Starting phenix.real_space_refine on Fri Mar 6 13:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wff_32464/03_2026/7wff_32464.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wff_32464/03_2026/7wff_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wff_32464/03_2026/7wff_32464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wff_32464/03_2026/7wff_32464.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wff_32464/03_2026/7wff_32464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wff_32464/03_2026/7wff_32464.map" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'PHE:plan': 1, 'ARG: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: {'ASN:plan1': 7, 'ARG:plan': 3, 'PHE:plan': 3, 'TYR:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} 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: 6.67, per 1000 atoms: 0.21 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: 2.62 Conformation dependent library (CDL) restraints added in 1.4 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: 0.95 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: 6.55 Time building geometry restraints manager: 3.48 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: 4.270 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: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.340 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.600 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.001 ARG G 175 TYR 0.038 0.002 TYR G 66 PHE 0.027 0.002 PHE F 149 TRP 0.033 0.002 TRP h 80 HIS 0.013 0.002 HIS F 265 Details of bonding type rmsd covalent geometry : bond 0.00637 (32910) covalent geometry : angle 0.94103 (44629) hydrogen bonds : bond 0.13822 ( 1681) hydrogen bonds : angle 6.66130 ( 4944) metal coordination : bond 0.06431 ( 4) metal coordination : angle 3.66977 ( 6) *********************** 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 : 1.104 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: 0.6622 (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: 0.8219 (mtpp) REVERT: B 300 GLU cc_start: 0.7134 (tt0) cc_final: 0.6824 (tt0) REVERT: B 351 MET cc_start: 0.8145 (tmm) cc_final: 0.7852 (ttt) REVERT: C 6 GLU cc_start: 0.6836 (tt0) cc_final: 0.6587 (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: 0.6574 (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: 0.8369 (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: 0.7230 (p) REVERT: E 42 ASN cc_start: 0.7721 (t0) cc_final: 0.6688 (t0) REVERT: E 50 ASP cc_start: 0.6935 (t0) cc_final: 0.6648 (t0) REVERT: E 56 GLN cc_start: 0.7146 (mp10) cc_final: 0.6646 (mp10) REVERT: E 78 LEU cc_start: 0.9070 (mt) cc_final: 0.8321 (mm) REVERT: F 21 LEU cc_start: 0.8641 (mm) cc_final: 0.8243 (mm) REVERT: F 240 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8429 (mmtm) REVERT: F 340 ARG cc_start: 0.8390 (tpt170) cc_final: 0.7968 (ptm-80) REVERT: F 344 PHE cc_start: 0.8750 (t80) cc_final: 0.8495 (t80) REVERT: F 381 MET cc_start: 0.8204 (ttp) cc_final: 0.7708 (ttp) REVERT: G 41 PHE cc_start: 0.8030 (t80) cc_final: 0.7496 (t80) REVERT: G 45 CYS cc_start: 0.8400 (m) cc_final: 0.8016 (m) REVERT: G 50 TYR cc_start: 0.8368 (m-10) cc_final: 0.8097 (m-10) REVERT: G 55 SER cc_start: 0.8108 (p) cc_final: 0.7830 (t) REVERT: G 152 PHE cc_start: 0.8326 (m-80) cc_final: 0.7945 (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: 0.7565 (t80) REVERT: b 206 ASN cc_start: 0.8799 (t0) cc_final: 0.8443 (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: 0.7203 (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: 0.8292 (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: 0.7690 (t70) REVERT: f 148 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8224 (tt0) REVERT: f 197 PHE cc_start: 0.8190 (t80) cc_final: 0.7890 (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: 0.6720 (tm-30) REVERT: g 160 ASP cc_start: 0.8318 (t70) cc_final: 0.7937 (t0) REVERT: g 172 TYR cc_start: 0.8489 (t80) cc_final: 0.8238 (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 116 GLN cc_start: 0.8419 (mm110) cc_final: 0.8193 (mm-40) REVERT: j 142 ILE cc_start: 0.8109 (mm) cc_final: 0.7831 (mm) REVERT: j 151 ASP cc_start: 0.7273 (p0) cc_final: 0.6951 (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: 0.1950 time to fit residues: 339.5680 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 : 1.108 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 196 HIS B 426 GLN B 459 ASN 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 62 GLN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.3654 r_free = 0.3654 target = 0.121878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100593 restraints weight = 67751.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103147 restraints weight = 32725.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104714 restraints weight = 20478.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.105539 restraints weight = 15407.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.106272 restraints weight = 13197.519| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32914 Z= 0.189 Angle : 0.735 27.637 44635 Z= 0.368 Chirality : 0.046 0.247 5062 Planarity : 0.005 0.074 5538 Dihedral : 6.833 58.882 4445 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.15 % Favored : 91.80 % Rotamer: Outliers : 2.43 % Allowed : 13.65 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.12), residues: 4011 helix: -0.68 (0.10), residues: 2181 sheet: -3.20 (0.24), residues: 328 loop : -2.97 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 88 TYR 0.023 0.002 TYR b 271 PHE 0.033 0.002 PHE f 118 TRP 0.024 0.002 TRP h 80 HIS 0.013 0.001 HIS a 309 Details of bonding type rmsd covalent geometry : bond 0.00432 (32910) covalent geometry : angle 0.71046 (44629) hydrogen bonds : bond 0.04481 ( 1681) hydrogen bonds : angle 5.07946 ( 4944) metal coordination : bond 0.01487 ( 4) metal coordination : angle 16.09980 ( 6) *********************** 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 936 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 852 time to evaluate : 1.101 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: 0.6149 (t60) cc_final: 0.5901 (t60) REVERT: A 163 ARG cc_start: 0.7265 (ttm110) cc_final: 0.6412 (ttp-170) REVERT: A 172 GLU cc_start: 0.8713 (tt0) cc_final: 0.8276 (tt0) REVERT: A 182 ILE cc_start: 0.8705 (mm) cc_final: 0.8502 (mm) REVERT: A 210 ARG cc_start: 0.7354 (mmm-85) cc_final: 0.6572 (mmt180) REVERT: A 338 TRP cc_start: 0.8330 (m100) cc_final: 0.7950 (m100) REVERT: B 128 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: B 182 LYS cc_start: 0.8791 (mttt) cc_final: 0.8136 (mtpp) REVERT: B 351 MET cc_start: 0.8277 (tmm) cc_final: 0.7877 (ttt) REVERT: C 84 MET cc_start: 0.7764 (tpt) cc_final: 0.7167 (tpt) REVERT: C 99 ILE cc_start: 0.8336 (mt) cc_final: 0.8130 (mm) REVERT: D 124 MET cc_start: 0.8824 (mmt) cc_final: 0.8334 (tpt) REVERT: D 128 TYR cc_start: 0.9154 (t80) cc_final: 0.8713 (t80) REVERT: D 150 GLU cc_start: 0.7255 (pp20) cc_final: 0.6665 (pp20) REVERT: D 503 TYR cc_start: 0.8806 (m-80) cc_final: 0.8596 (m-80) REVERT: E 31 LEU cc_start: 0.9120 (tp) cc_final: 0.8843 (tp) REVERT: E 35 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7791 (mm-30) REVERT: E 42 ASN cc_start: 0.8254 (t0) cc_final: 0.8032 (t0) REVERT: E 56 GLN cc_start: 0.7053 (mp10) cc_final: 0.6541 (mp10) REVERT: F 21 LEU cc_start: 0.8889 (mm) cc_final: 0.8370 (mm) REVERT: F 46 PHE cc_start: 0.8573 (t80) cc_final: 0.8287 (t80) REVERT: F 321 TYR cc_start: 0.8990 (m-80) cc_final: 0.8750 (m-10) REVERT: F 329 TYR cc_start: 0.8033 (m-80) cc_final: 0.7821 (m-80) REVERT: F 340 ARG cc_start: 0.8252 (tpt170) cc_final: 0.7824 (ptm-80) REVERT: F 619 ILE cc_start: 0.9304 (mm) cc_final: 0.8990 (mm) REVERT: G 41 PHE cc_start: 0.8059 (t80) cc_final: 0.7556 (t80) REVERT: G 50 TYR cc_start: 0.8591 (m-10) cc_final: 0.8339 (m-10) REVERT: G 56 HIS cc_start: 0.7975 (m-70) cc_final: 0.7469 (m-70) REVERT: G 152 PHE cc_start: 0.8431 (m-80) cc_final: 0.8064 (m-10) REVERT: a 200 LEU cc_start: 0.9344 (mt) cc_final: 0.9071 (mt) REVERT: a 237 MET cc_start: 0.7919 (mtt) cc_final: 0.7624 (mtt) REVERT: b 206 ASN cc_start: 0.8876 (t0) cc_final: 0.8395 (t0) REVERT: c 115 