Starting phenix.real_space_refine on Mon Oct 26 17:39:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n9v_0380/10_2026/6n9v_0380_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n9v_0380/10_2026/6n9v_0380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n9v_0380/10_2026/6n9v_0380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n9v_0380/10_2026/6n9v_0380.map" model { file = "/net/cci-nas-00/data/ceres_data/6n9v_0380/10_2026/6n9v_0380_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n9v_0380/10_2026/6n9v_0380_neut.cif" } resolution = 4.0 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 50 5.49 5 Mg 7 5.21 5 S 124 5.16 5 C 13409 2.51 5 N 3763 2.21 5 O 4172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21526 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1955 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 4, 'TRANS': 248} Chain breaks: 6 Chain: "B" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2117 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 4, 'TRANS': 270} Chain breaks: 3 Chain: "C" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2097 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 4, 'TRANS': 267} Chain breaks: 3 Chain: "D" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2056 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 262} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 3758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3758 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 472} Chain breaks: 6 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "F" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3549 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 446} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 5144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5144 Classifications: {'peptide': 645} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "P" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Unusual residues: {'DOC': 1} Classifications: {'RNA': 5, 'undetermined': 1} Modifications used: {'5*END': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 4, None: 1} Not linked: pdbres=" G P 5 " pdbres="DOC P 6 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "T" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 546 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 1, ' ZN': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {' MG': 2, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8294 SG CYS E 17 81.080 73.616 148.480 1.00182.63 S ATOM 8316 SG CYS E 20 79.419 75.737 150.798 1.00187.79 S ATOM 8429 SG CYS E 36 77.725 75.146 147.928 1.00162.86 S ATOM 8454 SG CYS E 39 80.413 77.076 147.426 1.00171.61 S Time building chain proxies: 4.53, per 1000 atoms: 0.21 Number of scatterers: 21526 At special positions: 0 Unit cell: (102.34, 131.58, 194.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 124 16.00 P 50 15.00 Mg 7 11.99 O 4172 8.00 N 3763 7.00 C 13409 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 235 " - pdb=" SG CYS F 241 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 908.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 17 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 39 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 20 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 36 " Number of angles added : 6 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4782 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 20 sheets defined 36.3% alpha, 13.6% beta 5 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.645A pdb=" N GLU A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 385 " --> pdb=" O TRP A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.919A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.536A pdb=" N GLU A 477 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 478 " --> pdb=" O HIS A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 478' Processing helix chain 'A' and resid 482 through 486 removed outlier: 3.635A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 486 " --> pdb=" O ILE A 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 486' Processing helix chain 'B' and resid 271 through 280 removed outlier: 3.543A pdb=" N ILE B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.806A pdb=" N ALA B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 removed outlier: 3.550A pdb=" N THR B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 374 removed outlier: 3.792A pdb=" N ILE B 373 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 374 " --> pdb=" O ARG B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 384 removed outlier: 3.718A pdb=" N GLU B 384 " --> pdb=" O GLN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.865A pdb=" N ASN B 388 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 415 Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 437 through 454 removed outlier: 3.660A pdb=" N MET B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 478 removed outlier: 3.888A pdb=" N GLY B 478 " --> pdb=" O HIS B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 279 removed outlier: 3.535A pdb=" N LEU C 279 " --> pdb=" O ILE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 319 through 332 removed outlier: 3.505A pdb=" N THR C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.532A pdb=" N ALA C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 Processing helix chain 'C' and resid 365 through 375 removed outlier: 3.619A pdb=" N LYS C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 384 removed outlier: 4.380A pdb=" N GLN C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 415 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 437 through 457 removed outlier: 3.933A pdb=" N MET C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 478 removed outlier: 4.046A pdb=" N GLY C 478 " --> pdb=" O HIS C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 293 through 299 removed outlier: 3.727A pdb=" N THR D 299 " --> pdb=" O ILE D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 332 removed outlier: 3.972A pdb=" N PHE D 321 " --> pdb=" O GLY D 317 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 332 " --> pdb=" O GLN D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 removed outlier: 4.190A pdb=" N THR D 349 " --> pdb=" O SER D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 removed outlier: 3.883A pdb=" N LYS D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG D 370 " --> pdb=" O ASP D 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 370' Processing helix chain 'D' and resid 371 through 376 removed outlier: 3.813A pdb=" N GLY D 376 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 removed outlier: 3.856A pdb=" N GLU D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU D 385 " --> pdb=" O TRP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 415 removed outlier: 3.648A pdb=" N ALA D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 456 removed outlier: 3.666A pdb=" N LEU D 445 " --> pdb=" O MET D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 478 removed outlier: 3.765A pdb=" N GLY D 478 " --> pdb=" O HIS D 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 95 removed outlier: 3.705A pdb=" N CYS E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 104 Processing helix chain 'E' and resid 159 through 169 Processing helix chain 'E' and resid 184 through 192 removed outlier: 3.668A pdb=" N THR E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS E 189 " --> pdb=" O ALA E 185 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA E 190 " --> pdb=" O LYS E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 199 removed outlier: 3.583A pdb=" N GLN E 198 " --> pdb=" O TYR E 195 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE E 199 " --> pdb=" O PHE E 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 195 through 199' Processing helix chain 'E' and resid 237 through 243 removed outlier: 3.509A pdb=" N CYS E 241 " --> pdb=" O ASP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 256 removed outlier: 3.711A pdb=" N GLN E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 317 through 328 removed outlier: 3.554A pdb=" N PHE E 321 " --> pdb=" O GLY E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 358 removed outlier: 4.379A pdb=" N THR E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA E 350 " --> pdb=" O VAL E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.717A pdb=" N ARG E 370 " --> pdb=" O ASP E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 387 removed outlier: 3.606A pdb=" N GLU E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU E 385 " --> pdb=" O TRP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 415 Processing helix chain 'E' and resid 440 