7228 (t0) REVERT: f 148 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8068 (tt0) REVERT: f 197 PHE cc_start: 0.7953 (t80) cc_final: 0.7697 (t80) REVERT: g 141 ARG cc_start: 0.7926 (mmp80) cc_final: 0.7681 (mmp80) REVERT: g 154 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7387 (tm-30) REVERT: g 160 ASP cc_start: 0.8282 (t70) cc_final: 0.7709 (t0) REVERT: h 97 GLU cc_start: 0.6624 (tt0) cc_final: 0.6378 (tt0) REVERT: h 158 TYR cc_start: 0.8359 (m-80) cc_final: 0.8073 (m-80) REVERT: i 178 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8476 (ttpp) REVERT: i 217 ARG cc_start: 0.8128 (tpt90) cc_final: 0.7824 (tpt-90) REVERT: j 151 ASP cc_start: 0.7479 (p0) cc_final: 0.7183 (p0) REVERT: j 156 ASN cc_start: 0.8693 (p0) cc_final: 0.8316 (p0) outliers start: 126 outliers final: 85 residues processed: 887 average time/residue: 0.4179 time to fit residues: 609.1915 Evaluate side-chains 829 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 739 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 465 HIS Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 575 PHE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 201 SER Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 378 LEU Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 204 CYS Chi-restraints excluded: chain b residue 213 PHE Chi-restraints excluded: chain c residue 93 ASN Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 82 HIS Chi-restraints excluded: chain d residue 103 CYS Chi-restraints excluded: chain d residue 107 LEU Chi-restraints excluded: chain d residue 125 ASP Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 157 HIS Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain f residue 122 TYR Chi-restraints excluded: chain f residue 132 PHE Chi-restraints excluded: chain f residue 192 TYR Chi-restraints excluded: chain g residue 111 SER Chi-restraints excluded: chain g residue 162 TYR Chi-restraints excluded: chain h residue 79 PHE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 201 THR Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 117 ILE Chi-restraints excluded: chain i residue 189 PHE Chi-restraints excluded: chain j residue 101 LEU Chi-restraints excluded: chain j residue 106 VAL Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 137 THR Chi-restraints excluded: chain j residue 196 GLN Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 226 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 205 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 386 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 357 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 HIS D 271 ASN ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 170 ASN a 248 ASN b 49 ASN c 157 ASN ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 HIS f 141 HIS ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.122850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.101699 restraints weight = 67277.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.104289 restraints weight = 31781.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.105921 restraints weight = 19540.223| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32914 Z= 0.168 Angle : 0.697 26.517 44635 Z= 0.346 Chirality : 0.046 0.274 5062 Planarity : 0.005 0.072 5538 Dihedral : 6.127 59.909 4439 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.08 % Favored : 91.90 % Rotamer: Outliers : 4.13 % Allowed : 20.15 % Favored : 75.72 % 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: -1.50 (0.13), residues: 4011 helix: 0.38 (0.11), residues: 2190 sheet: -2.87 (0.26), residues: 331 loop : -2.66 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP h 80 HIS 0.015 0.001 HIS B 465 PHE 0.028 0.001 PHE D 82 TYR 0.023 0.002 TYR g 172 ARG 0.007 0.000 ARG j 122 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 1681) hydrogen bonds : angle 4.58064 ( 4944) metal coordination : bond 0.01632 ( 4) metal coordination : angle 14.80397 ( 6) covalent geometry : bond 0.00390 (32910) covalent geometry : angle 0.67599 (44629) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 787 time to evaluate : 3.744 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: A 49 TRP cc_start: 0.6331 (t60) cc_final: 0.5830 (t60) REVERT: A 156 TYR cc_start: 0.7477 (t80) cc_final: 0.6911 (t80) REVERT: A 163 ARG cc_start: 0.7305 (ttm110) cc_final: 0.6411 (ttp-170) REVERT: A 174 PRO cc_start: 0.9172 (Cg_exo) cc_final: 0.8968 (Cg_endo) REVERT: A 198 GLN cc_start: 0.8073 (mt0) cc_final: 0.7818 (mt0) REVERT: A 210 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.6928 (mmt180) REVERT: A 305 PHE cc_start: 0.8236 (m-10) cc_final: 0.7952 (m-10) REVERT: B 128 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: B 182 LYS cc_start: 0.8846 (mttt) cc_final: 0.8194 (mtpp) REVERT: B 321 LYS cc_start: 0.8744 (mtpt) cc_final: 0.8423 (mtpt) REVERT: C 84 MET cc_start: 0.7675 (tpt) cc_final: 0.7167 (tpt) REVERT: D 76 TRP cc_start: 0.8462 (t60) cc_final: 0.8112 (t-100) REVERT: D 124 MET cc_start: 0.8822 (mmt) cc_final: 0.8394 (tpt) REVERT: D 364 LEU cc_start: 0.8266 (mt) cc_final: 