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8366 (mmtm) REVERT: d 71 ILE cc_start: 0.8510 (mt) cc_final: 0.8251 (mt) REVERT: e 160 ASP cc_start: 0.8003 (t0) cc_final: 0.7802 (t0) REVERT: f 126 GLN cc_start: 0.7257 (tt0) cc_final: 0.7046 (tt0) REVERT: f 148 GLU cc_start: 0.8341 (mt-10) cc_final: 0.8115 (tt0) REVERT: f 179 ASN cc_start: 0.5295 (OUTLIER) cc_final: 0.5053 (t0) REVERT: f 197 PHE cc_start: 0.8013 (t80) cc_final: 0.7705 (t80) REVERT: g 81 MET cc_start: 0.7891 (mtt) cc_final: 0.7565 (mtm) REVERT: g 160 ASP cc_start: 0.8334 (t70) cc_final: 0.7772 (t0) REVERT: h 97 GLU cc_start: 0.6639 (tt0) cc_final: 0.6220 (tt0) REVERT: h 120 MET cc_start: 0.7572 (ttp) cc_final: 0.7217 (ttt) REVERT: h 134 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7638 (mm-30) REVERT: i 84 ASP cc_start: 0.7403 (m-30) cc_final: 0.7133 (m-30) REVERT: j 151 ASP cc_start: 0.7426 (p0) cc_final: 0.7072 (p0) REVERT: j 156 ASN cc_start: 0.8762 (p0) cc_final: 0.8408 (p0) outliers start: 84 outliers final: 50 residues processed: 894 average time/residue: 0.1875 time to fit residues: 275.9394 Evaluate side-chains 785 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 733 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 316 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 91 LEU 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 191 LEU Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 631 LEU Chi-restraints excluded: chain F residue 715 ILE 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 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 f residue 179 ASN 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 82 VAL Chi-restraints excluded: chain i residue 113 VAL Chi-restraints excluded: chain i residue 117 ILE 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 213 VAL 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 108 optimal weight: 0.5980 chunk 147 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 305 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 346 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 245 GLN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 237 HIS ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 ASN ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 ASN F 663 ASN G 8 HIS ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 347 ASN c 157 ASN ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 82 HIS e 54 GLN f 204 ASN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 162 ASN ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.120012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098666 restraints weight = 68046.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101284 restraints weight = 32398.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102964 restraints weight = 19932.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103696 restraints weight = 14764.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.104390 restraints weight = 12702.217| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32914 Z= 0.205 Angle : 0.730 30.142 44635 Z= 0.362 Chirality : 0.047 0.259 5062 Planarity : 0.005 0.105 5538 Dihedral : 6.579 58.684 4441 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.55 % Favored : 91.42 % Rotamer: Outliers : 3.64 % Allowed : 16.22 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 4011 helix: -0.13 (0.11), residues: 2178 sheet: -3.04 (0.25), residues: 322 loop : -2.79 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG b 257 TYR 0.028 0.002 TYR a 160 PHE 0.041 0.002 PHE f 118 TRP 0.026 0.002 TRP h 80 HIS 0.008 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00478 (32910) covalent geometry : angle 0.70432 (44629) hydrogen bonds : bond 0.04270 ( 1681) hydrogen bonds : angle 4.87611 ( 4944) metal coordination : bond 0.01845 ( 4) metal coordination : angle 16.54037 ( 6) *********************** 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 935 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 809 time to evaluate : 1.317 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: 0.6265 (t60) cc_final: 0.5823 (t60) REVERT: A 156 TYR cc_start: 0.7537 (t80) cc_final: 0.6737 (t80) REVERT: A 163 ARG cc_start: 0.7274 (ttm110) cc_final: 0.6424 (ttp-170) REVERT: A 172 GLU cc_start: 0.8757 (tt0) cc_final: 0.8177 (tt0) REVERT: A 210 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.6873 (mmt180) REVERT: A 305 PHE cc_start: 0.8359 (m-10) cc_final: 0.8143 (m-10) REVERT: B 128 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7356 (pm20) REVERT: B 182 LYS cc_start: 0.8821 (mttt) cc_final: 0.8151 (mtpp) REVERT: B 218 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8555 (mm) REVERT: B 223 MET cc_start: 0.8597 (mmp) cc_final: 0.8395 (mmt) REVERT: B 379 ASP cc_start: 0.7092 (m-30) cc_final: 0.6860 (m-30) REVERT: C 84 MET cc_start: 0.7686 (tpt) cc_final: 0.7169 (tpt) REVERT: D 76 TRP cc_start: 0.8526 (t60) cc_final: 0.8097 (t-100) REVERT: D 102 ILE cc_start: 0.9322 (mm) cc_final: 0.9054 (tp) REVERT: D 124 MET cc_start: 0.8867 (mmt) cc_final: 0.8356 (tpt) REVERT: D 128 TYR cc_start: 0.9089 (t80) cc_final: 0.8852 (t80) REVERT: D 141 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9144 (tt) REVERT: D 150 GLU cc_start: 0.7349 (pp20) cc_final: 0.6868 (pp20) REVERT: E 1 MET cc_start: 0.7548 (tpt) cc_final: 0.7240 (tpt) REVERT: F 340 ARG cc_start: 0.8263 (tpt170) cc_final: 0.7861 (ptm-80) REVERT: G 50 TYR cc_start: 0.8588 (m-10) cc_final: 0.8291 (m-10) REVERT: G 66 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.6831 (t80) REVERT: G 81 MET cc_start: 0.7835 (ppp) cc_final: 0.7548 (ppp) REVERT: G 152 PHE cc_start: 0.8476 (m-80) cc_final: 0.8019 (m-10) REVERT: a 237 MET cc_start: 0.8094 (mtt) cc_final: 0.7804 (mtt) REVERT: b 206 ASN cc_start: 0.8732 (t0) cc_final: 0.8425 (t0) REVERT: c 115 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8299 (mmtm) REVERT: d 71 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8426 (mt) REVERT: f 127 ASN cc_start: 0.9101 (p0) cc_final: 0.8782 (p0) REVERT: f 148 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8140 (tt0) REVERT: f 197 PHE cc_start: 0.8111 (t80) cc_final: 0.7847 (t80) REVERT: g 154 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7372 (tm-30) REVERT: g 160 ASP cc_start: 0.8305 (t70) cc_final: 0.7754 (t0) REVERT: h 97 GLU cc_start: 0.6625 (tt0) cc_final: 0.6165 (tt0) REVERT: h 120 MET cc_start: 0.7693 (ttp) cc_final: 0.7422 (ttt) REVERT: h 158 TYR cc_start: 0.8346 (m-80) cc_final: 0.8086 (m-80) REVERT: i 217 ARG cc_start: 0.8259 (tpt90) cc_final: 0.7818 (tpt-90) REVERT: j 151 ASP cc_start: 0.7525 (p0) cc_final: 0.7225 (p0) REVERT: j 156 ASN cc_start: 0.8800 (p0) cc_final: 0.8467 (p0) outliers start: 126 outliers final: 81 residues processed: 881 average time/residue: 0.1895 time to fit residues: 275.6145 Evaluate side-chains 811 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 725 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 175 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 313 LEU 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 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 509 LEU Chi-restraints excluded: chain C residue 67 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 43 ILE 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 141 LEU 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 375 ILE Chi-restraints excluded: chain D residue 391 SER 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 57 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 466 SER Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 575 PHE Chi-restraints excluded: chain F residue 631 LEU 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 a residue 126 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain b residue 86 PHE Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 161 MET 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 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 c residue 146 ILE 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 f residue 204 ASN 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 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 114 VAL Chi-restraints excluded: chain j residue 137 THR Chi-restraints excluded: chain j residue 213 VAL 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 178 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 200 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 292 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 144 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 145 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 465 HIS ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 ASN ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 141 HIS f 204 ASN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 162 ASN i 194 ASN ** j 148 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 = 0.3656 r_free = 0.3656 target = 0.121866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100792 restraints weight = 67326.