through 457 removed outlier: 3.972A pdb=" N LEU E 445 " --> pdb=" O MET E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 478 removed outlier: 3.502A pdb=" N GLU E 477 " --> pdb=" O ALA E 474 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY E 478 " --> pdb=" O HIS E 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 474 through 478' Processing helix chain 'F' and resid 87 through 95 removed outlier: 3.787A pdb=" N CYS F 91 " --> pdb=" O SER F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 168 Processing helix chain 'F' and resid 184 through 191 removed outlier: 3.591A pdb=" N THR F 188 " --> pdb=" O ALA F 184 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 199 removed outlier: 3.974A pdb=" N GLN F 198 " --> pdb=" O TYR F 195 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE F 199 " --> pdb=" O PHE F 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 195 through 199' Processing helix chain 'F' and resid 209 through 219 removed outlier: 3.587A pdb=" N ARG F 213 " --> pdb=" O ASP F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 244 removed outlier: 3.811A pdb=" N CYS F 241 " --> pdb=" O ASP F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 256 removed outlier: 3.525A pdb=" N GLN F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 271 No H-bonds generated for 'chain 'F' and resid 269 through 271' Processing helix chain 'F' and resid 273 through 279 Processing helix chain 'F' and resid 295 through 299 Processing helix chain 'F' and resid 317 through 328 removed outlier: 3.505A pdb=" N PHE F 321 " --> pdb=" O GLY F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 358 removed outlier: 3.962A pdb=" N THR F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU F 351 " --> pdb=" O GLU F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 372 removed outlier: 3.718A pdb=" N LYS F 369 " --> pdb=" O SER F 365 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG F 370 " --> pdb=" O ASP F 366 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 378 through 386 removed outlier: 4.016A pdb=" N LEU F 385 " --> pdb=" O TRP F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 414 Processing helix chain 'F' and resid 440 through 457 Processing helix chain 'H' and resid 38 through 52 Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.509A pdb=" N LYS H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 124 through 132 Processing helix chain 'H' and resid 138 through 151 Processing helix chain 'H' and resid 165 through 186 removed outlier: 3.830A pdb=" N LYS H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 231 removed outlier: 3.575A pdb=" N GLU H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 246 removed outlier: 3.889A pdb=" N LEU H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 259 removed outlier: 4.031A pdb=" N GLU H 259 " --> pdb=" O ARG H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 348 Processing helix chain 'H' and resid 378 through 400 removed outlier: 4.481A pdb=" N ASP H 384 " --> pdb=" O GLN H 380 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 409 removed outlier: 3.638A pdb=" N ARG H 408 " --> pdb=" O ALA H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 453 Processing helix chain 'H' and resid 478 through 488 removed outlier: 3.628A pdb=" N ALA H 485 " --> pdb=" O LEU H 481 " (cutoff:3.500A) Processing helix chain 'H' and resid 504 through 514 removed outlier: 3.988A pdb=" N LYS H 508 " --> pdb=" O ASP H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 530 removed outlier: 3.683A pdb=" N TYR H 526 " --> pdb=" O LYS H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 544 through 555 removed outlier: 4.028A pdb=" N LYS H 552 " --> pdb=" O GLY H 548 " (cutoff:3.500A) Processing helix chain 'H' and resid 561 through 573 Processing helix chain 'H' and resid 608 through 637 removed outlier: 4.088A pdb=" N SER H 616 " --> pdb=" O THR H 612 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 617 " --> pdb=" O LEU H 613 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU H 620 " --> pdb=" O SER H 616 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE H 621 " --> pdb=" O ALA H 617 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS H 622 " --> pdb=" O GLY H 618 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE H 627 " --> pdb=" O LYS H 623 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU H 630 " --> pdb=" O ILE H 626 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU H 633 " --> pdb=" O THR H 629 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU H 635 " --> pdb=" O GLU H 631 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY H 637 " --> pdb=" O LEU H 633 " (cutoff:3.500A) Processing helix chain 'H' and resid 662 through 684 removed outlier: 4.573A pdb=" N GLN H 674 " --> pdb=" O ILE H 670 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU H 675 " --> pdb=" O GLU H 671 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP H 684 " --> pdb=" O VAL H 680 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA2, first strand: chain 'A' and resid 543 through 544 removed outlier: 7.008A pdb=" N VAL A 516 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR A 532 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A 514 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE A 499 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU A 306 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 462 " --> pdb=" O GLU A 306 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE A 308 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL F 266 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.606A pdb=" N VAL B 266 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 393 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 498 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 499 " --> pdb=" O LEU C 519 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 516 " --> pdb=" O GLY C 531 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY C 531 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE C 518 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE C 529 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 337 through 340 removed outlier: 6.368A pdb=" N GLU B 306 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL B 462 " --> pdb=" O GLU B 306 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE B 308 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 499 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 514 " --> pdb=" O TYR B 532 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TYR B 532 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL B 516 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 267 Processing sheet with id=AA6, first strand: chain 'D' and resid 266 through 267 removed outlier: 6.135A pdb=" N ILE E 308 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N CYS E 464 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL E 310 " --> pdb=" O CYS E 464 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL E 307 " --> pdb=" O THR E 498 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE E 500 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET E 309 " --> pdb=" O ILE E 500 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU E 502 " --> pdb=" O MET E 309 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N THR E 311 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 499 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL E 514 " --> pdb=" O TYR E 532 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR E 532 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL E 516 " --> pdb=" O ALA E 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 337 through 340 removed outlier: 5.976A pdb=" N ILE D 308 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL D 307 " --> pdb=" O THR D 498 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE D 500 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET D 309 " --> pdb=" O ILE D 500 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU D 502 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR D 311 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D 499 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL D 514 " --> pdb=" O TYR D 532 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR D 532 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL D 516 " --> pdb=" O ALA D 530 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 15 removed outlier: 3.831A pdb=" N TYR E 13 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN E 26 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 76 through 77 removed outlier: 6.421A pdb=" N GLN E 107 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL E 123 " --> pdb=" O GLN E 107 