Starting phenix.real_space_refine on Thu Jun 19 08:56:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxt_19579/06_2025/8rxt_19579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxt_19579/06_2025/8rxt_19579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rxt_19579/06_2025/8rxt_19579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxt_19579/06_2025/8rxt_19579.map" model { file = "/net/cci-nas-00/data/ceres_data/8rxt_19579/06_2025/8rxt_19579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxt_19579/06_2025/8rxt_19579.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 126 5.16 5 C 13984 2.51 5 N 3995 2.21 5 O 4141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22258 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3650 Classifications: {'peptide': 477} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 447} Chain breaks: 2 Chain: "B" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3650 Classifications: {'peptide': 477} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 447} Chain breaks: 2 Chain: "C" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3713 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 456} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3727 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 29, 'TRANS': 456} Chain breaks: 1 Chain: "E" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3727 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 29, 'TRANS': 456} Chain breaks: 1 Chain: "F" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3667 Classifications: {'peptide': 479} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 449} Chain breaks: 2 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ANP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.44, per 1000 atoms: 0.69 Number of scatterers: 22258 At special positions: 0 Unit cell: (136.095, 129, 148.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 P 12 15.00 O 4141 8.00 N 3995 7.00 C 13984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 2.7 seconds 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5458 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 28 sheets defined 51.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.591A pdb=" N ARG A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.766A pdb=" N ASN A 100 " --> pdb=" O PRO A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.502A pdb=" N ALA A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 223 through 232 removed outlier: 3.839A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 239 through 254 removed outlier: 3.920A pdb=" N GLU A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.505A pdb=" N LEU A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 294' Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.538A pdb=" N LEU A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'A' and resid 365 through 373 removed outlier: 3.558A pdb=" N LYS A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 406 through 425 removed outlier: 3.608A pdb=" N ILE A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.764A pdb=" N MET A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 441 " --> pdb=" O CYS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 removed outlier: 3.960A pdb=" N PHE A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 479 Processing helix chain 'A' and resid 485 through 496 removed outlier: 3.715A pdb=" N SER A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 495 " --> pdb=" O GLN A 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 44 through 56 removed outlier: 4.240A pdb=" N ARG B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 97 through 102 removed outlier: 3.649A pdb=" N ASN B 100 " --> pdb=" O PRO B 97 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 102 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.731A pdb=" N VAL B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 211 removed outlier: 3.705A pdb=" N ILE B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 239 through 253 removed outlier: 4.205A pdb=" N ARG B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 289 through 294 removed outlier: 3.574A pdb=" N ALA B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 308 through 322 removed outlier: 3.975A pdb=" N LEU B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Proline residue: B 318 - end of helix Processing helix chain 'B' and resid 365 through 373 Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.735A pdb=" N LEU B 378 " --> pdb=" O SER B 375 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 379 " --> pdb=" O ALA B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 375 through 