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103398 restraints weight = 31700.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.105063 restraints weight = 19449.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105958 restraints weight = 14369.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106603 restraints weight = 12173.263| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2860 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= 0.154 Angle : 0.692 27.734 44635 Z= 0.343 Chirality : 0.045 0.267 5062 Planarity : 0.005 0.069 5538 Dihedral : 6.341 59.348 4439 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.13 % Favored : 91.85 % Rotamer: Outliers : 3.79 % Allowed : 18.82 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.13), residues: 4011 helix: 0.15 (0.11), residues: 2206 sheet: -2.97 (0.25), residues: 328 loop : -2.74 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 61 TYR 0.023 0.002 TYR b 271 PHE 0.019 0.001 PHE E 45 TRP 0.026 0.001 TRP h 80 HIS 0.007 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00354 (32910) covalent geometry : angle 0.66894 (44629) hydrogen bonds : bond 0.04006 ( 1681) hydrogen bonds : angle 4.68069 ( 4944) metal coordination : bond 0.01498 ( 4) metal coordination : angle 15.37510 ( 6) *********************** 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 945 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 814 time to evaluate : 1.200 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: A 49 TRP cc_start: 0.6237 (t60) cc_final: 0.5808 (t60) REVERT: A 156 TYR cc_start: 0.7555 (t80) cc_final: 0.6925 (t80) REVERT: A 163 ARG cc_start: 0.7315 (ttm110) cc_final: 0.6446 (ttp-170) REVERT: A 172 GLU cc_start: 0.8676 (tt0) cc_final: 0.8410 (tt0) REVERT: A 198 GLN cc_start: 0.8055 (mt0) cc_final: 0.7695 (mm-40) REVERT: A 210 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.6864 (mmt180) REVERT: A 223 LEU cc_start: 0.6870 (mp) cc_final: 0.6467 (mp) REVERT: A 270 PHE cc_start: 0.8652 (m-80) cc_final: 0.8355 (m-80) REVERT: A 275 TYR cc_start: 0.7069 (m-80) cc_final: 0.6765 (m-80) REVERT: A 305 PHE cc_start: 0.8305 (m-10) cc_final: 0.8063 (m-10) REVERT: B 128 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: B 182 LYS cc_start: 0.8827 (mttt) cc_final: 0.8163 (mtpp) REVERT: B 379 ASP cc_start: 0.7053 (m-30) cc_final: 0.6790 (m-30) REVERT: C 84 MET cc_start: 0.7798 (tpt) cc_final: 0.7191 (tpt) REVERT: C 114 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8128 (mtpp) REVERT: D 124 MET cc_start: 0.8811 (mmt) cc_final: 0.8383 (tpt) REVERT: D 150 GLU cc_start: 0.7197 (pp20) cc_final: 0.6920 (pp20) REVERT: E 1 MET cc_start: 0.7480 (tpt) cc_final: 0.7131 (tpt) REVERT: F 27 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8290 (tt) REVERT: F 39 MET cc_start: 0.7628 (tpt) cc_final: 0.6959 (tpp) REVERT: F 254 MET cc_start: 0.8221 (mmp) cc_final: 0.7955 (mmm) REVERT: F 299 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8617 (tp) REVERT: F 340 ARG cc_start: 0.8300 (tpt170) cc_final: 0.7914 (ptm-80) REVERT: F 535 ARG cc_start: 0.6748 (mmm160) cc_final: 0.6488 (mmm-85) REVERT: G 66 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7131 (t80) REVERT: G 152 PHE cc_start: 0.8357 (m-80) cc_final: 0.7971 (m-10) REVERT: a 147 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7847 (mm-40) REVERT: a 237 MET cc_start: 0.8142 (mtt) cc_final: 0.7839 (mtt) REVERT: b 206 ASN cc_start: 0.8666 (t0) cc_final: 0.8460 (t0) REVERT: b 299 MET cc_start: 0.7098 (mtp) cc_final: 0.6636 (mtp) REVERT: c 115 LYS cc_start: 0.8538 (mmmm) cc_final: 0.8120 (mmtm) REVERT: e 160 ASP cc_start: 0.8031 (t0) cc_final: 0.7697 (t70) REVERT: f 148 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8003 (tt0) REVERT: f 197 PHE cc_start: 0.8023 (t80) cc_final: 0.7804 (t80) REVERT: g 92 ARG cc_start: 0.4121 (mmt90) cc_final: 0.3561 (tpp80) REVERT: g 141 ARG cc_start: 0.7912 (mmp80) cc_final: 0.7687 (mmp80) REVERT: g 160 ASP cc_start: 0.8307 (t70) cc_final: 0.7786 (t0) REVERT: h 97 GLU cc_start: 0.6620 (tt0) cc_final: 0.6334 (tt0) REVERT: h 158 TYR cc_start: 0.8358 (m-80) cc_final: 0.8076 (m-80) REVERT: i 165 MET cc_start: 0.7549 (mmm) cc_final: 0.6946 (mtt) REVERT: i 217 ARG cc_start: 0.8280 (tpt90) cc_final: 0.8038 (tpt-90) REVERT: j 151 ASP cc_start: 0.7694 (p0) cc_final: 0.7357 (p0) REVERT: j 156 ASN cc_start: 0.8750 (p0) cc_final: 0.8371 (p0) outliers start: 131 outliers final: 85 residues processed: 891 average time/residue: 0.1955 time to fit residues: 288.3710 Evaluate side-chains 812 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 723 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 183 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 313 LEU 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 211 LEU Chi-restraints excluded: chain B residue 218 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 420 LEU 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 D residue 14 THR Chi-restraints excluded: chain D residue 22 SER 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 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 433 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 27 LEU Chi-restraints excluded: chain F residue 48 LEU 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 368 GLU Chi-restraints excluded: chain F residue 575 PHE Chi-restraints excluded: chain F residue 631 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 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 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 378 LEU Chi-restraints excluded: chain b residue 49 ASN Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 86 PHE Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 161 MET Chi-restraints excluded: chain b residue 163 THR 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 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 f residue 204 ASN 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 h residue 185 ASN 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 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 349 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 329 optimal weight: 0.8980 chunk 383 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 322 optimal weight: 0.0470 chunk 16 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 465 HIS ** 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 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 ASN ** d 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 204 ASN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 194 ASN ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.122627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101527 restraints weight = 67585.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104138 restraints weight = 31832.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105821 restraints weight = 19517.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106654 restraints weight = 14334.