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA E 109 " --> pdb=" O GLN E 121 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN E 121 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TYR E 111 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 123 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS E 131 " --> pdb=" O VAL E 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 141 through 142 removed outlier: 7.800A pdb=" N VAL E 176 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL E 154 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU E 178 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N THR E 156 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE E 153 " --> pdb=" O ILE E 203 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY E 258 " --> pdb=" O VAL E 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 97 through 100 removed outlier: 3.585A pdb=" N SER F 120 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 175 through 176 removed outlier: 7.579A pdb=" N VAL F 176 " --> pdb=" O LYS F 152 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL F 154 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE F 202 " --> pdb=" O ARG F 229 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 391 through 392 removed outlier: 6.886A pdb=" N VAL F 337 " --> pdb=" O HIS F 392 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL F 307 " --> pdb=" O THR F 498 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ILE F 500 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET F 309 " --> pdb=" O ILE F 500 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU F 502 " --> pdb=" O MET F 309 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N THR F 311 " --> pdb=" O LEU F 502 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE F 499 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL F 514 " --> pdb=" O TYR F 532 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR F 532 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL F 516 " --> pdb=" O ALA F 530 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 32 through 34 removed outlier: 4.148A pdb=" N GLY H 21 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE H 2 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE H 56 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 232 through 233 Processing sheet with id=AB7, first strand: chain 'H' and resid 264 through 267 Processing sheet with id=AB8, first strand: chain 'H' and resid 419 through 421 Processing sheet with id=AB9, first strand: chain 'H' and resid 646 through 651 removed outlier: 7.106A pdb=" N GLN H 657 " --> pdb=" O MET H 649 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 574 through 579 removed outlier: 3.927A pdb=" N SER H 576 " --> pdb=" O LYS H 587 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 592 through 594 714 hydrogen bonds defined for protein. 2037 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue (no planarity definition) Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3578 1.31 - 1.44: 5726 1.44 - 1.56: 12338 1.56 - 1.69: 91 1.69 - 1.82: 202 Bond restraints: 21935 Sorted by residual: bond pdb=" O3B TTP B 700 " pdb=" PG TTP B 700 " ideal model delta sigma weight residual 1.748 1.593 0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" O3B TTP E 602 " pdb=" PG TTP E 602 " ideal model delta sigma weight residual 1.748 1.594 0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" O3B TTP C 700 " pdb=" PG TTP C 700 " ideal model delta sigma weight residual 1.748 1.594 0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" O3B TTP D 700 " pdb=" PG TTP D 700 " ideal model delta sigma weight residual 1.748 1.595 0.153 2.00e-02 2.50e+03 5.85e+01 bond pdb=" O3B TTP F 700 " pdb=" PG TTP F 700 " ideal model delta sigma weight residual 1.748 1.596 0.152 2.00e-02 2.50e+03 5.80e+01 ... (remaining 21930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 29244 2.90 - 5.79: 343 5.79 - 8.69: 57 8.69 - 11.59: 22 11.59 - 14.48: 27 Bond angle restraints: 29693 Sorted by residual: angle pdb=" N GLN B 364 " pdb=" CA GLN B 364 " pdb=" C GLN B 364 " ideal model delta sigma weight residual 113.21 120.12 -6.91 1.15e+00 7.56e-01 3.61e+01 angle pdb=" O4' DT T2039 " pdb=" C4' DT T2039 " pdb=" C3' DT T2039 " ideal model delta sigma weight residual 106.00 102.85 3.15 6.00e-01 2.78e+00 2.76e+01 angle pdb=" C2 TTP D 700 " pdb=" N3 TTP D 700 " pdb=" C4 TTP D 700 " ideal model delta sigma weight residual 128.28 113.80 14.48 3.00e+00 1.11e-01 2.33e+01 angle pdb=" C2 TTP F 700 " pdb=" N3 TTP F 700 " pdb=" C4 TTP F 700 " ideal model delta sigma weight residual 128.28 113.81 14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" C2 TTP E 602 " pdb=" N3 TTP E 602 " pdb=" C4 TTP E 602 " ideal model delta sigma weight residual 128.28 113.83 14.45 3.00e+00 1.11e-01 2.32e+01 ... (remaining 29688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.80: 12664 27.80 - 55.59: 402 55.59 - 83.39: 72 83.39 - 111.19: 1 111.19 - 138.99: 1 Dihedral angle restraints: 13140 sinusoidal: 5674 harmonic: 7466 Sorted by residual: dihedral pdb=" CD ARG H 604 " pdb=" NE ARG H 604 " pdb=" CZ ARG H 604 " pdb=" NH1 ARG H 604 " ideal model delta sinusoidal sigma weight residual 0.00 -73.24 73.24 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CD ARG B 363 " pdb=" NE ARG B 363 " pdb=" CZ ARG B 363 " pdb=" NH1 ARG B 363 " ideal model delta sinusoidal sigma weight residual 0.00 67.33 -67.33 1 1.00e+01 1.00e-02 5.90e+01 dihedral pdb=" CA ILE E 261 " pdb=" C ILE E 261 " pdb=" N PRO E 262 " pdb=" CA PRO E 262 " ideal model delta harmonic sigma weight residual -180.00 -149.15 -30.85 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 13137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2850 0.077 - 0.154: 412 0.154 - 0.231: 22 0.231 - 0.307: 5 0.307 - 0.384: 1 Chirality restraints: 3290 Sorted by residual: chirality pdb=" CA ILE E 261 " pdb=" N ILE E 261 " pdb=" C ILE E 261 " pdb=" CB ILE E 261 " both_signs ideal model delta sigma weight residual False 2.43 2.82 -0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" C4' TTP D 700 " pdb=" C3' TTP D 700 " pdb=" C5' TTP D 700 " pdb=" O4' TTP D 700 " both_signs ideal model delta sigma weight residual False -2.46 -2.75 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C4' TTP B 700 " pdb=" C3' TTP B 700 " pdb=" C5' TTP B 700 " pdb=" O4' TTP B 700 " both_signs ideal model delta sigma weight residual False -2.46 -2.75 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 3287 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 604 " 1.052 9.50e-02 1.11e+02 4.72e-01 1.34e+02 pdb=" NE ARG H 604 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG H 604 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG H 604 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG H 604 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 363 " 1.011 9.50e-02 1.11e+02 4.53e-01 1.24e+02 pdb=" NE ARG B 363 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG B 363 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 363 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 363 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 229 " 0.387 9.50e-02 1.11e+02 1.74e-01 1.84e+01 pdb=" NE ARG F 229 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG F 229 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG F 229 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 229 " 0.013 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 308 2.68 - 3.23: 17967 3.23 - 3.79: 31231 3.79 - 4.34: 41776 4.34 - 4.90: 69366 Nonbonded interactions: 160648 Sorted by model distance: nonbonded pdb=" O2B TTP F 700 " pdb="MG MG F 701 " model vdw 2.125 2.170 nonbonded pdb=" O2G TTP D 700 " pdb="MG MG D 701 " model vdw 2.142 2.170 nonbonded pdb=" O1G TTP B 700 " pdb="MG MG B 701 " model vdw 2.187 2.170 nonbonded pdb=" O1B TTP B 700 " pdb="MG MG B 701 " model vdw 2.187 2.170 nonbonded pdb=" OG SER B 319 " pdb="MG MG B 701 " model vdw 2.197 2.170 ... (remaining 160643 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 264 through 395 or resid 405 through 430 or resid 439 or ( \ resid 440 and (name N or name CA or name C or name O or name CB )) or resid 441 \ through 546)) selection = (chain 'B' and (resid 264 through 280 or resid 285 through 342 or resid 346 thro \ ugh 363 or resid 370 through 395 or resid 405 through 430 or resid 439 or (resid \ 440 and (name N or name CA or name C or name O or name CB )) or resid 441 throu \ gh 505 or resid 511 through 546)) selection = (chain 'C' and (resid 264 through 280 or resid 285 through 342 or resid 346 thro \ ugh 363 or resid 370 through 395 or resid 405 through 430 or resid 439 or (resid \ 440 and (name N or name CA or name C or name O or name CB )) or resid 441 throu \ gh 505 or resid 511 through 546)) selection = (chain 'D' and (resid 264 through 342 or resid 346 through 363 or resid 370 thro \ ugh 395 or resid 405 through 430 or resid 439 through 505 or resid 511 through 5 \ 46)) } ncs_group { reference = (chain 'E' and (resid 65 through 292 or resid 294 through 545)) selection = (chain 'F' and (resid 65 through 208 or resid 219 through 545)) } 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: 4.340 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.370 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 0.203 21941 Z= 0.324 Angle : 0.958 14.481 29701 Z= 0.496 Chirality : 0.053 0.384 3290 Planarity : 0.013 0.472 3660 Dihedral : 13.006 138.986 8355 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 0.41 % Allowed : 3.58 % Favored : 96.