379' Processing helix chain 'B' and resid 392 through 398 Processing helix chain 'B' and resid 399 through 403 removed outlier: 4.113A pdb=" N HIS B 402 " --> pdb=" O PRO B 399 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 403 " --> pdb=" O ASN B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 399 through 403' Processing helix chain 'B' and resid 406 through 425 Processing helix chain 'B' and resid 428 through 432 removed outlier: 3.563A pdb=" N LEU B 432 " --> pdb=" O ASN B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.714A pdb=" N GLU B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 458 removed outlier: 3.511A pdb=" N PHE B 450 " --> pdb=" O GLU B 446 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 452 " --> pdb=" O GLN B 448 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 479 Processing helix chain 'B' and resid 485 through 495 removed outlier: 3.880A pdb=" N SER B 494 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR B 495 " --> pdb=" O GLN B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 44 through 56 removed outlier: 4.377A pdb=" N ARG C 48 " --> pdb=" O GLU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 97 through 102 removed outlier: 4.175A pdb=" N LEU C 101 " --> pdb=" O PRO C 97 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 102' Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 142 through 148 removed outlier: 4.146A pdb=" N LEU C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 169 Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.774A pdb=" N TYR C 187 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.936A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 252 removed outlier: 3.512A pdb=" N ILE C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 322 removed outlier: 3.622A pdb=" N ARG C 316 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Proline residue: C 318 - end of helix Processing helix chain 'C' and resid 365 through 372 Processing helix chain 'C' and resid 375 through 382 Processing helix chain 'C' and resid 391 through 396 removed outlier: 4.033A pdb=" N GLU C 395 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU C 396 " --> pdb=" O SER C 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 396' Processing helix chain 'C' and resid 406 through 425 removed outlier: 3.752A pdb=" N ILE C 410 " --> pdb=" O GLN C 406 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 432 Processing helix chain 'C' and resid 433 through 441 Processing helix chain 'C' and resid 444 through 458 Processing helix chain 'C' and resid 461 through 478 Processing helix chain 'C' and resid 485 through 493 Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'D' and resid 40 through 56 removed outlier: 5.461A pdb=" N LYS D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ASP D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.642A pdb=" N ALA D 102 " --> pdb=" O THR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 159 through 170 Processing helix chain 'D' and resid 190 through 194 Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 223 through 232 removed outlier: 3.859A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 239 through 254 removed outlier: 4.210A pdb=" N GLU D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 254 " --> pdb=" O ASN D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 289 through 294 removed outlier: 3.614A pdb=" N LEU D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 289 through 294' Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.795A pdb=" N LEU D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 365 through 373 Processing helix chain 'D' and resid 375 through 380 Processing helix chain 'D' and resid 392 through 398 removed outlier: 3.797A pdb=" N LYS D 398 " --> pdb=" O GLU D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 424 removed outlier: 4.360A pdb=" N ALA D 409 " --> pdb=" O LYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 432 Processing helix chain 'D' and resid 433 through 441 removed outlier: 3.666A pdb=" N CYS D 441 " --> pdb=" O CYS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 458 Processing helix chain 'D' and resid 461 through 479 Processing helix chain 'D' and resid 485 through 493 Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 44 through 56 removed outlier: 4.334A pdb=" N ARG E 48 " --> pdb=" O GLU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 121 through 132 removed outlier: 4.374A pdb=" N ALA E 125 " --> pdb=" O ALA E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 159 through 170 Processing helix chain 'E' and resid 198 through 210 removed outlier: 3.724A pdb=" N ASN