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.107292 restraints weight = 12175.045| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32914 Z= 0.154 Angle : 0.694 26.824 44635 Z= 0.344 Chirality : 0.045 0.274 5062 Planarity : 0.005 0.070 5538 Dihedral : 6.180 59.659 4439 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.20 % Favored : 91.77 % Rotamer: Outliers : 3.85 % Allowed : 21.19 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.13), residues: 4011 helix: 0.31 (0.11), residues: 2199 sheet: -2.84 (0.26), residues: 325 loop : -2.71 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 61 TYR 0.035 0.002 TYR D 220 PHE 0.026 0.001 PHE D 82 TRP 0.026 0.001 TRP h 80 HIS 0.010 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00358 (32910) covalent geometry : angle 0.67195 (44629) hydrogen bonds : bond 0.03924 ( 1681) hydrogen bonds : angle 4.63626 ( 4944) metal coordination : bond 0.01458 ( 4) metal coordination : angle 14.82632 ( 6) *********************** 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 917 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 784 time to evaluate : 1.264 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: A 49 TRP cc_start: 0.6319 (t60) cc_final: 0.5776 (t60) REVERT: A 156 TYR cc_start: 0.7442 (t80) cc_final: 0.6865 (t80) REVERT: A 163 ARG cc_start: 0.7317 (ttm110) cc_final: 0.6419 (ttp-170) REVERT: A 174 PRO cc_start: 0.9203 (Cg_exo) cc_final: 0.8948 (Cg_endo) REVERT: A 198 GLN cc_start: 0.8100 (mt0) cc_final: 0.7693 (mm-40) REVERT: A 210 ARG cc_start: 0.7605 (mmm-85) cc_final: 0.6966 (mmt180) REVERT: A 305 PHE cc_start: 0.8307 (m-10) cc_final: 0.8037 (m-10) REVERT: B 128 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: B 182 LYS cc_start: 0.8832 (mttt) cc_final: 0.8150 (mtpp) REVERT: B 323 MET cc_start: 0.8379 (ppp) cc_final: 0.8130 (ppp) REVERT: B 379 ASP cc_start: 0.7082 (m-30) cc_final: 0.6806 (m-30) REVERT: B 405 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8365 (mp) REVERT: C 84 MET cc_start: 0.7804 (tpt) cc_final: 0.7142 (tpt) REVERT: C 114 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8225 (mtpp) REVERT: D 124 MET cc_start: 0.8769 (mmt) cc_final: 0.8406 (tpt) REVERT: D 156 LEU cc_start: 0.9079 (mt) cc_final: 0.8789 (mt) REVERT: E 1 MET cc_start: 0.7460 (tpt) cc_final: 0.6350 (tpt) REVERT: F 39 MET cc_start: 0.7646 (tpt) cc_final: 0.6977 (tpp) REVERT: F 340 ARG cc_start: 0.8225 (tpt170) cc_final: 0.7830 (ptm-80) REVERT: F 365 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.7371 (m90) REVERT: G 66 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7020 (t80) REVERT: G 117 ASP cc_start: 0.7512 (t0) cc_final: 0.7092 (t0) REVERT: G 152 PHE cc_start: 0.8328 (m-80) cc_final: 0.7919 (m-10) REVERT: a 147 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7847 (mm-40) REVERT: a 237 MET cc_start: 0.8115 (mtt) cc_final: 0.7834 (mtt) REVERT: a 246 ASN cc_start: 0.7687 (m-40) cc_final: 0.7211 (t0) REVERT: c 115 LYS cc_start: 0.8623 (mmmm) cc_final: 0.8175 (mmtm) REVERT: d 71 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8291 (mt) REVERT: d 111 SER cc_start: 0.8481 (m) cc_final: 0.8225 (m) REVERT: e 116 GLN cc_start: 0.7771 (tm130) cc_final: 0.7275 (tm-30) REVERT: e 160 ASP cc_start: 0.8056 (t0) cc_final: 0.7746 (t70) REVERT: f 91 PHE cc_start: 0.8289 (t80) cc_final: 0.8039 (t80) REVERT: f 148 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7954 (tt0) REVERT: f 197 PHE cc_start: 0.8062 (t80) cc_final: 0.7802 (t80) REVERT: f 229 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8397 (t) REVERT: g 92 ARG cc_start: 0.4275 (mmt90) cc_final: 0.3703 (tpp80) REVERT: g 141 ARG cc_start: 0.7911 (mmp80) cc_final: 0.7661 (mmp80) REVERT: g 154 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7413 (tm-30) REVERT: g 160 ASP cc_start: 0.8335 (t70) cc_final: 0.7758 (t0) REVERT: h 97 GLU cc_start: 0.6652 (tt0) cc_final: 0.6359 (tt0) REVERT: i 165 MET cc_start: 0.7577 (mmm) cc_final: 0.7036 (mtt) REVERT: j 151 ASP cc_start: 0.7763 (p0) cc_final: 0.7442 (p0) REVERT: j 156 ASN cc_start: 0.8725 (p0) cc_final: 0.8333 (p0) outliers start: 133 outliers final: 93 residues processed: 861 average time/residue: 0.1968 time to fit residues: 279.8195 Evaluate side-chains 828 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 729 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 208 LEU 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 131 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 229 ILE 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 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 14 THR 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 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 78 ASN Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 365 HIS Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 575 PHE 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 a residue 407 ILE 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 161 MET Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 213 PHE Chi-restraints excluded: chain c residue 93 ASN 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 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 122 TYR Chi-restraints excluded: chain f residue 132 PHE Chi-restraints excluded: chain f residue 192 TYR Chi-restraints excluded: chain f residue 204 ASN 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 82 VAL 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 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 345 optimal weight: 4.9990 chunk 346 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 373 optimal weight: 2.9990 chunk 394 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 313 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** 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 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 69 GLN e 54 GLN f 204 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.098045 restraints weight = 67708.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100605 restraints weight = 32019.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.102234 restraints weight = 19668.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103125 restraints weight = 14538.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.103787 restraints weight = 12267.659| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 32914 Z= 0.194 Angle : 0.727 28.283 44635 Z= 0.359 Chirality : 0.047 0.293 5062 Planarity : 0.005 0.070 5538 Dihedral : 6.228 59.577 4439 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.30 % Favored : 91.67 % Rotamer: Outliers : 4.02 % Allowed : 21.86 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 4011 helix: 0.38 (0.11), residues: 2199 sheet: -2.74 (0.27), residues: 325 loop : -2.66 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 282 TYR 0.034 0.002 TYR D 220 PHE 0.036 0.002 PHE E 45 TRP 0.026 0.002 TRP h 80 HIS 0.012 0.001 HIS e 86 Details of bonding type rmsd covalent geometry : bond 0.00454 (32910) covalent geometry : angle 0.70412 (44629) hydrogen bonds : bond 0.04023 ( 1681) hydrogen bonds : angle 4.64799 ( 4944) metal coordination : bond 0.01822 ( 4) metal coordination : angle 15.57850 ( 6) *********************** 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 915 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 776 time to evaluate : 1.335 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: 0.6314 (t60) cc_final: 0.5780 (t60) REVERT: A 156 TYR cc_start: 0.7399 (t80) cc_final: 0.6849 (t80) REVERT: A 163 ARG cc_start: 0.7351 (ttm110) cc_final: 0.6441 (ttp-170) REVERT: A 210 ARG cc_start: 0.7629 (mmm-85) cc_final: 0.7047 (mmt180) REVERT: A 275 TYR cc_start: 0.7407 (m-80) cc_final: 0.6593 (m-80) REVERT: A 305 PHE cc_start: 0.8341 (m-10) cc_final: 0.8080 (m-10) REVERT: B 128 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7692 (pm20) REVERT: B 182 LYS cc_start: 0.8842 (mttt) cc_final: 0.8182 (mtpp) REVERT: B 323 MET cc_start: 0.8441 (ppp) cc_final: 0.8177 (ppp) REVERT: B 405 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8294 (mp) REVERT: C 84 MET cc_start: 0.7844 (tpt) cc_final: 0.7256 (tpt) REVERT: D 124 MET cc_start: 0.8811 (mmt) cc_final: 0.8485 (tpt) REVERT: D 156 LEU cc_start: 0.9157 (mt) cc_final: 0.8835 (mt) REVERT: D 389 MET cc_start: 0.9137 (mmt) cc_final: 0.8917 (mmt) REVERT: E 19 TYR cc_start: 0.7892 (t80) cc_final: 0.7667 (t80) REVERT: E 56 GLN cc_start: 0.6868 (mp10) cc_final: 0.6521 (mp10) REVERT: F 39 MET cc_start: 0.7760 (tpt) cc_final: 0.7082 (tpp) REVERT: F 49 SER cc_start: 0.9086 (m) cc_final: 0.8801 (p) REVERT: F 299 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8680 (tp) REVERT: F 340 ARG cc_start: 0.8279 (tpt170) cc_final: 