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 1.79 % 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: -4.08 (0.13), residues: 2581 helix: -3.01 (0.11), residues: 896 sheet: -1.31 (0.24), residues: 451 loop : -3.00 (0.14), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.013 0.001 TYR H 648 PHE 0.024 0.002 PHE H 686 TRP 0.046 0.002 TRP H 700 HIS 0.008 0.001 HIS C 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.32 (21935) covalent geometry : angle 0.94813 / 0.50 (29693) SS BOND : bond 0.00041 / 0.03 ( 1) SS BOND : angle 1.14604 / 0.47 ( 2) hydrogen bonds : bond 0.16082 / 10.78 ( 727) hydrogen bonds : angle 6.61097 / 4.31 ( 2063) metal coordination : bond 0.15127 / 11.24 ( 4) metal coordination : angle 9.71235 / 7.09 ( 6) Misc. bond : bond 0.00077 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 651 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.7700 (m-10) cc_final: 0.7377 (m-90) REVERT: A 361 ARG cc_start: 0.6894 (mmm-85) cc_final: 0.6516 (ttm110) REVERT: A 394 TYR cc_start: 0.8148 (t80) cc_final: 0.7888 (t80) REVERT: A 412 MET cc_start: 0.8187 (ttm) cc_final: 0.7755 (ttm) REVERT: A 443 ASP cc_start: 0.7981 (t0) cc_final: 0.7590 (t0) REVERT: A 515 LEU cc_start: 0.8919 (tt) cc_final: 0.8452 (mp) REVERT: B 352 ASP cc_start: 0.7800 (m-30) cc_final: 0.7342 (m-30) REVERT: B 375 ASN cc_start: 0.8788 (p0) cc_final: 0.8182 (p0) REVERT: B 437 ASP cc_start: 0.7747 (t70) cc_final: 0.7255 (p0) REVERT: B 497 ASP cc_start: 0.8896 (m-30) cc_final: 0.8121 (t0) REVERT: C 300 LEU cc_start: 0.8993 (mt) cc_final: 0.8759 (tt) REVERT: C 494 GLN cc_start: 0.8997 (mt0) cc_final: 0.8677 (mt0) REVERT: D 316 MET cc_start: 0.9055 (mmp) cc_final: 0.8483 (mmm) REVERT: D 370 ARG cc_start: 0.8404 (ptp-170) cc_final: 0.8191 (ttp-110) REVERT: D 405 LEU cc_start: 0.9035 (tp) cc_final: 0.8761 (tt) REVERT: D 409 LEU cc_start: 0.9672 (mt) cc_final: 0.9447 (mt) REVERT: D 456 THR cc_start: 0.8565 (p) cc_final: 0.7985 (p) REVERT: E 187 LYS cc_start: 0.9418 (tppt) cc_final: 0.9087 (ttpt) REVERT: E 251 MET cc_start: 0.8332 (mmm) cc_final: 0.7958 (mmt) REVERT: E 255 TRP cc_start: 0.8609 (m100) cc_final: 0.8088 (m100) REVERT: E 256 ASN cc_start: 0.8300 (m110) cc_final: 0.7892 (t0) REVERT: E 303 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.6878 (mtt-85) REVERT: E 370 ARG cc_start: 0.8243 (ptp-170) cc_final: 0.7835 (tmm-80) REVERT: E 497 ASP cc_start: 0.8258 (m-30) cc_final: 0.7996 (t0) REVERT: E 542 LEU cc_start: 0.9305 (mm) cc_final: 0.9064 (mt) REVERT: F 91 CYS cc_start: 0.8710 (m) cc_final: 0.8385 (p) REVERT: F 142 PHE cc_start: 0.6956 (t80) cc_final: 0.6661 (t80) REVERT: F 163 LEU cc_start: 0.9005 (mt) cc_final: 0.8805 (mt) REVERT: F 166 MET cc_start: 0.8699 (mtp) cc_final: 0.8394 (mtp) REVERT: F 359 ARG cc_start: 0.7191 (mmt-90) cc_final: 0.6811 (mmp80) REVERT: F 412 MET cc_start: 0.8870 (mtt) cc_final: 0.8648 (mtm) REVERT: F 425 HIS cc_start: 0.7202 (t-90) cc_final: 0.6509 (t-170) REVERT: F 526 ASP cc_start: 0.8834 (p0) cc_final: 0.8454 (p0) REVERT: H 130 TYR cc_start: 0.8383 (m-80) cc_final: 0.8169 (m-80) REVERT: H 179 LYS cc_start: 0.8103 (tmtt) cc_final: 0.7592 (pttp) REVERT: H 332 VAL cc_start: 0.8824 (p) cc_final: 0.8419 (m) REVERT: H 585 GLN cc_start: 0.7169 (mm-40) cc_final: 0.6567 (tt0) REVERT: H 630 GLU cc_start: 0.7993 (pt0) cc_final: 0.7746 (pm20) REVERT: H 677 MET cc_start: 0.8281 (tpt) cc_final: 0.7832 (tpt) outliers start: 9 outliers final: 1 residues processed: 657 average time/residue: 0.1807 time to fit residues: 172.9694 Evaluate side-chains 303 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 303 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.0060 chunk 111 optimal weight: 1.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 296 ASN ** B 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN B 536 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 HIS D 358 ASN ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 HIS E 70 ASN E 129 ASN E 145 HIS ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN E 253 GLN E 325 GLN E 358 ASN ** E 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 444 ASN E 494 GLN F 107 GLN F 136 HIS ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 475 HIS F 512 ASN H 62 HIS H 230 ASN H 331 HIS H 423 ASN H 439 GLN H 520 ASN H 607 HIS ** H 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 640 HIS H 685 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.117288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.085887 restraints weight = 42274.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.087427 restraints weight = 24010.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088164 restraints weight = 16193.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.088825 restraints weight = 13989.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.089723 restraints weight = 12489.308| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21941 Z= 0.128 Angle : 0.596 10.997 29701 Z= 0.310 Chirality : 0.043 0.167 3290 Planarity : 0.004 0.094 3660 Dihedral : 12.141 137.251 3426 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.54 % Allowed : 11.14 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -2.83 (0.15), residues: 2581 helix: -1.44 (0.15), residues: 924 sheet: -0.93 (0.24), residues: 462 loop : -2.61 (0.15), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 77 TYR 0.012 0.001 TYR H 530 PHE 0.028 0.001 PHE C 523 TRP 0.021 0.002 TRP H 351 HIS 0.007 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (21935) covalent geometry : angle 0.59399 / 0.31 (29693) SS BOND : bond 0.00194 / 0.12 ( 1) SS BOND : angle 1.71030 / 0.73 ( 2) hydrogen bonds : bond 0.04244 / 2.86 ( 727) hydrogen bonds : angle 4.98932 / 3.26 ( 2063) metal coordination : bond 0.00700 / 0.41 ( 4) metal coordination : angle 3.20317 / 2.37 ( 6) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 338 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 ARG cc_start: 0.6806 (mmm-85) cc_final: 0.6566 (ttm110) REVERT: A 394 TYR cc_start: 0.7992 (t80) cc_final: 0.7778 (t80) REVERT: A 515 LEU cc_start: 0.9060 (tt) cc_final: 0.8663 (tp) REVERT: A 532 TYR cc_start: 0.7995 (m-80) cc_final: 0.7727 (m-80) REVERT: B 333 MET cc_start: 0.8180 (mpp) cc_final: 0.7934 (mtm) REVERT: B 348 GLU cc_start: 0.7457 (mp0) cc_final: 0.7244 (mp0) REVERT: B 352 ASP cc_start: 0.7777 (m-30) cc_final: 0.7271 (m-30) REVERT: B 375 ASN cc_start: 0.8507 (p0) cc_final: 0.8251 (p0) REVERT: B 437 ASP cc_start: 0.7786 (t70) cc_final: 0.7329 (p0) REVERT: B 497 ASP cc_start: 0.9030 (m-30) cc_final: 0.8047 (t0) REVERT: C 300 LEU cc_start: 0.8999 (mt) cc_final: 0.8644 (tt) REVERT: C 494 GLN cc_start: 0.9088 (mt0) cc_final: 0.8710 (mt0) REVERT: D 312 SER cc_start: 0.8930 (p) cc_final: 0.8064 (m) REVERT: D 316 MET cc_start: 0.8949 (mmp) cc_final: 0.8538 (mmm) REVERT: D 499 ILE cc_start: 0.9306 (mp) cc_final: 0.8918 (mm) REVERT: E 121 GLN cc_start: 0.7465 (mt0) cc_final: 0.7238 (mt0) REVERT: E 187 LYS cc_start: 0.9292 (tppt) cc_final: 0.9029 (ttpt) REVERT: E 197 ASP cc_start: 0.7669 (m-30) cc_final: 0.7437 (m-30) REVERT: E 256 ASN cc_start: 0.8333 (m110) cc_final: 0.7888 (t0) REVERT: E 306 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6945 (mt-10) REVERT: E 370 ARG cc_start: 0.8155 (ptp-170) cc_final: 0.7880 (tmm-80) REVERT: E 497 ASP cc_start: 0.8317 (m-30) cc_final: 0.8001 (t0) REVERT: F 88 LYS cc_start: 0.6764 (pptt) cc_final: 0.6242 (tmtt) REVERT: F 91 CYS cc_start: 0.8648 (m) cc_final: 0.8146 (p) REVERT: F 142 PHE cc_start: 0.7254 (t80) cc_final: 0.6505 (t80) REVERT: F 218 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6761 (tp30) REVERT: F 412 MET cc_start: 0.8969 (mtt) cc_final: 0.8760 (mtm) REVERT: H 179 LYS cc_start: 0.8072 (tmtt) cc_final: 0.7594 (pttp) REVERT: H 378 GLU cc_start: 0.7939 (mp0) cc_final: 0.7658 (mp0) REVERT: H 530 TYR cc_start: 0.8056 (m-80) cc_final: 0.7795 (m-80) REVERT: H 585 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6490 (tt0) REVERT: H 677 MET cc_start: 0.8288 (tpt) cc_final: 0.7849 (tpt) outliers start: 34 outliers final: 23 residues processed: 363 average time/residue: 0.1570 time to fit residues: 86.5839 Evaluate side-chains 289 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 266 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 485 ASP Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 545 LYS Chi-restraints excluded: chain H residue 607 HIS Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [210, 255, 81, 237, 164, 105, 80, 36, 42, 229, 170] chunk 210 optimal weight: 0.9980 chunk 255 optimal weight: 5.9990 chunk 81 optimal weight: 0.4980 chunk 237 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 229 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 HIS ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.083763 restraints weight = 43037.