E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 210 " --> pdb=" O ILE E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 removed outlier: 3.728A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 254 removed outlier: 3.834A pdb=" N GLU E 245 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 280 Processing helix chain 'E' and resid 289 through 294 removed outlier: 3.559A pdb=" N ALA E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 308 through 322 removed outlier: 3.654A pdb=" N LEU E 312 " --> pdb=" O ASN E 308 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU E 317 " --> pdb=" O GLU E 313 " (cutoff:3.500A) Proline residue: E 318 - end of helix Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'E' and resid 375 through 380 Processing helix chain 'E' and resid 392 through 398 Processing helix chain 'E' and resid 406 through 425 Processing helix chain 'E' and resid 433 through 441 removed outlier: 3.558A pdb=" N CYS E 441 " --> pdb=" O CYS E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 458 Processing helix chain 'E' and resid 461 through 479 Processing helix chain 'E' and resid 485 through 494 removed outlier: 3.608A pdb=" N SER E 494 " --> pdb=" O GLN E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 44 through 56 removed outlier: 4.186A pdb=" N ARG F 48 " --> pdb=" O GLU F 44 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 93 Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.811A pdb=" N ASN F 100 " --> pdb=" O PRO F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 159 through 170 removed outlier: 3.587A pdb=" N VAL F 163 " --> pdb=" O ASN F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 194 Processing helix chain 'F' and resid 198 through 211 Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.742A pdb=" N LYS F 229 " --> pdb=" O THR F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 235 removed outlier: 3.584A pdb=" N LEU F 235 " --> pdb=" O SER F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 254 removed outlier: 4.188A pdb=" N ARG F 253 " --> pdb=" O ILE F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 280 Processing helix chain 'F' and resid 289 through 294 removed outlier: 3.872A pdb=" N ALA F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 308 through 315 removed outlier: 3.629A pdb=" N LEU F 312 " --> pdb=" O ASN F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 322 Processing helix chain 'F' and resid 365 through 371 removed outlier: 3.578A pdb=" N ARG F 369 " --> pdb=" O ASP F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 375 through 380 Processing helix chain 'F' and resid 392 through 397 Processing helix chain 'F' and resid 406 through 425 Processing helix chain 'F' and resid 428 through 432 removed outlier: 3.709A pdb=" N LEU F 432 " --> pdb=" O ASN F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 441 Processing helix chain 'F' and resid 444 through 458 removed outlier: 3.704A pdb=" N PHE F 450 " --> pdb=" O GLU F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 479 Processing helix chain 'F' and resid 485 through 495 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 9 removed outlier: 6.077A pdb=" N SER A 31 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL A 67 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR A 33 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU A 69 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL A 35 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AA3, first strand: chain 'A' and resid 109 through 110 removed outlier: 3.682A pdb=" N GLU A 109 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.649A pdb=" N ARG A 268 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY A 218 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 327 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 12 removed outlier: 3.722A pdb=" N VAL B 15 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER B 31 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL B 67 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR B 33 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU B 69 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL B 35 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 104 through 107 removed outlier: 6.555A pdb=" N GLU B 105 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N ALA B 139 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N ILE B 107 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA B 157 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE B 138 " --> pdb=" O ALA B 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 109 through 110 removed outlier: 3.584A pdb=" N GLU B 109 