0.7804 (ptm-80) REVERT: F 365 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7608 (m90) REVERT: G 66 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7120 (t80) REVERT: G 117 ASP cc_start: 0.7594 (t0) cc_final: 0.7164 (t0) REVERT: G 151 ASP cc_start: 0.7915 (t0) cc_final: 0.7396 (t0) REVERT: G 152 PHE cc_start: 0.8392 (m-80) cc_final: 0.8137 (m-10) REVERT: a 237 MET cc_start: 0.8195 (mtt) cc_final: 0.7878 (mtt) REVERT: a 246 ASN cc_start: 0.7701 (m-40) cc_final: 0.7196 (t0) REVERT: b 206 ASN cc_start: 0.8731 (t0) cc_final: 0.8425 (m-40) REVERT: c 115 LYS cc_start: 0.8716 (mmmm) cc_final: 0.8245 (mmtm) REVERT: d 71 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8305 (mt) REVERT: d 111 SER cc_start: 0.8585 (m) cc_final: 0.8310 (m) REVERT: e 116 GLN cc_start: 0.7839 (tm130) cc_final: 0.7634 (tm-30) REVERT: e 160 ASP cc_start: 0.8149 (t0) cc_final: 0.7914 (t0) REVERT: f 148 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7837 (tt0) REVERT: f 197 PHE cc_start: 0.8102 (t80) cc_final: 0.7836 (t80) REVERT: f 229 VAL cc_start: 0.8644 (OUTLIER) cc_final: 0.8422 (t) REVERT: g 141 ARG cc_start: 0.7903 (mmp80) cc_final: 0.7615 (mmp80) REVERT: g 154 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7436 (tm-30) REVERT: g 160 ASP cc_start: 0.8411 (t70) cc_final: 0.7846 (t0) REVERT: h 97 GLU cc_start: 0.6621 (tt0) cc_final: 0.6153 (tt0) REVERT: i 217 ARG cc_start: 0.8292 (tpt90) cc_final: 0.7971 (tpt-90) REVERT: j 151 ASP cc_start: 0.7829 (p0) cc_final: 0.7464 (p0) REVERT: j 156 ASN cc_start: 0.8775 (p0) cc_final: 0.8405 (p0) outliers start: 139 outliers final: 108 residues processed: 861 average time/residue: 0.1948 time to fit residues: 277.2075 Evaluate side-chains 846 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 731 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 246 THR 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 218 LEU Chi-restraints excluded: chain B residue 229 ILE 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 442 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 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 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 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 286 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 365 HIS Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 575 PHE 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 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 86 PHE Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 161 MET Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 213 PHE Chi-restraints excluded: chain c residue 93 ASN Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain c residue 186 HIS 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 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 122 TYR Chi-restraints excluded: chain f residue 132 PHE Chi-restraints excluded: chain f residue 192 TYR Chi-restraints excluded: chain f residue 204 ASN Chi-restraints excluded: chain f residue 229 VAL Chi-restraints excluded: chain g residue 107 LEU 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 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 114 VAL Chi-restraints excluded: chain j residue 196 GLN Chi-restraints excluded: chain j residue 213 VAL Chi-restraints excluded: chain j residue 218 ILE 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 356 optimal weight: 0.9980 chunk 391 optimal weight: 9.9990 chunk 362 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 274 optimal weight: 0.0770 chunk 3 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 231 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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** ** 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** ** a 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 ASN e 193 ASN f 204 ASN f 225 GLN ** h 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.122114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101165 restraints weight = 67816.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.103766 restraints weight = 32109.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105415 restraints weight = 19676.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106289 restraints weight = 14544.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106939 restraints weight = 12313.107| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 32914 Z= 0.147 Angle : 0.703 26.342 44635 Z= 0.347 Chirality : 0.045 0.284 5062 Planarity : 0.005 0.071 5538 Dihedral : 6.101 59.491 4439 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.16 % Allowed : 22.41 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 4011 helix: 0.50 (0.11), residues: 2187 sheet: -2.65 (0.26), residues: 332 loop : -2.61 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG b 172 TYR 0.034 0.002 TYR B 164 PHE 0.035 0.001 PHE D 82 TRP 0.023 0.001 TRP h 80 HIS 0.010 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00339 (32910) covalent geometry : angle 0.68309 (44629) hydrogen bonds : bond 0.03877 ( 1681) hydrogen bonds : angle 4.55859 ( 4944) metal coordination : bond 0.01368 ( 4) metal coordination : angle 14.38677 ( 6) *********************** 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 938 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 794 time to evaluate : 1.385 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: A 49 TRP cc_start: 0.6257 (t60) cc_final: 0.5695 (t60) REVERT: A 156 TYR cc_start: 0.7381 (t80) cc_final: 0.7028 (t80) REVERT: A 210 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.7078 (mmt180) REVERT: A 275 TYR cc_start: 0.7098 (m-80) cc_final: 0.6786 (m-80) REVERT: A 305 PHE cc_start: 0.8321 (m-10) cc_final: 0.8039 (m-10) REVERT: B 128 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: B 182 LYS cc_start: 0.8837 (mttt) cc_final: 0.8159 (mtpp) REVERT: B 295 TRP cc_start: 0.8110 (t60) cc_final: 0.7570 (t60) REVERT: B 405 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8205 (mp) REVERT: B 466 MET cc_start: 0.7776 (tpp) cc_final: 0.7458 (tpp) REVERT: C 84 MET cc_start: 0.7853 (tpt) cc_final: 0.7246 (tpt) REVERT: D 124 MET cc_start: 0.8753 (mmt) cc_final: 0.8428 (tpt) REVERT: D 156 LEU cc_start: 0.9121 (mt) cc_final: 0.8609 (mt) REVERT: E 56 GLN cc_start: 0.6757 (mp10) cc_final: 0.6456 (mp10) REVERT: F 39 MET cc_start: 0.7622 (tpt) cc_final: 0.7220 (tpp) REVERT: F 299 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8586 (tp) REVERT: F 340 ARG cc_start: 0.8237 (tpt170) cc_final: 0.7790 (ptm-80) REVERT: F 365 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7497 (m90) REVERT: G 66 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7299 (t80) REVERT: G 117 ASP cc_start: 0.7517 (t0) cc_final: 0.7096 (t0) REVERT: G 152 PHE cc_start: 0.8252 (m-80) cc_final: 0.7949 (m-10) REVERT: a 147 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7857 (mm-40) REVERT: a 237 MET cc_start: 0.8215 (mtt) cc_final: 0.7920 (mtt) REVERT: a 246 ASN cc_start: 0.7550 (m-40) cc_final: 0.7111 (t0) REVERT: b 206 ASN cc_start: 0.8817 (t0) cc_final: 0.8344 (m-40) REVERT: c 115 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8231 (mmtm) REVERT: d 71 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8270 (mt) REVERT: e 160 ASP cc_start: 0.8049 (t0) cc_final: 0.7738 (t70) REVERT: f 148 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7835 (tt0) REVERT: f 197 PHE cc_start: 0.8032 (t80) cc_final: 0.7790 (t80) REVERT: f 229 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8365 (t) REVERT: g 92 ARG cc_start: 0.4233 (mmt90) cc_final: 0.3680 (tpp80) REVERT: g 141 ARG cc_start: 0.7976 (mmp80) cc_final: 0.7768 (mmp80) REVERT: g 144 ASP cc_start: 0.6479 (p0) cc_final: 0.6163 (p0) REVERT: g 160 ASP cc_start: 0.8391 (t70) cc_final: 0.7828 (t0) REVERT: h 97 GLU cc_start: 0.6624 (tt0) cc_final: 0.6368 (tt0) REVERT: i 178 LYS cc_start: 0.8876 (ttpp) cc_final: 0.8583 (ttpp) REVERT: i 217 ARG cc_start: 0.8330 (tpt90) cc_final: 0.7992 (tpt-90) REVERT: j 151 ASP cc_start: 0.7594 (p0) cc_final: 0.7339 (p0) REVERT: j 156 ASN cc_start: 0.8734 (p0) cc_final: 0.8361 (p0) outliers start: 144 outliers final: 106 residues processed: 881 average time/residue: 0.1921 time to