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.083776 restraints weight = 29309.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.084653 restraints weight = 21741.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.085152 restraints weight = 18602.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.085226 restraints weight = 16987.011| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21941 Z= 0.135 Angle : 0.560 9.655 29701 Z= 0.291 Chirality : 0.043 0.182 3290 Planarity : 0.004 0.062 3660 Dihedral : 11.658 134.208 3422 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.08 % Allowed : 12.18 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -2.18 (0.15), residues: 2581 helix: -0.65 (0.17), residues: 929 sheet: -0.65 (0.24), residues: 455 loop : -2.44 (0.15), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 439 TYR 0.014 0.001 TYR C 411 PHE 0.019 0.001 PHE F 452 TRP 0.034 0.002 TRP F 260 HIS 0.006 0.001 HIS B 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (21935) covalent geometry : angle 0.55855 / 0.29 (29693) SS BOND : bond 0.00079 / 0.05 ( 1) SS BOND : angle 1.47185 / 0.63 ( 2) hydrogen bonds : bond 0.03734 / 2.52 ( 727) hydrogen bonds : angle 4.56288 / 3.01 ( 2063) metal coordination : bond 0.00637 / 0.36 ( 4) metal coordination : angle 2.77068 / 1.91 ( 6) Misc. bond : bond 0.00025 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 278 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.7875 (m-10) cc_final: 0.7416 (m-90) REVERT: A 361 ARG cc_start: 0.6946 (mmm-85) cc_final: 0.6663 (ttm110) REVERT: A 394 TYR cc_start: 0.8021 (t80) cc_final: 0.7788 (t80) REVERT: A 468 ASN cc_start: 0.8737 (t0) cc_final: 0.8533 (t0) REVERT: A 515 LEU cc_start: 0.9203 (tt) cc_final: 0.8674 (tp) REVERT: A 532 TYR cc_start: 0.8038 (m-80) cc_final: 0.7781 (m-80) REVERT: A 537 LYS cc_start: 0.6966 (mmtt) cc_final: 0.6659 (tppt) REVERT: B 375 ASN cc_start: 0.8582 (p0) cc_final: 0.8339 (p0) REVERT: B 437 ASP cc_start: 0.7839 (t70) cc_final: 0.7388 (p0) REVERT: B 497 ASP cc_start: 0.9131 (m-30) cc_final: 0.8037 (t0) REVERT: B 542 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8812 (pp) REVERT: C 300 LEU cc_start: 0.8998 (mt) cc_final: 0.8639 (tt) REVERT: C 333 MET cc_start: 0.8573 (mmt) cc_final: 0.8277 (mmt) REVERT: C 341 MET cc_start: 0.9028 (mmt) cc_final: 0.8806 (mmt) REVERT: D 312 SER cc_start: 0.9055 (p) cc_final: 0.8149 (m) REVERT: D 316 MET cc_start: 0.9017 (mmp) cc_final: 0.8616 (mmm) REVERT: D 499 ILE cc_start: 0.9241 (mp) cc_final: 0.8874 (mm) REVERT: E 187 LYS cc_start: 0.9287 (tppt) cc_final: 0.9027 (ttpt) REVERT: E 197 ASP cc_start: 0.7786 (m-30) cc_final: 0.7511 (m-30) REVERT: E 370 ARG cc_start: 0.8143 (ptp-170) cc_final: 0.7892 (tmm-80) REVERT: E 497 ASP cc_start: 0.8373 (m-30) cc_final: 0.8107 (t0) REVERT: F 88 LYS cc_start: 0.6727 (pptt) cc_final: 0.6430 (tmtt) REVERT: F 91 CYS cc_start: 0.8326 (m) cc_final: 0.8124 (m) REVERT: F 142 PHE cc_start: 0.7194 (t80) cc_final: 0.6704 (t80) REVERT: F 162 MET cc_start: 0.8425 (tmm) cc_final: 0.7933 (tmm) REVERT: F 169 GLN cc_start: 0.8244 (mp10) cc_final: 0.8032 (mp10) REVERT: H 90 ASP cc_start: 0.8570 (t0) cc_final: 0.8086 (t0) REVERT: H 179 LYS cc_start: 0.8102 (tmtt) cc_final: 0.7601 (pttp) REVERT: H 378 GLU cc_start: 0.8089 (mp0) cc_final: 0.7783 (mp0) REVERT: H 461 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8276 (pp) REVERT: H 585 GLN cc_start: 0.7353 (mm-40) cc_final: 0.6614 (pt0) REVERT: H 630 GLU cc_start: 0.8055 (pt0) cc_final: 0.7761 (pt0) REVERT: H 677 MET cc_start: 0.8399 (tpt) cc_final: 0.8076 (tpt) outliers start: 46 outliers final: 34 residues processed: 312 average time/residue: 0.1569 time to fit residues: 75.5376 Evaluate side-chains 285 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 249 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 503 GLU Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain F residue 247 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 545 LYS Chi-restraints excluded: chain H residue 607 HIS Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [249, 40, 13, 229, 126, 201, 218, 107, 58, 12, 31] chunk 249 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 ASN A 465 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 239 ASN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 607 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.079175 restraints weight = 43777.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080169 restraints weight = 25509.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.080399 restraints weight = 19456.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.080799 restraints weight = 17153.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.081270 restraints weight = 15268.600| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 21941 Z= 0.201 Angle : 0.616 10.368 29701 Z= 0.315 Chirality : 0.045 0.180 3290 Planarity : 0.004 0.057 3660 Dihedral : 11.628 129.807 3422 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.72 % Allowed : 12.91 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.72 (0.16), residues: 2581 helix: -0.01 (0.18), residues: 934 sheet: -0.70 (0.24), residues: 471 loop : -2.29 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 323 TYR 0.026 0.002 TYR A 547 PHE 0.019 0.002 PHE E 523 TRP 0.019 0.002 TRP E 42 HIS 0.006 0.001 HIS H 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (21935) covalent geometry : angle 0.61457 / 0.31 (29693) SS BOND : bond 0.00163 / 0.10 ( 1) SS BOND : angle 1.39763 / 0.56 ( 2) hydrogen bonds : bond 0.04107 / 2.78 ( 727) hydrogen bonds : angle 4.47370 / 2.99 ( 2063) metal coordination : bond 0.00533 / 0.31 ( 4) metal coordination : angle 3.11063 / 2.10 ( 6) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 248 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.7961 (m-10) cc_final: 0.7606 (m-90) REVERT: A 537 LYS cc_start: 0.6852 (mmtt) cc_final: 0.6552 (tppt) REVERT: B 375 ASN cc_start: 0.8599 (p0) cc_final: 0.8396 (p0) REVERT: B 437 ASP cc_start: 0.7813 (t70) cc_final: 0.7394 (p0) REVERT: B 542 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8886 (pp) REVERT: C 333 MET cc_start: 0.8669 (mmt) cc_final: 0.8419 (mmt) REVERT: C 441 MET cc_start: 0.8350 (tpp) cc_final: 0.8050 (tpp) REVERT: D 316 MET cc_start: 0.9120 (mmp) cc_final: 0.8627 (mmm) REVERT: D 499 ILE cc_start: 0.9208 (mp) cc_final: 0.8869 (mm) REVERT: E 187 LYS cc_start: 0.9342 (tppt) cc_final: 0.9091 (ttpt) REVERT: E 197 ASP cc_start: 0.7730 (m-30) cc_final: 0.7494 (m-30) REVERT: E 497 ASP cc_start: 0.8439 (m-30) cc_final: 0.8143 (t0) REVERT: F 88 LYS cc_start: 0.6866 (pptt) cc_final: 0.6245 (tttm) REVERT: F 91 CYS cc_start: 0.8442 (m) cc_final: 0.8180 (p) REVERT: F 142 PHE cc_start: 0.7332 (t80) cc_final: 0.6610 (t80) REVERT: F 162 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7899 (tmm) REVERT: F 341 MET cc_start: 0.7917 (mmt) cc_final: 0.7646 (mmt) REVERT: F 359 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.7512 (mtp85) REVERT: H 17 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8344 (mppt) REVERT: H 146 MET cc_start: 0.8598 (mmm) cc_final: 0.8132 (tpt) REVERT: H 179 LYS cc_start: 0.8127 (tmtt) cc_final: 0.7593 (pttp) REVERT: H 378 GLU cc_start: 0.8207 (mp0) cc_final: 0.7945 (mp0) REVERT: H 585 GLN cc_start: 0.7311 (mm-40) cc_final: 0.6606 (pt0) REVERT: H 630 GLU cc_start: 0.8091 (pt0) cc_final: 0.7666 (pt0) REVERT: H 677 MET cc_start: 0.8482 (tpt) cc_final: 0.8189 (tpt) outliers start: 60 outliers final: 40 residues processed: 292 average time/residue: 0.1570 time to fit residues: 70.6263 Evaluate side-chains 268 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 489 SER Chi-restraints excluded: chain D residue 466 LEU Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 17 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 545 LYS Chi-restraints excluded: chain H residue 607 HIS Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [111, 60, 7, 18, 154, 132, 37, 62, 20, 115, 230] chunk 111 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 132 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 230 optimal weight: 2.