0.8033 (mt) REVERT: D 503 TYR cc_start: 0.8648 (m-80) cc_final: 0.8426 (m-80) REVERT: F 39 MET cc_start: 0.7655 (tpt) cc_final: 0.7087 (tpp) REVERT: F 46 PHE cc_start: 0.8560 (t80) cc_final: 0.8321 (t80) REVERT: F 340 ARG cc_start: 0.8221 (tpt170) cc_final: 0.7801 (ptm-80) REVERT: G 50 TYR cc_start: 0.8559 (m-10) cc_final: 0.8358 (m-10) REVERT: G 66 TYR cc_start: 0.7709 (OUTLIER) cc_final: 0.6928 (t80) REVERT: G 152 PHE cc_start: 0.8392 (m-80) cc_final: 0.7960 (m-10) REVERT: a 147 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7805 (mm-40) REVERT: a 246 ASN cc_start: 0.7625 (m-40) cc_final: 0.7157 (t0) REVERT: b 299 MET cc_start: 0.7391 (mtp) cc_final: 0.6661 (mtp) REVERT: c 115 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8350 (mmtm) REVERT: d 71 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8409 (mt) REVERT: e 116 GLN cc_start: 0.7812 (tm130) cc_final: 0.7608 (tm-30) REVERT: e 160 ASP cc_start: 0.7887 (t0) cc_final: 0.7382 (t0) REVERT: f 91 PHE cc_start: 0.8234 (t80) cc_final: 0.8006 (t80) REVERT: f 148 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8021 (tt0) REVERT: f 197 PHE cc_start: 0.8037 (t80) cc_final: 0.7803 (t80) REVERT: f 229 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8383 (t) REVERT: g 141 ARG cc_start: 0.7895 (mmp80) cc_final: 0.7649 (mmp80) REVERT: g 160 ASP cc_start: 0.8287 (t70) cc_final: 0.7714 (t0) REVERT: g 172 TYR cc_start: 0.8555 (t80) cc_final: 0.8157 (t80) REVERT: g 176 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7501 (mm-30) REVERT: h 97 GLU cc_start: 0.6660 (tt0) cc_final: 0.6382 (tt0) REVERT: h 134 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7339 (mm-30) REVERT: i 178 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8482 (ttpp) REVERT: i 217 ARG cc_start: 0.8111 (tpt90) cc_final: 0.7839 (tpt-90) REVERT: j 114 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7749 (m) REVERT: j 151 ASP cc_start: 0.7590 (p0) cc_final: 0.7324 (p0) REVERT: j 156 ASN cc_start: 0.8729 (p0) cc_final: 0.8335 (p0) outliers start: 143 outliers final: 96 residues processed: 863 average time/residue: 0.4066 time to fit residues: 576.0677 Evaluate side-chains 834 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 733 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 575 PHE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 162 LEU Chi-restraints excluded: chain a residue 201 SER Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain b residue 49 ASN Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 204 CYS Chi-restraints excluded: chain b residue 213 PHE Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 93 ASN Chi-restraints excluded: chain c residue 103 LEU Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 82 HIS Chi-restraints excluded: chain d residue 103 CYS Chi-restraints excluded: chain d residue 125 ASP Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 157 HIS Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 86 HIS Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 199 VAL Chi-restraints excluded: chain f residue 122 TYR Chi-restraints excluded: chain f residue 132 PHE Chi-restraints excluded: chain f residue 192 TYR Chi-restraints excluded: chain f residue 229 VAL Chi-restraints excluded: chain g residue 111 SER Chi-restraints excluded: chain g residue 162 TYR Chi-restraints excluded: chain h residue 79 PHE Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 201 THR Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 117 ILE Chi-restraints excluded: chain i residue 167 VAL Chi-restraints excluded: chain j residue 101 LEU Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 196 GLN Chi-restraints excluded: chain j residue 218 ILE Chi-restraints excluded: chain j residue 226 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 311 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 chunk 70 optimal weight: 0.0170 chunk 392 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 198 optimal weight: 0.6980 chunk 281 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 196 GLN ** 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 = 0.3691 r_free = 0.3691 target = 0.124384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103535 restraints weight = 67707.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.106083 restraints weight = 32356.