fit residues: 279.8038 Evaluate side-chains 847 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 734 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 175 LEU Chi-restraints excluded: chain A residue 208 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 218 LEU Chi-restraints excluded: chain B residue 229 ILE 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 442 LEU 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 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 380 ILE Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 432 MET 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 365 HIS Chi-restraints excluded: chain F residue 368 GLU 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 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 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 281 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 383 ASN Chi-restraints excluded: chain a residue 407 ILE 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 161 MET Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 204 CYS 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 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 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 122 TYR Chi-restraints excluded: chain f residue 132 PHE Chi-restraints excluded: chain f residue 140 ILE Chi-restraints excluded: chain f residue 192 TYR Chi-restraints excluded: chain f residue 204 ASN Chi-restraints excluded: chain f residue 229 VAL Chi-restraints excluded: chain g residue 107 LEU 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 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 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 389 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 74 optimal weight: 0.0010 chunk 217 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 363 optimal weight: 0.8980 chunk 285 optimal weight: 2.9990 chunk 40 optimal weight: 0.0970 chunk 61 optimal weight: 0.9980 chunk 373 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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 E 44 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 HIS F 638 ASN a 158 GLN b 49 ASN e 86 HIS ** e 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 193 ASN f 204 ASN f 215 ASN f 225 GLN ** h 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.123101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.102016 restraints weight = 67499.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104630 restraints weight = 32164.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.106086 restraints weight = 19813.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.107239 restraints weight = 14983.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107598 restraints weight = 12363.823| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32914 Z= 0.144 Angle : 0.715 25.302 44635 Z= 0.353 Chirality : 0.046 0.301 5062 Planarity : 0.005 0.069 5538 Dihedral : 6.017 59.871 4439 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.93 % Allowed : 23.71 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 4011 helix: 0.59 (0.11), residues: 2186 sheet: -2.45 (0.28), residues: 314 loop : -2.63 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 175 TYR 0.035 0.002 TYR B 164 PHE 0.037 0.001 PHE E 45 TRP 0.031 0.001 TRP h 80 HIS 0.010 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00332 (32910) covalent geometry : angle 0.69673 (44629) hydrogen bonds : bond 0.03808 ( 1681) hydrogen bonds : angle 4.53397 ( 4944) metal coordination : bond 0.01293 ( 4) metal coordination : angle 13.76472 ( 6) *********************** 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 934 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 798 time to evaluate : 1.140 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: 0.6305 (t60) cc_final: 0.5671 (t60) REVERT: A 156 TYR cc_start: 0.7253 (t80) cc_final: 0.6963 (t80) REVERT: A 194 ILE cc_start: 0.9027 (pt) cc_final: 0.8721 (pt) REVERT: A 210 ARG cc_start: 0.7616 (mmm-85) cc_final: 0.7121 (mmt180) REVERT: A 275 TYR cc_start: 0.7417 (m-80) cc_final: 0.6500 (m-80) REVERT: A 305 PHE cc_start: 0.8281 (m-10) cc_final: 0.7993 (m-10) REVERT: B 128 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: B 182 LYS cc_start: 0.8806 (mttt) cc_final: 0.8164 (mtpp) REVERT: B 224 TYR cc_start: 0.8022 (p90) cc_final: 0.7761 (p90) REVERT: B 295 TRP cc_start: 0.8094 (t60) cc_final: 0.7506 (t60) REVERT: B 466 MET cc_start: 0.7820 (tpp) cc_final: 0.7497 (tpp) REVERT: C 84 MET cc_start: 0.7896 (tpt) cc_final: 0.7268 (tpt) REVERT: D 124 MET cc_start: 0.8774 (mmt) cc_final: 0.8443 (tpt) REVERT: E 56 GLN cc_start: 0.6848 (mp10) cc_final: 0.6548 (mp10) REVERT: F 39 MET cc_start: 0.7588 (tpt) cc_final: 0.7116 (tpp) REVERT: F 299 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8566 (tp) REVERT: F 340 ARG cc_start: 0.8192 (tpt170) cc_final: 0.7754 (ptm-80) REVERT: F 365 HIS cc_start: 0.7732 (OUTLIER) cc_final: 0.7500 (m90) REVERT: G 41 PHE cc_start: 0.8124 (t80) cc_final: 0.7813 (t80) REVERT: G 66 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7288 (t80) REVERT: G 117 ASP cc_start: 0.7515 (t0) cc_final: 0.7125 (t0) REVERT: G 151 ASP cc_start: 0.7826 (t0) cc_final: 0.7246 (t70) REVERT: G 152 PHE cc_start: 0.8280 (m-80) cc_final: 0.7195 (m-10) REVERT: a 237 MET cc_start: 0.8196 (mtt) cc_final: 0.7944 (mtt) REVERT: a 246 ASN cc_start: 0.7444 (m-40) cc_final: 0.7061 (t0) REVERT: b 206 ASN cc_start: 0.8774 (t0) cc_final: 0.8324 (m-40) REVERT: c 115 LYS cc_start: 0.8637 (mmmm) cc_final: 0.8237 (mmtm) REVERT: d 71 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8236 (mt) REVERT: e 155 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7149 (mm-30) REVERT: e 156 MET cc_start: 0.7233 (mmt) cc_final: 0.7030 (mmt) REVERT: e 160 ASP cc_start: 0.7935 (t0) cc_final: 0.7643 (t70) REVERT: f 148 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7834 (tt0) REVERT: f 197 PHE cc_start: 0.7972 (t80) cc_final: 0.7647 (t80) REVERT: g 144 ASP cc_start: 0.6499 (p0) cc_final: 0.6265 (p0) REVERT: g 160 ASP cc_start: 0.8395 (t70) cc_final: 0.7826 (t0) REVERT: i 178 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8601 (ttpp) REVERT: i 190 SER cc_start: 0.7771 (t) cc_final: 0.7546 (t) REVERT: j 146 MET cc_start: 0.6784 (ptp) cc_final: 0.5432 (ptp) REVERT: j 151 ASP cc_start: 0.7592 (p0) cc_final: 0.7314 (p0) REVERT: j 156 ASN cc_start: 0.8717 (p0) cc_final: 0.8351 (p0) REVERT: j 198 PHE cc_start: 0.8286 (p90) cc_final: 0.7621 (p90) outliers start: 136 outliers final: 104 residues processed: 877 average time/residue: 0.1857 time to fit residues: 270.6279 Evaluate side-chains 862 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 753 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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 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 218 LEU Chi-restraints excluded: chain B residue 229 ILE 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 420 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 485 ILE 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 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 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 368 ASP Chi-restraints excluded: chain D residue 369 GLU 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 286 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 365 HIS Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 638 ASN Chi-restraints excluded: chain F residue 675 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 39 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 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 a residue 383 ASN Chi-restraints excluded: chain a residue 407 ILE Chi-restraints excluded: chain a residue 446 THR Chi-restraints excluded: chain b residue 48 ASN Chi-restraints excluded: chain b residue 49 ASN Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 131 SER Chi-restraints excluded: chain b residue 161 MET Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 204 CYS 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 140 LEU Chi-restraints excluded: chain c residue 186 HIS 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 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 140 ILE 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 14 optimal weight: 0.6980 chunk 247 optimal weight: 0.0040 chunk 148 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 362 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 145 optimal weight: 0.2980 chunk 153 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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** ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 638 ASN b 49 ASN ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 237 GLN h 126 ASN ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 148 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 = 0.3682 r_free = 0.3682 target = 0.123394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102510 restraints weight = 67540.