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 HIS ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.081125 restraints weight = 42801.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.082242 restraints weight = 24965.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.082452 restraints weight = 19423.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.082909 restraints weight = 16740.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.083196 restraints weight = 14867.730| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21941 Z= 0.103 Angle : 0.512 10.699 29701 Z= 0.265 Chirality : 0.042 0.196 3290 Planarity : 0.003 0.057 3660 Dihedral : 11.414 129.607 3422 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.08 % Allowed : 14.36 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.43 (0.16), residues: 2581 helix: 0.28 (0.18), residues: 927 sheet: -0.59 (0.24), residues: 470 loop : -2.14 (0.16), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 439 TYR 0.020 0.001 TYR A 394 PHE 0.015 0.001 PHE E 452 TRP 0.042 0.001 TRP E 147 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (21935) covalent geometry : angle 0.51092 / 0.27 (29693) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 0.94340 / 0.39 ( 2) hydrogen bonds : bond 0.03308 / 2.21 ( 727) hydrogen bonds : angle 4.23378 / 2.84 ( 2063) metal coordination : bond 0.00329 / 0.17 ( 4) metal coordination : angle 2.42933 / 1.59 ( 6) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.7955 (m-10) cc_final: 0.7585 (m-90) REVERT: A 537 LYS cc_start: 0.6744 (mmtt) cc_final: 0.6451 (tppt) REVERT: B 375 ASN cc_start: 0.8601 (p0) cc_final: 0.8399 (p0) REVERT: B 437 ASP cc_start: 0.7692 (t70) cc_final: 0.7353 (p0) REVERT: B 487 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.6894 (ttm-80) REVERT: B 542 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8846 (pp) REVERT: C 441 MET cc_start: 0.8307 (tpp) cc_final: 0.8026 (tpp) REVERT: D 316 MET cc_start: 0.9050 (mmp) cc_final: 0.8598 (mmm) REVERT: D 499 ILE cc_start: 0.9197 (mp) cc_final: 0.8875 (mm) REVERT: E 41 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7780 (pttt) REVERT: E 187 LYS cc_start: 0.9347 (tppt) cc_final: 0.9096 (ttpt) REVERT: E 197 ASP cc_start: 0.7821 (m-30) cc_final: 0.7596 (m-30) REVERT: E 208 MET cc_start: 0.3026 (mmp) cc_final: 0.2687 (mmp) REVERT: E 251 MET cc_start: 0.8768 (tpp) cc_final: 0.8244 (mmt) REVERT: E 306 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6979 (mt-10) REVERT: F 88 LYS cc_start: 0.6853 (pptt) cc_final: 0.6167 (tttm) REVERT: F 91 CYS cc_start: 0.8418 (m) cc_final: 0.8165 (p) REVERT: F 142 PHE cc_start: 0.7250 (t80) cc_final: 0.6754 (t80) REVERT: F 162 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7946 (tmm) REVERT: F 169 GLN cc_start: 0.8311 (mp10) cc_final: 0.8057 (mp10) REVERT: F 203 ILE cc_start: 0.8385 (mm) cc_final: 0.8130 (mm) REVERT: F 341 MET cc_start: 0.7826 (mmt) cc_final: 0.7580 (mmt) REVERT: H 17 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8408 (mppt) REVERT: H 146 MET cc_start: 0.8562 (mmm) cc_final: 0.8149 (tpt) REVERT: H 179 LYS cc_start: 0.8102 (tmtt) cc_final: 0.7562 (pttp) REVERT: H 378 GLU cc_start: 0.8126 (mp0) cc_final: 0.7875 (mp0) REVERT: H 391 MET cc_start: 0.7635 (tmm) cc_final: 0.7005 (tmm) REVERT: H 514 GLU cc_start: 0.5436 (OUTLIER) cc_final: 0.4717 (pp20) REVERT: H 585 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6614 (pt0) REVERT: H 630 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7703 (pp20) REVERT: H 677 MET cc_start: 0.8468 (tpt) cc_final: 0.8157 (tpt) outliers start: 46 outliers final: 30 residues processed: 286 average time/residue: 0.1603 time to fit residues: 70.5822 Evaluate side-chains 269 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 17 LYS Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 537 ILE Chi-restraints excluded: chain H residue 545 LYS Chi-restraints excluded: chain H residue 630 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [258, 34, 17, 128, 95, 0, 245, 153, 248, 183, 180] chunk 258 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 HIS ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.077265 restraints weight = 44101.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.077961 restraints weight = 27075.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.078595 restraints weight = 19671.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.079450 restraints weight = 16533.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.079399 restraints weight = 14798.739| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 21941 Z= 0.252 Angle : 0.630 10.721 29701 Z= 0.321 Chirality : 0.046 0.371 3290 Planarity : 0.004 0.056 3660 Dihedral : 11.630 129.025 3422 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.94 % Allowed : 14.67 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.41 (0.16), residues: 2581 helix: 0.32 (0.18), residues: 932 sheet: -0.59 (0.24), residues: 475 loop : -2.15 (0.16), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 274 TYR 0.021 0.002 TYR A 547 PHE 0.015 0.002 PHE C 523 TRP 0.028 0.002 TRP F 260 HIS 0.007 0.001 HIS H 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.25 (21935) covalent geometry : angle 0.62822 / 0.32 (29693) SS BOND : bond 0.00021 / 0.01 ( 1) SS BOND : angle 0.89173 / 0.35 ( 2) hydrogen bonds : bond 0.04172 / 2.83 ( 727) hydrogen bonds : angle 4.46064 / 3.01 ( 2063) metal coordination : bond 0.00525 / 0.32 ( 4) metal coordination : angle 3.32901 / 2.24 ( 6) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 242 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8093 (m-10) cc_final: 0.7755 (m-90) REVERT: A 537 LYS cc_start: 0.6905 (mmtt) cc_final: 0.6574 (tppt) REVERT: B 437 ASP cc_start: 0.7796 (t70) cc_final: 0.7447 (p0) REVERT: B 542 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8977 (pp) REVERT: D 316 MET cc_start: 0.9113 (mmp) cc_final: 0.8625 (mmm) REVERT: D 523 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: E 187 LYS cc_start: 0.9423 (tppt) cc_final: 0.9166 (ttpt) REVERT: E 197 ASP cc_start: 0.7789 (m-30) cc_final: 0.7530 (m-30) REVERT: E 306 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7157 (mt-10) REVERT: F 88 LYS cc_start: 0.7045 (pptt) cc_final: 0.6216 (tttm) REVERT: F 91 CYS cc_start: 0.8581 (m) cc_final: 0.8228 (p) REVERT: F 142 PHE cc_start: 0.7506 (t80) cc_final: 0.6993 (t80) REVERT: F 169 GLN cc_start: 0.8430 (mp10) cc_final: 0.8082 (mp10) REVERT: F 341 MET cc_start: 0.8046 (mmt) cc_final: 0.7813 (mmt) REVERT: F 359 ARG cc_start: 0.7916 (mmt-90) cc_final: 0.7627 (mtp85) REVERT: H 17 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8475 (mppt) REVERT: H 146 MET cc_start: 0.8599 (mmm) cc_final: 0.8145 (tpt) REVERT: H 179 LYS cc_start: 0.8091 (tmtt) cc_final: 0.7552 (pttp) REVERT: H 359 LYS cc_start: 0.7863 (pmmt) cc_final: 0.7574 (mmtt) REVERT: H 378 GLU cc_start: 0.8226 (mp0) cc_final: 0.7991 (mp0) REVERT: H 514 GLU cc_start: 0.5288 (OUTLIER) cc_final: 0.4754 (pp20) REVERT: H 585 GLN cc_start: 0.7363 (mm-40) cc_final: 0.6608 (pt0) REVERT: H 630 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7755 (pt0) REVERT: H 677 MET cc_start: 0.8514 (tpt) cc_final: 0.8227 (tpt) outliers start: 65 outliers final: 43 residues processed: 287 average time/residue: 0.1557 time to fit residues: 69.3387 Evaluate side-chains 275 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 193 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 380 GLN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 17 LYS Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 545 LYS Chi-restraints excluded: chain H residue 630 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [132, 228, 68, 146, 87, 150, 69, 194, 143, 114, 206] chunk 132 optimal weight: 0.6980 chunk 228 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 146 optimal weight: 0.4980 chunk 87 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 206 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 512 ASN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.110386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.081324 restraints weight = 42938.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080177 restraints weight = 30947.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.080942 restraints weight = 26636.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.081491 restraints weight = 21773.