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 267 through 268 removed outlier: 6.885A pdb=" N ARG B 268 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 344 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 10 removed outlier: 6.463A pdb=" N THR C 33 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU C 69 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL C 35 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.359A pdb=" N LEU C 136 " --> pdb=" O PHE C 155 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ALA C 157 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE C 138 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 109 through 110 Processing sheet with id=AB4, first strand: chain 'C' and resid 267 through 268 removed outlier: 6.823A pdb=" N ARG C 268 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 214 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 215 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE C 388 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER C 217 " --> pdb=" O ILE C 388 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 3 through 11 Processing sheet with id=AB6, first strand: chain 'D' and resid 104 through 106 Processing sheet with id=AB7, first strand: chain 'D' and resid 109 through 110 removed outlier: 3.795A pdb=" N GLU D 109 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 267 through 268 removed outlier: 6.678A pdb=" N ARG D 268 " --> pdb=" O PHE D 300 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY D 297 " --> pdb=" O GLN D 340 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE D 342 " --> pdb=" O GLY D 297 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ALA D 344 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU D 301 " --> pdb=" O ALA D 344 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY D 218 " --> pdb=" O MET D 345 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 326 through 327 Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 9 Processing sheet with id=AC2, first strand: chain 'E' and resid 104 through 107 removed outlier: 3.765A pdb=" N ALA E 139 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU E 136 " --> pdb=" O PHE E 155 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ALA E 157 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE E 138 " --> pdb=" O ALA E 157 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 109 through 110 Processing sheet with id=AC4, first strand: chain 'E' and resid 267 through 268 removed outlier: 6.672A pdb=" N ARG E 268 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 386 " --> pdb=" O LEU E 215 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 323 through 325 Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 9 removed outlier: 3.661A pdb=" N LEU F 69 " --> pdb=" O VAL F 35 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 104 through 107 removed outlier: 3.638A pdb=" N ALA F 139 " --> pdb=" O ILE F 107 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 109 through 110 removed outlier: 3.555A pdb=" N GLU F 109 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 267 through 268 removed outlier: 6.703A pdb=" N ARG F 268 " --> pdb=" O PHE F 300 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 323 through 326 removed outlier: 3.704A pdb=" N PHE F 335 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE F 326 " --> pdb=" O ILE F 333 " (cutoff:3.500A) 993 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.34 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4204 1.33 - 1.45: 4989 1.45 - 1.57: 13250 1.57 - 1.70: 31 1.70 - 1.82: 199 Bond restraints: 22673 Sorted by residual: bond pdb=" O3A ANP E 601 " pdb=" PB ANP E 601 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" O3A ANP A 601 " pdb=" PB ANP A 601 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" O3A ANP B 601 " pdb=" PB ANP B 601 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" O3A ANP E 602 " pdb=" PB ANP E 602 " ideal model delta sigma weight residual 1.700 1.566 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" N3B ANP E 601 " pdb=" PG ANP E 601 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.72e+01 ... (remaining 22668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 30367 3.60 - 7.20: 290 7.20 - 10.80: 38 10.80 - 14.40: 15 14.40 - 18.00: 5 Bond angle restraints: 30715 Sorted by residual: angle pdb=" CA PRO D 288 " pdb=" N PRO D 288 " pdb=" CD PRO D 288 " ideal model delta sigma weight residual 112.00 99.17 12.83 1.40e+00 5.10e-01 8.40e+01 angle pdb=" CA PRO A 276 " pdb=" N PRO A 276 " pdb=" CD PRO A 276 " ideal model delta sigma weight residual 112.00 100.08 11.92 1.40e+00 5.10e-01 7.24e+01 angle