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.105149 restraints weight = 32282.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.106787 restraints weight = 19793.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107728 restraints weight = 14656.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.108266 restraints weight = 12345.941| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32914 Z= 0.153 Angle : 0.733 25.328 44635 Z= 0.363 Chirality : 0.046 0.272 5062 Planarity : 0.005 0.079 5538 Dihedral : 5.990 59.754 4439 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.05 % Favored : 91.92 % Rotamer: Outliers : 3.64 % Allowed : 24.52 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.13), residues: 4011 helix: 0.60 (0.11), residues: 2190 sheet: -2.38 (0.28), residues: 315 loop : -2.59 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 175 TYR 0.038 0.002 TYR B 164 PHE 0.033 0.001 PHE D 82 TRP 0.037 0.001 TRP h 80 HIS 0.010 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00360 (32910) covalent geometry : angle 0.71601 (44629) hydrogen bonds : bond 0.03887 ( 1681) hydrogen bonds : angle 4.54147 ( 4944) metal coordination : bond 0.01339 ( 4) metal coordination : angle 13.67814 ( 6) *********************** 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 904 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 778 time to evaluate : 1.099 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: 0.6307 (t60) cc_final: 0.5693 (t60) REVERT: A 156 TYR cc_start: 0.7206 (t80) cc_final: 0.6965 (t80) REVERT: A 210 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.7145 (mmt180) REVERT: A 275 TYR cc_start: 0.7146 (m-80) cc_final: 0.6844 (m-80) REVERT: A 305 PHE cc_start: 0.8299 (m-10) cc_final: 0.8012 (m-10) REVERT: B 128 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7688 (pm20) REVERT: B 182 LYS cc_start: 0.8854 (mttt) cc_final: 0.8169 (mtpp) REVERT: B 224 TYR cc_start: 0.8083 (p90) cc_final: 0.7800 (p90) REVERT: B 295 TRP cc_start: 0.8116 (t60) cc_final: 0.7545 (t60) REVERT: B 447 TYR cc_start: 0.7783 (m-80) cc_final: 0.7052 (m-80) REVERT: B 466 MET cc_start: 0.7807 (tpp) cc_final: 0.7503 (tpp) REVERT: C 84 MET cc_start: 0.7850 (tpt) cc_final: 0.7253 (tpt) REVERT: D 124 MET cc_start: 0.8775 (mmt) cc_final: 0.8437 (tpt) REVERT: E 56 GLN cc_start: 0.6876 (mp10) cc_final: 0.6593 (mp10) REVERT: F 39 MET cc_start: 0.7597 (tpt) cc_final: 0.7021 (tpp) REVERT: F 152 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7532 (mt-10) REVERT: F 265 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7777 (p-80) REVERT: F 269 MET cc_start: 0.9372 (ttt) cc_final: 0.8942 (ttt) REVERT: F 299 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8568 (tp) REVERT: F 340 ARG cc_start: 0.8143 (tpt170) cc_final: 0.7788 (ptm-80) REVERT: G 41 PHE cc_start: 0.8141 (t80) cc_final: 0.7860 (t80) REVERT: G 66 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7333 (t80) REVERT: G 117 ASP cc_start: 0.7364 (t0) cc_final: 0.7020 (t0) REVERT: G 152 PHE cc_start: 0.8345 (m-80) cc_final: 0.7993 (m-10) REVERT: a 237 MET cc_start: 0.8160 (mtt) cc_final: 0.7878 (mtt) REVERT: a 246 ASN cc_start: 0.7396 (m-40) cc_final: 0.7050 (t0) REVERT: b 206 ASN cc_start: 0.8785 (t0) cc_final: 0.8377 (m-40) REVERT: c 115 LYS cc_start: 0.8553 (mmmm) cc_final: 0.8113 (mmtm) REVERT: d 71 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8271 (mt) REVERT: e 155 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7224 (mm-30) REVERT: e 160 ASP cc_start: 0.7932 (t0) cc_final: 0.7692 (t70) REVERT: f 148 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7826 (tt0) REVERT: f 197 PHE cc_start: 0.7980 (t80) cc_final: 0.7669 (t80) REVERT: g 129 ASP cc_start: 0.7430 (t0) cc_final: 0.7229 (t0) REVERT: g 160 ASP cc_start: 0.8414 (t70) cc_final: 0.7792 (t0) REVERT: i 88 GLU cc_start: 0.7237 (pm20) cc_final: 0.7032 (pm20) REVERT: i 165 MET cc_start: 0.7561 (mmm) cc_final: 0.7014 (mtt) REVERT: i 178 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8684 (ttpp) REVERT: i 190 SER cc_start: 0.7726 (t) cc_final: 0.7513 (t) REVERT: j 146 MET cc_start: 0.6808 (ptp) cc_final: 0.5466 (ptp) REVERT: j 151 ASP cc_start: 0.7754 (p0) cc_final: 0.7454 (p0) REVERT: j 156 ASN cc_start: 0.8715 (p0) cc_final: 0.8351 (p0) REVERT: j 198 PHE cc_start: 0.8308 (p90) cc_final: 0.7659 (p90) outliers start: 126 outliers final: 107 residues processed: 849 average time/residue: 0.1875 time to fit residues: 263.7825 Evaluate side-chains 846 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 734 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 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 218 LEU Chi-restraints excluded: chain B residue 229 ILE 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 420 LEU Chi-restraints excluded: chain B residue 442 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 C residue 117 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 64 ASP 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 368 ASP Chi-restraints excluded: chain D residue 369 GLU 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 14 ILE 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 94 SER Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 265 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 638 ASN 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 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 281 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 383 ASN Chi-restraints excluded: chain a residue 407 ILE Chi-restraints excluded: chain a residue 446 THR Chi-restraints excluded: chain b residue 49 ASN Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 86 PHE Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 131 SER Chi-restraints excluded: chain b residue 161 MET Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 204 CYS Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 103 LEU Chi-restraints excluded: chain c residue 140 LEU Chi-restraints excluded: chain c residue 186 HIS 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 60 ASN 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 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 114 VAL Chi-restraints excluded: chain j residue 196 GLN Chi-restraints excluded: chain j residue 213 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 124 optimal weight: 0.7980 chunk 330 optimal weight: 9.9990 chunk 174 optimal weight: 0.6980 chunk 220 optimal weight: 0.9990 chunk 320 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 353 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 290 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** B 196 HIS ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 HIS ** 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 638 ASN ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 49 ASN e 86 HIS ** e 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 148 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 = 0.3676 r_free = 0.3676 target = 0.123137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.102246 restraints weight = 68098.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.104848 restraints weight = 32456.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.106474 restraints weight = 19844.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107346 restraints weight = 14663.