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.081604 restraints weight = 18516.726| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21941 Z= 0.101 Angle : 0.520 9.595 29701 Z= 0.268 Chirality : 0.042 0.203 3290 Planarity : 0.003 0.054 3660 Dihedral : 11.408 129.409 3422 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.95 % Allowed : 15.85 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.17 (0.16), residues: 2581 helix: 0.55 (0.18), residues: 929 sheet: -0.50 (0.25), residues: 470 loop : -2.01 (0.16), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 303 TYR 0.019 0.001 TYR A 547 PHE 0.015 0.001 PHE F 71 TRP 0.053 0.001 TRP E 147 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (21935) covalent geometry : angle 0.51893 / 0.27 (29693) SS BOND : bond 0.00077 / 0.05 ( 1) SS BOND : angle 0.61810 / 0.26 ( 2) hydrogen bonds : bond 0.03231 / 2.16 ( 727) hydrogen bonds : angle 4.14482 / 2.79 ( 2063) metal coordination : bond 0.00277 / 0.15 ( 4) metal coordination : angle 2.45259 / 1.60 ( 6) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 239 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8073 (m-10) cc_final: 0.7684 (m-90) REVERT: A 426 ILE cc_start: 0.8590 (pt) cc_final: 0.8362 (tt) REVERT: A 537 LYS cc_start: 0.6811 (mmtt) cc_final: 0.6504 (tppt) REVERT: B 352 ASP cc_start: 0.8694 (t0) cc_final: 0.8485 (t0) REVERT: B 437 ASP cc_start: 0.7717 (t70) cc_final: 0.7337 (p0) REVERT: B 487 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.6911 (ttm-80) REVERT: B 533 MET cc_start: 0.8051 (mtm) cc_final: 0.7571 (mtm) REVERT: C 441 MET cc_start: 0.8340 (tpp) cc_final: 0.7957 (tpp) REVERT: D 316 MET cc_start: 0.9017 (mmp) cc_final: 0.8505 (mmm) REVERT: D 499 ILE cc_start: 0.9191 (mp) cc_final: 0.8894 (mm) REVERT: E 41 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7898 (pttt) REVERT: E 124 ARG cc_start: 0.7070 (ttm-80) cc_final: 0.6866 (tpt170) REVERT: E 162 MET cc_start: 0.8213 (tmm) cc_final: 0.7999 (tmm) REVERT: E 187 LYS cc_start: 0.9391 (tppt) cc_final: 0.9147 (ttpt) REVERT: E 197 ASP cc_start: 0.7818 (m-30) cc_final: 0.7573 (m-30) REVERT: E 251 MET cc_start: 0.8772 (tpp) cc_final: 0.8277 (mmt) REVERT: E 260 TRP cc_start: 0.8374 (p-90) cc_final: 0.8124 (p-90) REVERT: E 306 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7142 (mt-10) REVERT: E 404 ARG cc_start: 0.6243 (OUTLIER) cc_final: 0.4670 (pmt-80) REVERT: F 88 LYS cc_start: 0.7039 (pptt) cc_final: 0.6225 (tttm) REVERT: F 91 CYS cc_start: 0.8356 (m) cc_final: 0.8119 (p) REVERT: F 162 MET cc_start: 0.8495 (tmm) cc_final: 0.8219 (tmm) REVERT: F 169 GLN cc_start: 0.8394 (mp10) cc_final: 0.8074 (mp10) REVERT: F 203 ILE cc_start: 0.8407 (mm) cc_final: 0.8119 (mm) REVERT: F 341 MET cc_start: 0.7998 (mmt) cc_final: 0.7784 (mmt) REVERT: F 359 ARG cc_start: 0.7825 (mmt-90) cc_final: 0.7596 (mtp85) REVERT: H 146 MET cc_start: 0.8581 (mmm) cc_final: 0.8114 (tpt) REVERT: H 378 GLU cc_start: 0.8179 (mp0) cc_final: 0.7964 (mp0) REVERT: H 391 MET cc_start: 0.7676 (tmm) cc_final: 0.7034 (tmm) REVERT: H 514 GLU cc_start: 0.5529 (OUTLIER) cc_final: 0.4860 (pp20) REVERT: H 585 GLN cc_start: 0.7366 (mm-40) cc_final: 0.6632 (pt0) REVERT: H 630 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7670 (pp20) REVERT: H 677 MET cc_start: 0.8448 (tpt) cc_final: 0.8135 (tpt) outliers start: 43 outliers final: 31 residues processed: 270 average time/residue: 0.1541 time to fit residues: 63.9831 Evaluate side-chains 268 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 630 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [21, 163, 236, 71, 152, 241, 251, 145, 185, 85, 11] chunk 21 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 241 optimal weight: 0.5980 chunk 251 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 ASN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 ASN ** F 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.106838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.076436 restraints weight = 43947.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.077104 restraints weight = 26568.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.077590 restraints weight = 19953.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.078247 restraints weight = 16926.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.078383 restraints weight = 15173.421| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 21941 Z= 0.249 Angle : 0.654 11.933 29701 Z= 0.329 Chirality : 0.046 0.185 3290 Planarity : 0.004 0.053 3660 Dihedral : 11.651 127.976 3422 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.49 % Allowed : 15.67 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.20 (0.16), residues: 2581 helix: 0.53 (0.18), residues: 928 sheet: -0.58 (0.24), residues: 478 loop : -2.02 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 504 TYR 0.025 0.002 TYR A 394 PHE 0.016 0.002 PHE C 523 TRP 0.023 0.002 TRP E 147 HIS 0.007 0.001 HIS H 683 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.25 (21935) covalent geometry : angle 0.65233 / 0.33 (29693) SS BOND : bond 0.00104 / 0.06 ( 1) SS BOND : angle 0.84802 / 0.31 ( 2) hydrogen bonds : bond 0.04267 / 2.91 ( 727) hydrogen bonds : angle 4.41516 / 2.97 ( 2063) metal coordination : bond 0.00476 / 0.30 ( 4) metal coordination : angle 3.46050 / 2.32 ( 6) Misc. bond : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8151 (m-10) cc_final: 0.7756 (m-90) REVERT: B 437 ASP cc_start: 0.7873 (t70) cc_final: 0.7481 (p0) REVERT: D 306 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7542 (mm-30) REVERT: D 316 MET cc_start: 0.9125 (mmp) cc_final: 0.8605 (mmm) REVERT: D 523 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: E 19 ASN cc_start: 0.8877 (t0) cc_final: 0.8452 (m-40) REVERT: E 187 LYS cc_start: 0.9463 (tppt) cc_final: 0.9206 (ttpt) REVERT: E 197 ASP cc_start: 0.7776 (m-30) cc_final: 0.7524 (m-30) REVERT: E 208 MET cc_start: 0.2978 (mmp) cc_final: 0.2564 (mmp) REVERT: E 260 TRP cc_start: 0.8418 (p-90) cc_final: 0.8087 (p-90) REVERT: E 306 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7300 (mt-10) REVERT: E 404 ARG cc_start: 0.6159 (OUTLIER) cc_final: 0.5119 (pmt-80) REVERT: F 88 LYS cc_start: 0.7045 (pptt) cc_final: 0.6134 (tttm) REVERT: F 91 CYS cc_start: 0.8519 (m) cc_final: 0.8184 (p) REVERT: F 97 TRP cc_start: 0.7969 (p-90) cc_final: 0.7632 (p-90) REVERT: F 142 PHE cc_start: 0.7225 (t80) cc_final: 0.7014 (t80) REVERT: F 169 GLN cc_start: 0.8470 (mp10) cc_final: 0.8070 (mp10) REVERT: F 203 ILE cc_start: 0.8399 (mm) cc_final: 0.8142 (mm) REVERT: F 359 ARG cc_start: 0.7954 (mmt-90) cc_final: 0.7683 (mtp85) REVERT: F 446 MET cc_start: 0.9311 (mmm) cc_final: 0.8979 (tpt) REVERT: H 146 MET cc_start: 0.8613 (mmm) cc_final: 0.8119 (tpt) REVERT: H 223 LEU cc_start: 0.8240 (tp) cc_final: 0.7902 (tp) REVERT: H 359 LYS cc_start: 0.7898 (pmmt) cc_final: 0.7579 (mmtt) REVERT: H 378 GLU cc_start: 0.8263 (mp0) cc_final: 0.8046 (mp0) REVERT: H 514 GLU cc_start: 0.5259 (OUTLIER) cc_final: 0.4873 (pp20) REVERT: H 585 GLN cc_start: 0.7372 (mm-40) cc_final: 0.6616 (pt0) REVERT: H 630 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: H 677 MET cc_start: 0.8469 (tpt) cc_final: 0.8174 (tpt) outliers start: 55 outliers final: 40 residues processed: 271 average time/residue: 0.1487 time to fit residues: 62.6668 Evaluate side-chains 262 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 527 THR Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 489 SER Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 630 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [174, 12, 186, 69, 258, 159, 84, 206, 228, 29, 8] chunk 174 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 258 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 84 optimal weight: 0.8980 chunk 206 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 ASN F 244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.109474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.080070 restraints weight = 42946.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.079143 restraints weight = 29950.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.079514 restraints weight = 26219.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.080038 restraints weight = 21506.