pdb=" CA PRO A 377 " pdb=" N PRO A 377 " pdb=" CD PRO A 377 " ideal model delta sigma weight residual 112.00 100.22 11.78 1.40e+00 5.10e-01 7.08e+01 angle pdb=" CA PRO E 97 " pdb=" N PRO E 97 " pdb=" CD PRO E 97 " ideal model delta sigma weight residual 112.00 100.67 11.33 1.40e+00 5.10e-01 6.55e+01 angle pdb=" N PRO C 177 " pdb=" CA PRO C 177 " pdb=" C PRO C 177 " ideal model delta sigma weight residual 110.70 118.96 -8.26 1.22e+00 6.72e-01 4.58e+01 ... (remaining 30710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.58: 12403 18.58 - 37.17: 1294 37.17 - 55.75: 284 55.75 - 74.34: 81 74.34 - 92.92: 43 Dihedral angle restraints: 14105 sinusoidal: 5745 harmonic: 8360 Sorted by residual: dihedral pdb=" CA ASN D 284 " pdb=" C ASN D 284 " pdb=" N PRO D 285 " pdb=" CA PRO D 285 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ILE A 12 " pdb=" C ILE A 12 " pdb=" N GLY A 13 " pdb=" CA GLY A 13 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LYS C 255 " pdb=" C LYS C 255 " pdb=" N LEU C 256 " pdb=" CA LEU C 256 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 14102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3115 0.063 - 0.125: 412 0.125 - 0.188: 25 0.188 - 0.251: 4 0.251 - 0.313: 5 Chirality restraints: 3561 Sorted by residual: chirality pdb=" CG LEU E 173 " pdb=" CB LEU E 173 " pdb=" CD1 LEU E 173 " pdb=" CD2 LEU E 173 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C3' ANP A 601 " pdb=" C2' ANP A 601 " pdb=" C4' ANP A 601 " pdb=" O3' ANP A 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C3' ANP B 601 " pdb=" C2' ANP B 601 " pdb=" C4' ANP B 601 " pdb=" O3' ANP B 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3558 not shown) Planarity restraints: 3968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 275 " 0.102 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO A 276 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 96 " -0.091 5.00e-02 4.00e+02 1.29e-01 2.66e+01 pdb=" N PRO E 97 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO E 97 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO E 97 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 176 " 0.082 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO D 177 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO D 177 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO D 177 " 0.062 5.00e-02 4.00e+02 ... (remaining 3965 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1276 2.73 - 3.27: 23868 3.27 - 3.82: 34634 3.82 - 4.36: 41010 4.36 - 4.90: 70304 Nonbonded interactions: 171092 Sorted by model distance: nonbonded pdb=" O ASP A 383 " pdb=" NZ LYS A 496 " model vdw 2.188 3.120 nonbonded pdb=" O ALA D 146 " pdb=" OG1 THR D 149 " model vdw 2.195 3.040 nonbonded pdb=" O ASN D 429 " pdb=" NZ LYS D 470 " model vdw 2.203 3.120 nonbonded pdb=" O THR C 401 " pdb=" ND1 HIS C 402 " model vdw 2.215 3.120 nonbonded pdb=" OG SER A 147 " pdb=" O PRO A 177 " model vdw 2.239 3.040 ... (remaining 171087 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 1 through 500) selection = (chain 'B' and resid 1 through 500) selection = (chain 'C' and (resid 1 through 181 or resid 191 through 500)) selection = (chain 'D' and (resid 1 through 181 or resid 191 through 500)) selection = (chain 'E' and (resid 1 through 181 or resid 191 through 500)) selection = (chain 'F' and (resid 1 through 180 or resid 190 through 500)) } 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: 10.430 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: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 50.190 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.008 0.829 22674 Z= 0.595 Angle : 0.916 18.004 30715 Z= 0.450 Chirality : 0.044 0.313 3561 Planarity : 0.007 0.145 3968 Dihedral : 16.934 92.924 8647 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.33 % Favored : 93.01 % Rotamer: Outliers : 0.62 % Allowed : 19.28 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2861 helix: 0.30 (0.15), residues: 1232 sheet: 0.50 (0.25), residues: 480 loop : -0.55 (0.20), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 191 HIS 0.015 0.001 HIS C 295 PHE 0.032 0.001 PHE C 231 TYR 0.020 0.002 TYR C 166 ARG 0.011 0.001 ARG F 48 Details of bonding type rmsd hydrogen bonds : bond 0.17862 ( 993) hydrogen bonds : angle 6.90763 ( 2808) covalent geometry : bond 0.00514 (22673) covalent geometry : angle 0.91590 (30715) Misc. bond : bond 0.82870 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 653 time to evaluate : 2.691 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 226 MET cc_start: 0.7279 (tpt) cc_final: 0.7073 (ptm) REVERT: A 299 LEU cc_start: 0.8824 (tt) cc_final: 0.8559 (tt) REVERT: A 455 MET