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107704 restraints weight = 20157.163| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32914 Z= 0.139 Angle : 0.681 25.002 44635 Z= 0.339 Chirality : 0.045 0.273 5062 Planarity : 0.005 0.072 5538 Dihedral : 5.982 59.034 4439 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.88 % Favored : 92.10 % Rotamer: Outliers : 3.56 % Allowed : 21.86 % Favored : 74.59 % 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 (0.13), residues: 4011 helix: 0.54 (0.11), residues: 2181 sheet: -2.71 (0.26), residues: 328 loop : -2.59 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP h 80 HIS 0.035 0.001 HIS e 86 PHE 0.032 0.001 PHE e 147 TYR 0.032 0.002 TYR f 102 ARG 0.015 0.000 ARG G 175 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 1681) hydrogen bonds : angle 4.50920 ( 4944) metal coordination : bond 0.01340 ( 4) metal coordination : angle 13.98567 ( 6) covalent geometry : bond 0.00317 (32910) covalent geometry : angle 0.66194 (44629) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 825 time to evaluate : 3.471 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: A 49 TRP cc_start: 0.6301 (t60) cc_final: 0.5782 (t60) REVERT: A 156 TYR cc_start: 0.7372 (t80) cc_final: 0.6873 (t80) REVERT: A 198 GLN cc_start: 0.8051 (mt0) cc_final: 0.7760 (mt0) REVERT: A 210 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.6947 (mmt180) REVERT: A 252 LYS cc_start: 0.6013 (mmtt) cc_final: 0.5708 (mtmm) REVERT: A 275 TYR cc_start: 0.7304 (m-80) cc_final: 0.6752 (m-80) REVERT: A 305 PHE cc_start: 0.8190 (m-10) cc_final: 0.7900 (m-10) REVERT: B 128 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7304 (pm20) REVERT: B 134 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9119 (mm) REVERT: B 182 LYS cc_start: 0.8841 (mttt) cc_final: 0.8196 (mtpp) REVERT: C 84 MET cc_start: 0.7731 (tpt) cc_final: 0.7180 (tpt) REVERT: D 76 TRP cc_start: 0.8339 (t60) cc_final: 0.7998 (t-100) REVERT: D 124 MET cc_start: 0.8761 (mmt) cc_final: 0.8393 (tpt) REVERT: D 156 LEU cc_start: 0.9071 (mt) cc_final: 0.8788 (mt) REVERT: D 364 LEU cc_start: 0.8132 (mt) cc_final: 0.7873 (mt) REVERT: D 503 TYR cc_start: 0.8558 (m-80) cc_final: 0.8332 (m-80) REVERT: F 39 MET cc_start: 0.7567 (tpt) cc_final: 0.6925 (tpp) REVERT: F 299 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8559 (tp) REVERT: F 340 ARG cc_start: 0.8185 (tpt170) cc_final: 0.7755 (ptm-80) REVERT: G 41 PHE cc_start: 0.8092 (t80) cc_final: 0.7855 (t80) REVERT: G 50 TYR cc_start: 0.8619 (m-10) cc_final: 0.8347 (m-10) REVERT: G 66 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7125 (t80) REVERT: G 117 ASP cc_start: 0.7445 (t0) cc_final: 0.7048 (t0) REVERT: G 152 PHE cc_start: 0.8276 (m-80) cc_final: 0.7827 (m-10) REVERT: a 246 ASN cc_start: 0.7424 (m-40) cc_final: 0.7013 (t0) REVERT: c 115 LYS cc_start: 0.8643 (mmmm) cc_final: 0.8217 (mmtm) REVERT: c 178 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8580 (tm-30) REVERT: e 160 ASP cc_start: 0.7791 (t0) cc_final: 0.7304 (t0) REVERT: f 148 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7865 (tt0) REVERT: f 197 PHE cc_start: 0.7941 (t80) cc_final: 0.7703 (t80) REVERT: g 141 ARG cc_start: 0.7779 (mmp80) cc_final: 0.7575 (mmp80) REVERT: g 160 ASP cc_start: 0.8341 (t70) cc_final: 0.7709 (t0) REVERT: h 158 TYR cc_start: 0.8322 (m-80) cc_final: 0.8110 (m-80) REVERT: i 178 LYS cc_start: 0.8842 (ttpp) cc_final: 0.8630 (ttpp) REVERT: i 217 ARG cc_start: 0.8110 (tpt90) cc_final: 0.7855 (tpt-90) REVERT: j 114 VAL cc_start: 0.8034 (OUTLIER) cc_final: 0.7784 (m) REVERT: j 151 ASP cc_start: 0.7549 (p0) cc_final: 0.7301 (p0) REVERT: j 156 ASN cc_start: 0.8680 (p0) cc_final: 0.8294 (p0) outliers start: 123 outliers final: 90 residues processed: 892 average time/residue: 0.4162 time to fit residues: 609.6277 Evaluate side-chains 840 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 745 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 575 PHE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 162 LEU Chi-restraints excluded: chain a residue 201 SER Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain b residue 48 ASN Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 131 SER Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 204 CYS Chi-restraints excluded: chain b residue 213 PHE Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 93 ASN Chi-restraints excluded: chain c residue 133 ILE Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 82 HIS Chi-restraints excluded: chain d residue 103 CYS Chi-restraints excluded: chain d residue 125 ASP Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 157 HIS Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 68 GLU Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 199 VAL Chi-restraints excluded: chain f residue 99 SER Chi-restraints excluded: chain f residue 122 TYR Chi-restraints excluded: chain f residue 132 PHE Chi-restraints excluded: chain f residue 192 TYR Chi-restraints excluded: chain g residue 111 SER Chi-restraints excluded: chain g residue 162 TYR Chi-restraints excluded: chain g residue 182 ILE Chi-restraints excluded: chain h residue 79 PHE Chi-restraints excluded: chain h residue 135 ASP Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 167 VAL Chi-restraints excluded: chain j residue 114 VAL Chi-restraints excluded: chain j residue 137 THR Chi-restraints excluded: chain j residue 196 GLN Chi-restraints excluded: chain j residue 226 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 395 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 387 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 196 optimal weight: 6.9990 chunk 223 optimal weight: 0.0670 chunk 49 optimal weight: 0.8980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 HIS ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 158 GLN b 49 ASN ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.124648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103896 restraints weight = 67615.