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.080361 restraints weight = 18683.934| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21941 Z= 0.105 Angle : 0.539 11.986 29701 Z= 0.275 Chirality : 0.043 0.322 3290 Planarity : 0.003 0.053 3660 Dihedral : 11.352 128.592 3422 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.90 % Allowed : 16.12 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -1.01 (0.17), residues: 2581 helix: 0.69 (0.18), residues: 922 sheet: -0.47 (0.24), residues: 475 loop : -1.89 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 323 TYR 0.019 0.001 TYR A 547 PHE 0.017 0.001 PHE F 71 TRP 0.024 0.001 TRP E 42 HIS 0.003 0.001 HIS C 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (21935) covalent geometry : angle 0.53745 / 0.27 (29693) SS BOND : bond 0.00076 / 0.05 ( 1) SS BOND : angle 0.54537 / 0.21 ( 2) hydrogen bonds : bond 0.03301 / 2.22 ( 727) hydrogen bonds : angle 4.12059 / 2.78 ( 2063) metal coordination : bond 0.00256 / 0.15 ( 4) metal coordination : angle 2.61812 / 1.70 ( 6) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8125 (m-10) cc_final: 0.7729 (m-90) REVERT: B 306 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7988 (mm-30) REVERT: B 437 ASP cc_start: 0.7711 (t70) cc_final: 0.7372 (p0) REVERT: B 487 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.6958 (ttm-80) REVERT: C 441 MET cc_start: 0.8273 (tpp) cc_final: 0.7857 (tpp) REVERT: D 316 MET cc_start: 0.9018 (mmp) cc_final: 0.8568 (mmm) REVERT: E 19 ASN cc_start: 0.8770 (t0) cc_final: 0.8445 (m-40) REVERT: E 41 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7176 (pttt) REVERT: E 124 ARG cc_start: 0.7113 (ttm-80) cc_final: 0.6898 (tpt170) REVERT: E 187 LYS cc_start: 0.9439 (tppt) cc_final: 0.9202 (ttpt) REVERT: E 197 ASP cc_start: 0.7784 (m-30) cc_final: 0.7564 (m-30) REVERT: E 208 MET cc_start: 0.3106 (mmp) cc_final: 0.2789 (mmp) REVERT: E 251 MET cc_start: 0.8791 (tpp) cc_final: 0.8280 (mmt) REVERT: E 260 TRP cc_start: 0.8339 (p-90) cc_final: 0.8086 (p-90) REVERT: E 306 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7240 (mt-10) REVERT: E 404 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.4684 (pmt-80) REVERT: F 88 LYS cc_start: 0.7059 (pptt) cc_final: 0.6179 (tttm) REVERT: F 91 CYS cc_start: 0.8457 (m) cc_final: 0.8148 (p) REVERT: F 169 GLN cc_start: 0.8417 (mp10) cc_final: 0.8048 (mp10) REVERT: F 203 ILE cc_start: 0.8382 (mm) cc_final: 0.8094 (mm) REVERT: H 146 MET cc_start: 0.8566 (mmm) cc_final: 0.8131 (tpt) REVERT: H 359 LYS cc_start: 0.7799 (pmmt) cc_final: 0.7527 (mmtt) REVERT: H 378 GLU cc_start: 0.8187 (mp0) cc_final: 0.7982 (mp0) REVERT: H 514 GLU cc_start: 0.5466 (OUTLIER) cc_final: 0.4950 (pp20) REVERT: H 585 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6601 (pt0) REVERT: H 614 LEU cc_start: 0.7720 (mt) cc_final: 0.7381 (mt) REVERT: H 630 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7633 (pp20) REVERT: H 677 MET cc_start: 0.8469 (tpt) cc_final: 0.8163 (tpt) outliers start: 42 outliers final: 32 residues processed: 269 average time/residue: 0.1602 time to fit residues: 66.5139 Evaluate side-chains 262 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 366 ASP Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 461 LEU Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 630 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [134, 138, 261, 139, 193, 95, 217, 135, 126, 169, 10] chunk 134 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 193 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.079680 restraints weight = 43279.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.079671 restraints weight = 28394.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.079934 restraints weight = 25317.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.080446 restraints weight = 20735.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.080753 restraints weight = 17506.236| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21941 Z= 0.118 Angle : 0.547 13.288 29701 Z= 0.278 Chirality : 0.043 0.222 3290 Planarity : 0.003 0.053 3660 Dihedral : 11.282 128.946 3422 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.95 % Allowed : 16.30 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.88 (0.17), residues: 2581 helix: 0.78 (0.18), residues: 923 sheet: -0.45 (0.24), residues: 475 loop : -1.78 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 339 TYR 0.020 0.001 TYR A 394 PHE 0.017 0.001 PHE F 71 TRP 0.049 0.001 TRP E 147 HIS 0.003 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (21935) covalent geometry : angle 0.54567 / 0.28 (29693) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 0.65234 / 0.24 ( 2) hydrogen bonds : bond 0.03264 / 2.21 ( 727) hydrogen bonds : angle 4.07209 / 2.75 ( 2063) metal coordination : bond 0.00260 / 0.14 ( 4) metal coordination : angle 2.56764 / 1.68 ( 6) Misc. bond : bond 0.00002 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 226 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 329 TRP cc_start: 0.8198 (m-10) cc_final: 0.7814 (m-90) REVERT: B 306 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8105 (mm-30) REVERT: B 437 ASP cc_start: 0.7758 (t70) cc_final: 0.7366 (p0) REVERT: B 487 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7230 (ttm-80) REVERT: C 441 MET cc_start: 0.8312 (tpp) cc_final: 0.7894 (tpp) REVERT: D 306 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7380 (mm-30) REVERT: D 316 MET cc_start: 0.9034 (mmp) cc_final: 0.8569 (mmm) REVERT: E 19 ASN cc_start: 0.8713 (t0) cc_final: 0.8374 (m-40) REVERT: E 124 ARG cc_start: 0.7115 (ttm-80) cc_final: 0.6905 (tpt170) REVERT: E 187 LYS cc_start: 0.9418 (tppt) cc_final: 0.9193 (ttpt) REVERT: E 197 ASP cc_start: 0.7795 (m-30) cc_final: 0.7570 (m-30) REVERT: E 251 MET cc_start: 0.8802 (tpp) cc_final: 0.8293 (mmt) REVERT: E 260 TRP cc_start: 0.8310 (p-90) cc_final: 0.8065 (p-90) REVERT: E 306 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7251 (mt-10) REVERT: E 404 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.4701 (pmt-80) REVERT: F 88 LYS cc_start: 0.7123 (pptt) cc_final: 0.6225 (tttm) REVERT: F 91 CYS cc_start: 0.8383 (m) cc_final: 0.8123 (p) REVERT: F 97 TRP cc_start: 0.7885 (p-90) cc_final: 0.7550 (p-90) REVERT: F 169 GLN cc_start: 0.8362 (mp10) cc_final: 0.8008 (mp10) REVERT: F 203 ILE cc_start: 0.8394 (mm) cc_final: 0.8103 (mm) REVERT: H 146 MET cc_start: 0.8562 (mmm) cc_final: 0.8131 (tpt) REVERT: H 514 GLU cc_start: 0.5448 (OUTLIER) cc_final: 0.4994 (pp20) REVERT: H 585 GLN cc_start: 0.7376 (mm-40) cc_final: 0.6631 (pt0) REVERT: H 630 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7604 (pp20) REVERT: H 677 MET cc_start: 0.8389 (tpt) cc_final: 0.8100 (tpt) outliers start: 43 outliers final: 35 residues processed: 258 average time/residue: 0.1528 time to fit residues: 61.3247 Evaluate side-chains 261 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain B residue 309 MET Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 471 LYS Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 489 SER Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 404 ARG Chi-restraints excluded: chain E residue 509 ASP Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 482 SER Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain H residue 337 SER Chi-restraints excluded: chain H residue 505 ILE Chi-restraints excluded: chain H residue 514 GLU Chi-restraints excluded: chain H residue 630 GLU Chi-restraints excluded: chain H residue 686 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: [61, 117, 84, 90, 11, 149, 231, 263, 262, 134, 253] chunk 61 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 149 optimal weight: 0.0030 chunk 231 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 262 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.109342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.078346 restraints weight = 43570.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.078848 restraints weight = 32698.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.079491 restraints weight = 23800.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.080060 restraints weight = 20941.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.080165 restraints weight = 18691.671| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21941 Z= 0.124 Angle : 0.555 12.809 29701 Z= 0.282 Chirality : 0.043 0.211 3290 Planarity : 0.003 0.053 3660 Dihedral : 11.251 129.047 3422 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.04 % Allowed : 16.71 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % 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: -0.84 (0.17), residues: 2581 helix: 0.79 (0.18), residues: 930 sheet: -0.43 (0.24), residues: 476 loop : -1.74 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 339 TYR 0.018 0.001 TYR A 547 PHE 0.017 0.001 PHE F 71 TRP 0.035 0.001 TRP E 147 HIS 0.004 0.001 HIS B 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (21935) covalent geometry : angle 0.55427 / 0.28 (29693) SS BOND : bond 0.00024 / 0.02 ( 1) SS BOND : angle 0.57564 / 0.21 ( 2) hydrogen bonds : bond 0.03262 / 2.20 ( 727) hydrogen bonds : angle 4.05944 / 2.74 ( 2063) metal coordination : bond 0.00272 / 0.14 ( 4) metal coordination : angle 2.61356 / 1.71 ( 6) Misc. bond : bond 0.00006 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3184.05 seconds wall clock time: 55 minutes 57.02 seconds (3357.02 seconds total)