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.107820 restraints weight = 12424.811| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 32914 Z= 0.154 Angle : 0.741 25.136 44635 Z= 0.366 Chirality : 0.047 0.282 5062 Planarity : 0.005 0.070 5538 Dihedral : 5.967 59.761 4439 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.64 % Allowed : 24.86 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 4011 helix: 0.61 (0.11), residues: 2191 sheet: -2.35 (0.28), residues: 317 loop : -2.60 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG b 172 TYR 0.038 0.002 TYR B 164 PHE 0.033 0.001 PHE D 82 TRP 0.035 0.001 TRP h 80 HIS 0.010 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00363 (32910) covalent geometry : angle 0.72437 (44629) hydrogen bonds : bond 0.03908 ( 1681) hydrogen bonds : angle 4.54425 ( 4944) metal coordination : bond 0.01327 ( 4) metal coordination : angle 13.41218 ( 6) ********************** 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 905 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 779 time to evaluate : 1.130 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: 0.6281 (t60) cc_final: 0.5680 (t60) REVERT: A 156 TYR cc_start: 0.7192 (t80) cc_final: 0.6991 (t80) REVERT: A 210 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7132 (mmt180) REVERT: A 275 TYR cc_start: 0.7276 (m-80) cc_final: 0.6276 (m-80) REVERT: A 305 PHE cc_start: 0.8282 (m-10) cc_final: 0.7990 (m-10) REVERT: B 181 MET cc_start: 0.8801 (tpp) cc_final: 0.8179 (tpp) REVERT: B 182 LYS cc_start: 0.8854 (mttt) cc_final: 0.8168 (mtpp) REVERT: B 224 TYR cc_start: 0.8058 (p90) cc_final: 0.7774 (p90) REVERT: B 295 TRP cc_start: 0.8119 (t60) cc_final: 0.7523 (t60) REVERT: B 447 TYR cc_start: 0.7792 (m-80) cc_final: 0.7081 (m-10) REVERT: B 448 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8460 (mm) REVERT: B 466 MET cc_start: 0.7912 (tpp) cc_final: 0.7607 (tpp) REVERT: C 84 MET cc_start: 0.7886 (tpt) cc_final: 0.7297 (tpt) REVERT: D 124 MET cc_start: 0.8765 (mmt) cc_final: 0.8440 (tpt) REVERT: E 56 GLN cc_start: 0.6890 (mp10) cc_final: 0.6592 (mp10) REVERT: F 39 MET cc_start: 0.7620 (tpt) cc_final: 0.7032 (tpp) REVERT: F 152 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7499 (mt-10) REVERT: F 265 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.7858 (p-80) REVERT: F 269 MET cc_start: 0.9351 (ttt) cc_final: 0.8924 (ttt) REVERT: F 299 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8534 (tp) REVERT: F 340 ARG cc_start: 0.8088 (tpt170) cc_final: 0.7719 (ptm-80) REVERT: G 41 PHE cc_start: 0.8165 (t80) cc_final: 0.7933 (t80) REVERT: G 66 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7401 (t80) REVERT: G 112 MET cc_start: 0.8268 (mmp) cc_final: 0.7921 (mmp) REVERT: G 117 ASP cc_start: 0.7403 (t0) cc_final: 0.6974 (t0) REVERT: G 152 PHE cc_start: 0.8344 (m-80) cc_final: 0.8001 (m-10) REVERT: a 237 MET cc_start: 0.8225 (mtt) cc_final: 0.7940 (mtt) REVERT: a 246 ASN cc_start: 0.7358 (m-40) cc_final: 0.6792 (t0) REVERT: b 206 ASN cc_start: 0.8732 (t0) cc_final: 0.8337 (m-40) REVERT: c 115 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8128 (mmtm) REVERT: e 122 MET cc_start: 0.7434 (mmt) cc_final: 0.7203 (mmt) REVERT: e 155 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7285 (mm-30) REVERT: e 160 ASP cc_start: 0.7942 (t0) cc_final: 0.7663 (t70) REVERT: f 148 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7813 (tt0) REVERT: f 197 PHE cc_start: 0.8059 (t80) cc_final: 0.7763 (t80) REVERT: f 216 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7489 (mp0) REVERT: g 129 ASP cc_start: 0.7471 (t0) cc_final: 0.7258 (t0) REVERT: g 160 ASP cc_start: 0.8372 (t70) cc_final: 0.7850 (t0) REVERT: i 165 MET cc_start: 0.7591 (mmm) cc_final: 0.7044 (mtt) REVERT: i 178 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8540 (ttpp) REVERT: i 190 SER cc_start: 0.7748 (t) cc_final: 0.7527 (t) REVERT: j 119 GLU cc_start: 0.7985 (tp30) cc_final: 0.7263 (tp30) REVERT: j 146 MET cc_start: 0.6659 (ptp) cc_final: 0.5336 (ptp) REVERT: j 151 ASP cc_start: 0.7755 (p0) cc_final: 0.7474 (p0) REVERT: j 156 ASN cc_start: 0.8725 (p0) cc_final: 0.8366 (p0) REVERT: j 198 PHE cc_start: 0.8345 (p90) cc_final: 0.7636 (p90) REVERT: j 239 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7722 (ttm110) outliers start: 126 outliers final: 104 residues processed: 848 average time/residue: 0.1803 time to fit residues: 255.0684 Evaluate side-chains 864 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 756 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 B residue 99 ILE Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 229 ILE 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 420 LEU Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 485 ILE 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 C residue 117 LEU Chi-restraints excluded: chain D residue 44 CYS Chi-restraints excluded: chain D residue 64 ASP 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 368 ASP Chi-restraints excluded: chain D residue 369 GLU 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 14 ILE Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 265 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 368 GLU 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 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 281 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 331 LEU Chi-restraints excluded: chain a residue 383 ASN Chi-restraints excluded: chain a residue 407 ILE Chi-restraints excluded: chain a residue 446 THR Chi-restraints excluded: chain b residue 65 LEU Chi-restraints excluded: chain b residue 86 PHE Chi-restraints excluded: chain b residue 96 ASP Chi-restraints excluded: chain b residue 131 SER Chi-restraints excluded: chain b residue 161 MET Chi-restraints excluded: chain b residue 163 THR Chi-restraints excluded: chain b residue 204 CYS Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain c residue 103 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 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 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 114 VAL Chi-restraints excluded: chain j residue 173 PHE Chi-restraints excluded: chain j residue 196 GLN Chi-restraints excluded: chain j residue 213 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 92 optimal weight: 0.9980 chunk 234 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 266 optimal weight: 0.1980 chunk 113 optimal weight: 0.5980 chunk 206 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 GLN ** 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 638 ASN ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 248 ASN b 49 ASN ** 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 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.124008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.103418 restraints weight = 68090.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105972 restraints weight = 33012.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107564 restraints weight = 20519.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108414 restraints weight = 15280.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109081 restraints weight = 12977.427| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 32914 Z= 0.152 Angle : 0.743 24.952 44635 Z= 0.368 Chirality : 0.047 0.315 5062 Planarity : 0.005 0.075 5538 Dihedral : 5.935 59.938 4439 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 3.53 % Allowed : 25.38 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 4011 helix: 0.63 (0.11), residues: 2187 sheet: -2.30 (0.28), residues: 316 loop : -2.61 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 175 TYR 0.047 0.002 TYR D 220 PHE 0.032 0.001 PHE E 45 TRP 0.038 0.002 TRP h 80 HIS 0.012 0.001 HIS D 344 Details of bonding type rmsd covalent geometry : bond 0.00355 (32910) covalent geometry : angle 0.72676 (44629) hydrogen bonds : bond 0.03881 ( 1681) hydrogen bonds : angle 4.54798 ( 4944) metal coordination : bond 0.01274 ( 4) metal coordination : angle 13.22431 ( 6) =============================================================================== Job complete usr+sys time: 6698.72 seconds wall clock time: 116 minutes 37.09 seconds (6997.09 seconds total)