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.106455 restraints weight = 32375.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.108104 restraints weight = 20074.069| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 32914 Z= 0.142 Angle : 0.699 24.592 44635 Z= 0.345 Chirality : 0.045 0.275 5062 Planarity : 0.005 0.072 5538 Dihedral : 5.921 59.847 4439 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.80 % Favored : 92.17 % Rotamer: Outliers : 3.21 % Allowed : 23.33 % Favored : 73.46 % 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: -1.24 (0.13), residues: 4011 helix: 0.62 (0.11), residues: 2182 sheet: -2.68 (0.26), residues: 340 loop : -2.56 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP h 80 HIS 0.009 0.001 HIS D 344 PHE 0.036 0.001 PHE e 147 TYR 0.041 0.002 TYR f 102 ARG 0.007 0.000 ARG G 175 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 1681) hydrogen bonds : angle 4.49827 ( 4944) metal coordination : bond 0.01301 ( 4) metal coordination : angle 13.70465 ( 6) covalent geometry : bond 0.00328 (32910) covalent geometry : angle 0.68036 (44629) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 817 time to evaluate : 3.494 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: A 49 TRP cc_start: 0.6319 (t60) cc_final: 0.5706 (t60) REVERT: A 156 TYR cc_start: 0.7365 (t80) cc_final: 0.7028 (t80) REVERT: A 198 GLN cc_start: 0.8064 (mt0) cc_final: 0.7542 (mt0) REVERT: A 210 ARG cc_start: 0.7513 (mmm-85) cc_final: 0.6964 (mmt180) REVERT: A 252 LYS cc_start: 0.6046 (mmtt) cc_final: 0.5693 (mtmm) REVERT: A 305 PHE cc_start: 0.8181 (m-10) cc_final: 0.7877 (m-10) REVERT: B 128 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7315 (pm20) REVERT: B 134 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9089 (mm) REVERT: B 182 LYS cc_start: 0.8849 (mttt) cc_final: 0.8165 (mtpp) REVERT: B 211 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7184 (mp) REVERT: B 218 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8346 (mm) REVERT: B 405 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8236 (mp) REVERT: B 447 TYR cc_start: 0.7766 (m-80) cc_final: 0.7166 (m-10) REVERT: C 84 MET cc_start: 0.7744 (tpt) cc_final: 0.7222 (tpt) REVERT: D 76 TRP cc_start: 0.8337 (t60) cc_final: 0.8003 (t-100) REVERT: D 124 MET cc_start: 0.8754 (mmt) cc_final: 0.8392 (tpt) REVERT: D 156 LEU cc_start: 0.9067 (mt) cc_final: 0.8662 (mt) REVERT: D 503 TYR cc_start: 0.8534 (m-80) cc_final: 0.8290 (m-80) REVERT: E 56 GLN cc_start: 0.6732 (mp10) cc_final: 0.6510 (mp10) REVERT: F 39 MET cc_start: 0.7560 (tpt) cc_final: 0.7005 (tpp) REVERT: F 299 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8544 (tp) REVERT: F 340 ARG cc_start: 0.8147 (tpt170) cc_final: 0.7666 (ptm-80) REVERT: G 41 PHE cc_start: 0.7997 (t80) cc_final: 0.7777 (t80) REVERT: G 50 TYR cc_start: 0.8613 (m-10) cc_final: 0.8400 (m-10) REVERT: G 66 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.7133 (t80) REVERT: G 117 ASP cc_start: 0.7314 (t0) cc_final: 0.6961 (t0) REVERT: G 152 PHE cc_start: 0.8246 (m-80) cc_final: 0.7850 (m-10) REVERT: a 246 ASN cc_start: 0.7346 (m-40) cc_final: 0.6885 (t0) REVERT: c 115 LYS cc_start: 0.8647 (mmmm) cc_final: 0.8253 (mmtm) REVERT: c 178 GLN cc_start: 0.9083 (tm-30) cc_final: 0.8583 (tm-30) REVERT: e 160 ASP cc_start: 0.7738 (t0) cc_final: 0.7299 (t0) REVERT: f 148 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7820 (tt0) REVERT: f 197 PHE cc_start: 0.7966 (t80) cc_final: 0.7704 (t80) REVERT: g 160 ASP cc_start: 0.8353 (t70) cc_final: 0.7749 (t0) REVERT: g 172 TYR cc_start: 0.8364 (t80) cc_final: 0.7539 (t80) REVERT: g 176 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7379 (mm-30) REVERT: h 158 TYR cc_start: 0.8333 (m-80) cc_final: 0.8114 (m-80) REVERT: i 178 LYS cc_start: 0.8835 (ttpp) cc_final: 0.8467 (ttpp) REVERT: i 190 SER cc_start: 0.7862 (t) cc_final: 0.7606 (t) REVERT: i 217 ARG cc_start: 0.8120 (tpt90) cc_final: 0.7877 (tpt-90) REVERT: j 151 ASP cc_start: 0.7656 (p0) cc_final: 0.7341 (p0) REVERT: j 156 ASN cc_start: 0.8684 (p0) cc_final: 0.8305 (p0) outliers start: 111 outliers final: 83 residues processed: 879 average time/residue: 0.4102 time to fit residues: 590.0121 Evaluate side-chains 852 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 762 time to evaluate : 3.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 575 PHE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 162 LEU Chi-restraints excluded: chain a residue 201 SER Chi-restraints excluded: chain a residue 281 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain b residue 49 ASN Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 131 SER Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 93 ASN Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 82 HIS Chi-restraints excluded: chain d residue 103 CYS Chi-restraints excluded: chain d residue 125 ASP Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 157 HIS Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 199 VAL Chi-restraints excluded: chain f residue 122 TYR Chi-restraints excluded: chain f residue 132 PHE Chi-restraints excluded: chain f residue 192 TYR Chi-restraints excluded: chain g residue 111 SER Chi-restraints excluded: chain g residue 162 TYR Chi-restraints excluded: chain h residue 79 PHE Chi-restraints excluded: chain h residue 135 ASP Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 201 THR Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 167 VAL Chi-restraints excluded: chain j residue 101 LEU Chi-restraints excluded: chain j residue 106 VAL Chi-restraints excluded: chain j residue 137 THR Chi-restraints excluded: chain j residue 196 GLN Chi-restraints excluded: chain j residue 218 ILE Chi-restraints excluded: chain j residue 226 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 43 optimal weight: 0.7980 chunk 360 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 194 optimal weight: 30.0000 chunk 97 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 311 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 ASN ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 193 ASN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.123595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102661 restraints weight = 67679.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105242 restraints weight = 32855.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106831 restraints weight = 20514.105| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 32914 Z= 0.163 Angle : 0.722 25.682 44635 Z= 0.356 Chirality : 0.046 0.278 5062 Planarity : 0.005 0.073 5538 Dihedral : 5.961 59.553 4439 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.03 % Favored : 91.95 % Rotamer: Outliers : 3.67 % Allowed : 23.68 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 4011 helix: 0.58 (0.11), residues: 2189 sheet: -2.56 (0.26), residues: 340 loop : -2.57 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP h 80 HIS 0.010 0.001 HIS D 344 PHE 0.040 0.001 PHE e 147 TYR 0.036 0.002 TYR B 164 ARG 0.016 0.000 ARG G 175 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 1681) hydrogen bonds : angle 4.52819 ( 4944) metal coordination : bond 0.01457 ( 4) metal coordination : angle 14.33992 ( 6) covalent geometry : bond 0.00387 (32910) covalent geometry : angle 0.70284 (44629) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 782 time to evaluate : 3.871 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: A 49 TRP cc_start: 0.6368 (t60) cc_final: 0.5745 (t60) REVERT: A 156 TYR cc_start: 0.7287 (t80) cc_final: 0.6994 (t80) REVERT: A 181 SER cc_start: 0.8689 (t) cc_final: 0.8475 (p) REVERT: A 210 ARG cc_start: 0.7494 (mmm-85) cc_final: 0.6956 (mmt180) REVERT: A 305 PHE cc_start: 0.8222 (m-10) cc_final: 0.7917 (m-10) REVERT: B 128 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7348 (pm20) REVERT: B 134 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9114 (mm) REVERT: B 182 LYS cc_start: 0.8853 (mttt) cc_final: 0.8148 (mtpp) REVERT: B 218 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8416 (mm) REVERT: B 405 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8277 (mp) REVERT: B 447 TYR cc_start: 0.7802 (m-80) cc_final: 0.7350 (m-80) REVERT: C 84 MET cc_start: 0.7666 (tpt) cc_final: 0.7193 (tpt) REVERT: D 86 MET cc_start: 0.8659 (mmt) cc_final: 0.8428 (mmt) REVERT: D 124 MET cc_start: 0.8782 (mmt) cc_final: 0.8432 (tpt) REVERT: D 503 TYR cc_start: 0.8564 (m-80) cc_final: 0.8310 (m-80) REVERT: E 56 GLN cc_start: 0.6730 (mp10) cc_final: 0.6445 (mp10) REVERT: F 39 MET cc_start: 0.7602 (tpt) cc_final: 0.7026 (tpp) REVERT: F 299 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8543 (tp) REVERT: F 340 ARG cc_start: 0.8227 (tpt170) cc_final: 0.7714 (ptm-80) REVERT: G 50 TYR cc_start: 0.8609 (m-10) cc_final: 0.8305 (m-10) REVERT: G 66 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7093 (t80) REVERT: G 117 ASP cc_start: 0.7331 (t0) cc_final: 0.6993 (t0) REVERT: G 151 ASP cc_start: 0.7876 (t0) cc_final: 0.7608 (t70) REVERT: a 246 ASN cc_start: 0.7298 (m-40) cc_final: 0.6835 (t0) REVERT: c 115 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8166 (mmtm) REVERT: e 156 MET cc_start: 0.7255 (mmt) cc_final: 0.7007 (mmt) REVERT: e 160 ASP cc_start: 0.7783 (t0) cc_final: 0.7330 (t0) REVERT: f 148 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7818 (tt0) REVERT: f 197 PHE cc_start: 0.8039 (t80) cc_final: 0.7766 (t80) REVERT: g 160 ASP cc_start: 0.8370 (t70) cc_final: 0.7769 (t0) REVERT: i 178 LYS cc_start: 0.8836 (ttpp) cc_final: 0.8543 (ttpp) REVERT: i 190 SER cc_start: 0.7841 (t) cc_final: 0.7615 (t) REVERT: j 151 ASP cc_start: 0.7451 (p0) cc_final: 0.7208 (p0) REVERT: j 156 ASN cc_start: 0.8638 (p0) cc_final: 0.8245 (p0) outliers start: 127 outliers final: 96 residues processed: 852 average time/residue: 0.4136 time to fit residues: 578.8017 Evaluate side-chains 846 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 744 time to evaluate : 3.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 575 PHE Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 109 PHE Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 162 LEU Chi-restraints excluded: chain a residue 201 SER Chi-restraints excluded: chain a residue 281 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 407 ILE Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 331 VAL Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 93 ASN Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 82 HIS Chi-restraints excluded: chain d residue 103 CYS Chi-restraints excluded: chain d residue 125 ASP Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 157 HIS Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 112 THR Chi-restraints excluded: chain e residue 199 VAL Chi-restraints excluded: chain f residue 122 TYR Chi-restraints excluded: chain f residue 132 PHE Chi-restraints excluded: chain f residue 192 TYR Chi-restraints excluded: chain g residue 111 SER Chi-restraints excluded: chain g residue 162 TYR Chi-restraints excluded: chain g residue 182 ILE Chi-restraints excluded: chain h residue 79 PHE Chi-restraints excluded: chain h residue 120 MET Chi-restraints excluded: chain h residue 135 ASP Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 201 THR Chi-restraints excluded: chain i residue 82 VAL Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 167 VAL Chi-restraints excluded: chain i residue 189 PHE Chi-restraints excluded: chain j residue 101 LEU Chi-restraints excluded: chain j residue 106 VAL Chi-restraints excluded: chain j residue 137 THR Chi-restraints excluded: chain j residue 218 ILE Chi-restraints excluded: chain j residue 226 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 260 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 344 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 chunk 317 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 338 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 365 HIS G 62 GLN a 170 ASN a 259 GLN ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 HIS ** e 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 193 ASN f 215 ASN ** h 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095738 restraints weight = 68724.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098253 restraints weight = 33222.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099836 restraints weight = 20710.565| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 32914 Z= 0.268 Angle : 0.817 29.561 44635 Z= 0.404 Chirality : 0.050 0.316 5062 Planarity : 0.005 0.080 5538 Dihedral : 6.332 59.175 4439 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.87 % Allowed : 23.88 % Favored : 72.25 % 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: -1.41 (0.13), residues: 4011 helix: 0.39 (0.11), residues: 2196 sheet: -2.53 (0.27), residues: 330 loop : -2.60 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP h 80 HIS 0.011 0.001 HIS D 344 PHE 0.040 0.002 PHE j 145 TYR 0.038 0.002 TYR B 164 ARG 0.018 0.001 ARG G 175 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 1681) hydrogen bonds : angle 4.78663 ( 4944) metal coordination : bond 0.02116 ( 4) metal coordination : angle 16.77642 ( 6) covalent geometry : bond 0.00632 (32910) covalent geometry : angle 0.79310 (44629) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 771 time to evaluate : 3.770 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: A 49 TRP cc_start: 0.6386 (t60) cc_final: 0.5785 (t60) REVERT: A 156 TYR cc_start: 0.7386 (t80) cc_final: 0.6896 (t80) REVERT: A 210 ARG cc_start: 0.7697 (mmm-85) cc_final: 0.7186 (mmt180) REVERT: A 326 PRO cc_start: 0.6636 (Cg_exo) cc_final: 0.6342 (Cg_endo) REVERT: B 128 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: B 182 LYS cc_start: 0.8862 (mttt) cc_final: 0.8169 (mtpp) REVERT: B 213 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: B 218 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8627 (mm) REVERT: B 295 TRP cc_start: 0.8382 (t60) cc_final: 0.7792 (t60) REVERT: B 405 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8342 (mp) REVERT: B 447 TYR cc_start: 0.7985 (m-80) cc_final: 0.7768 (m-80) REVERT: B 448 LEU cc_start: 0.8740 (mm) cc_final: 0.8453 (mm) REVERT: C 84 MET cc_start: 0.7779 (tpt) cc_final: 0.7292 (tpt) REVERT: D 124 MET cc_start: 0.8842 (mmt) cc_final: 0.8499 (tpt) REVERT: D 503 TYR cc_start: 0.8692 (m-80) cc_final: 0.8475 (m-80) REVERT: E 56 GLN cc_start: 0.6868 (mp10) cc_final: 0.6661 (mp10) REVERT: F 340 ARG cc_start: 0.8390 (tpt170) cc_final: 0.7916 (ptm-80) REVERT: G 66 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7233 (t80) REVERT: G 117 ASP cc_start: 0.7602 (t0) cc_final: 0.7190 (t0) REVERT: a 147 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7938 (mm-40) REVERT: a 246 ASN cc_start: 0.7533 (m-40) cc_final: 0.7087 (t0) REVERT: a 248 ASN cc_start: 0.7728 (t0) cc_final: 0.7403 (t0) REVERT: b 341 MET cc_start: 0.8845 (tmm) cc_final: 0.8464 (tmm) REVERT: c 115 LYS cc_start: 0.8750 (mmmm) cc_final: 0.8230 (mmtm) REVERT: e 160 ASP cc_start: 0.8239 (t0) cc_final: 0.7812 (t70) REVERT: f 148 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7855 (tt0) REVERT: f 197 PHE cc_start: 0.8233 (t80) cc_final: 0.8004 (t80) REVERT: g 160 ASP cc_start: 0.8487 (t70) cc_final: 0.7898 (t0) REVERT: g 176 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7527 (mm-30) REVERT: i 178 LYS cc_start: 0.8881 (ttpp) cc_final: 0.8584 (ttpp) REVERT: j 151 ASP cc_start: 0.7838 (p0) cc_final: 0.7559 (p0) REVERT: j 156 ASN cc_start: 0.8803 (p0) cc_final: 0.8488 (p0) outliers start: 134 outliers final: 102 residues processed: 854 average time/residue: 0.4892 time to fit residues: 684.9839 Evaluate side-chains 830 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 723 time to evaluate : 5.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 369 GLU Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 468 LYS Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 575 PHE Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain F residue 694 ILE Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 162 LEU Chi-restraints excluded: chain a residue 201 SER Chi-restraints excluded: chain a residue 220 ASP Chi-restraints excluded: chain a residue 281 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 407 ILE Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 131 SER Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 204 CYS Chi-restraints excluded: chain b residue 331 VAL Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 93 ASN Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 103 CYS Chi-restraints excluded: chain d residue 125 ASP Chi-restraints excluded: chain d residue 144 LEU Chi-restraints excluded: chain d residue 157 HIS Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 86 HIS Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 199 VAL Chi-restraints excluded: chain f residue 122 TYR Chi-restraints excluded: chain f residue 132 PHE Chi-restraints excluded: chain f residue 192 TYR Chi-restraints excluded: chain g residue 107 LEU Chi-restraints excluded: chain g residue 111 SER Chi-restraints excluded: chain h residue 79 PHE Chi-restraints excluded: chain h residue 135 ASP Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 201 THR Chi-restraints excluded: chain i residue 82 VAL Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 117 ILE Chi-restraints excluded: chain i residue 167 VAL Chi-restraints excluded: chain i residue 189 PHE Chi-restraints excluded: chain j residue 101 LEU Chi-restraints excluded: chain j residue 106 VAL Chi-restraints excluded: chain j residue 218 ILE Chi-restraints excluded: chain j residue 226 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 31 optimal weight: 0.9990 chunk 283 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 228 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 157 optimal weight: 0.8980 chunk 167 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 193 ASN ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.121479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100140 restraints weight = 67720.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.102750 restraints weight = 32190.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.104348 restraints weight = 19837.547| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 32914 Z= 0.166 Angle : 0.773 26.935 44635 Z= 0.382 Chirality : 0.048 0.310 5062 Planarity : 0.005 0.083 5538 Dihedral : 6.176 57.111 4439 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.92 % Allowed : 25.61 % Favored : 71.47 % 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 (0.13), residues: 4011 helix: 0.49 (0.11), residues: 2193 sheet: -2.58 (0.27), residues: 342 loop : -2.60 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP h 80 HIS 0.011 0.001 HIS D 344 PHE 0.042 0.002 PHE G 41 TYR 0.039 0.002 TYR B 164 ARG 0.018 0.001 ARG G 175 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 1681) hydrogen bonds : angle 4.69491 ( 4944) metal coordination : bond 0.01352 ( 4) metal coordination : angle 14.79516 ( 6) covalent geometry : bond 0.00390 (32910) covalent geometry : angle 0.75365 (44629) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8022 Ramachandran restraints generated. 4011 Oldfield, 0 Emsley, 4011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 774 time to evaluate : 4.308 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: A 49 TRP cc_start: 0.6313 (t60) cc_final: 0.5694 (t60) REVERT: A 156 TYR cc_start: 0.7375 (t80) cc_final: 0.7106 (t80) REVERT: A 210 ARG cc_start: 0.7526 (mmm-85) cc_final: 0.7079 (mmt180) REVERT: A 305 PHE cc_start: 0.8395 (m-80) cc_final: 0.8073 (m-80) REVERT: B 128 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: B 182 LYS cc_start: 0.8854 (mttt) cc_final: 0.8167 (mtpp) REVERT: B 295 TRP cc_start: 0.8228 (t60) cc_final: 0.7639 (t60) REVERT: B 405 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8292 (mp) REVERT: B 447 TYR cc_start: 0.7870 (m-80) cc_final: 0.7535 (m-80) REVERT: D 63 MET cc_start: 0.7941 (ttm) cc_final: 0.7561 (mtp) REVERT: D 124 MET cc_start: 0.8739 (mmt) cc_final: 0.8421 (tpt) REVERT: D 503 TYR cc_start: 0.8639 (m-80) cc_final: 0.8375 (m-80) REVERT: E 56 GLN cc_start: 0.6814 (mp10) cc_final: 0.6516 (mp10) REVERT: F 39 MET cc_start: 0.7703 (tpt) cc_final: 0.7355 (tpp) REVERT: F 49 SER cc_start: 0.9095 (m) cc_final: 0.8676 (p) REVERT: F 299 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8804 (tp) REVERT: F 340 ARG cc_start: 0.8286 (tpt170) cc_final: 0.7799 (ptm-80) REVERT: G 66 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7267 (t80) REVERT: G 117 ASP cc_start: 0.7466 (t0) cc_final: 0.7100 (t0) REVERT: G 151 ASP cc_start: 0.7840 (t0) cc_final: 0.7413 (t0) REVERT: G 152 PHE cc_start: 0.8377 (m-80) cc_final: 0.8102 (m-10) REVERT: a 246 ASN cc_start: 0.7449 (m-40) cc_final: 0.6791 (t0) REVERT: a 248 ASN cc_start: 0.7612 (t0) cc_final: 0.7251 (t0) REVERT: b 206 ASN cc_start: 0.8861 (t0) cc_final: 0.8494 (m-40) REVERT: c 115 LYS cc_start: 0.8566 (mmmm) cc_final: 0.8140 (mmtm) REVERT: e 160 ASP cc_start: 0.8099 (t0) cc_final: 0.7567 (t70) REVERT: f 148 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7818 (tt0) REVERT: f 197 PHE cc_start: 0.8097 (t80) cc_final: 0.7853 (t80) REVERT: g 129 ASP cc_start: 0.7668 (t0) cc_final: 0.7458 (t0) REVERT: g 160 ASP cc_start: 0.8385 (t70) cc_final: 0.7830 (t0) REVERT: i 178 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8487 (ttpp) REVERT: j 146 MET cc_start: 0.7199 (ptp) cc_final: 0.6740 (ptp) REVERT: j 151 ASP cc_start: 0.7814 (p0) cc_final: 0.7533 (p0) REVERT: j 156 ASN cc_start: 0.8742 (p0) cc_final: 0.8382 (p0) outliers start: 101 outliers final: 85 residues processed: 834 average time/residue: 0.4653 time to fit residues: 639.7750 Evaluate side-chains 823 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 734 time to evaluate : 5.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 393 PHE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 380 ILE Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 575 PHE Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain a residue 122 ILE Chi-restraints excluded: chain a residue 126 VAL Chi-restraints excluded: chain a residue 162 LEU Chi-restraints excluded: chain a residue 201 SER Chi-restraints excluded: chain a residue 281 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 407 ILE Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 131 SER Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 331 VAL Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 93 ASN Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 103 CYS Chi-restraints excluded: chain d residue 125 ASP Chi-restraints excluded: chain d residue 157 HIS Chi-restraints excluded: chain e residue 60 ASN Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain e residue 199 VAL Chi-restraints excluded: chain f residue 99 SER Chi-restraints excluded: chain f residue 122 TYR Chi-restraints excluded: chain f residue 132 PHE Chi-restraints excluded: chain f residue 192 TYR Chi-restraints excluded: chain g residue 111 SER Chi-restraints excluded: chain g residue 182 ILE Chi-restraints excluded: chain h residue 135 ASP Chi-restraints excluded: chain h residue 141 THR Chi-restraints excluded: chain h residue 185 ASN Chi-restraints excluded: chain h residue 201 THR Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 167 VAL Chi-restraints excluded: chain i residue 189 PHE Chi-restraints excluded: chain j residue 101 LEU Chi-restraints excluded: chain j residue 106 VAL Chi-restraints excluded: chain j residue 170 ASP Chi-restraints excluded: chain j residue 218 ILE Chi-restraints excluded: chain j residue 226 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 13 optimal weight: 10.0000 chunk 288 optimal weight: 0.0670 chunk 290 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 638 ASN ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 193 ASN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.121846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100751 restraints weight = 67967.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103350 restraints weight = 32195.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.104999 restraints weight = 19804.670| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 32914 Z= 0.166 Angle : 0.771 26.241 44635 Z= 0.382 Chirality : 0.048 0.285 5062 Planarity : 0.005 0.080 5538 Dihedral : 6.098 56.025 4439 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 2.95 % Allowed : 25.93 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4011 helix: 0.53 (0.11), residues: 2180 sheet: -2.49 (0.27), residues: 339 loop : -2.56 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP h 80 HIS 0.010 0.001 HIS D 344 PHE 0.047 0.002 PHE e 147 TYR 0.040 0.002 TYR B 164 ARG 0.018 0.001 ARG G 175 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 1681) hydrogen bonds : angle 4.67391 ( 4944) metal coordination : bond 0.01354 ( 4) metal coordination : angle 14.20547 ( 6) covalent geometry : bond 0.00392 (32910) covalent geometry : angle 0.75357 (44629) =============================================================================== Job complete usr+sys time: 13962.70 seconds wall clock time: 246 minutes 19.57 seconds (14779.57 seconds total)