cc_start: 0.8182 (mmm) cc_final: 0.7566 (mmm) REVERT: A 467 ARG cc_start: 0.9044 (mtm180) cc_final: 0.8734 (ptp-170) REVERT: A 489 LEU cc_start: 0.9035 (mt) cc_final: 0.8743 (mp) REVERT: C 205 VAL cc_start: 0.9504 (t) cc_final: 0.9284 (t) REVERT: C 299 LEU cc_start: 0.9093 (tp) cc_final: 0.8881 (tt) REVERT: C 381 ARG cc_start: 0.8701 (mmm-85) cc_final: 0.8333 (ttp80) REVERT: C 450 PHE cc_start: 0.9014 (t80) cc_final: 0.8784 (t80) REVERT: D 42 VAL cc_start: 0.6976 (p) cc_final: 0.6584 (p) REVERT: D 209 CYS cc_start: 0.7997 (m) cc_final: 0.7410 (m) REVERT: D 212 HIS cc_start: 0.8599 (m-70) cc_final: 0.8368 (m90) REVERT: D 227 MET cc_start: 0.8869 (mmt) cc_final: 0.8581 (mmm) REVERT: D 346 ASN cc_start: 0.8953 (m-40) cc_final: 0.8591 (t0) REVERT: E 132 ASP cc_start: 0.8233 (t0) cc_final: 0.8007 (t0) REVERT: E 310 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8312 (tm-30) REVERT: E 324 ILE cc_start: 0.8738 (tt) cc_final: 0.8518 (tp) REVERT: E 474 THR cc_start: 0.8526 (m) cc_final: 0.8301 (p) REVERT: F 432 LEU cc_start: 0.8453 (mt) cc_final: 0.8242 (mt) outliers start: 15 outliers final: 3 residues processed: 659 average time/residue: 0.3362 time to fit residues: 337.1708 Evaluate side-chains 451 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 448 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 MET Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain F residue 451 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 135 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 258 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 ASN A 133 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 HIS C 310 GLN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN D 55 ASN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN E 24 HIS E 130 HIS E 199 HIS ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 GLN ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.103659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.075701 restraints weight = 73624.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.077845 restraints weight = 40120.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079335 restraints weight = 26840.000| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 22674 Z= 0.327 Angle : 0.899 13.618 30715 Z= 0.443 Chirality : 0.048 0.263 3561 Planarity : 0.007 0.089 3968 Dihedral : 9.344 113.102 3176 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.17 % Favored : 92.24 % Rotamer: Outliers : 5.55 % Allowed : 20.68 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2861 helix: -0.00 (0.14), residues: 1283 sheet: 0.09 (0.24), residues: 498 loop : -0.90 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 262 HIS 0.010 0.002 HIS A 323 PHE 0.024 0.003 PHE B 81 TYR 0.023 0.003 TYR C 465 ARG 0.015 0.001 ARG A 309 Details of bonding type rmsd hydrogen bonds : bond 0.04555 ( 993) hydrogen bonds : angle 5.79592 ( 2808) covalent geometry : bond 0.00696 (22673) covalent geometry : angle 0.89888 (30715) Misc. bond : bond 0.00139 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 460 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8885 (pt) REVERT: A 229 LYS cc_start: 0.9166 (pttp) cc_final: 0.8943 (pttt) REVERT: A 301 LEU cc_start: 0.9534 (mm) cc_final: 0.9306 (mm) REVERT: A 320 GLU cc_start: 0.9364 (mm-30) cc_final: 0.9004 (mp0) REVERT: A 417 MET cc_start: 0.8835 (tpp) cc_final: 0.8282 (mmt) REVERT: A 455 MET cc_start: 0.8987 (mmm) cc_final: 0.8736 (mmm) REVERT: A 489 LEU cc_start: 0.9342 (mt) cc_final: 0.9142 (mp) REVERT: B 105 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8157 (mt-10) REVERT: B 306 GLU cc_start: 0.8964 (tp30) cc_final: 0.8285 (tp30) REVERT: B 417 MET cc_start: 0.9346 (mmt) cc_final: 0.8986 (mmt) REVERT: B 443 LEU cc_start: 0.8600 (tp) cc_final: 0.8379 (tp) REVERT: B 466 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.7266 (t70) REVERT: B 496 LYS cc_start: 0.9117 (tppp) cc_final: 0.8639 (tppp) REVERT: C 226 MET cc_start: 0.7586 (tpt) cc_final: 0.7330 (tpt) REVERT: C 313 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7713 (mp0) REVERT: C 450 PHE cc_start: 0.9393 (t80) cc_final: 0.9058 (t80) REVERT: D 17 GLN cc_start: 0.8222 (mp10) cc_final: 0.7931 (mp10) REVERT: D 212 HIS cc_start: 0.8738 (m-70) cc_final: 0.8506 (m-70) REVERT: D 226 MET cc_start: 0.8758 (mtm) cc_final: 0.8179 (mtm) REVERT: D 253 ARG cc_start: 0.9363 (mtp180) cc_final: 0.9007 (ttp-170) REVERT: D 325 CYS cc_start: 0.9027 (m) cc_final: 0.8679 (m) REVERT: D 335 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7762 (m-10) REVERT: D 479 ASN cc_start: 0.9397 (OUTLIER) cc_final: 0.8878 (m110) REVERT: E 229 LYS cc_start: 0.9251 (ptmt) cc_final: 0.8958 (pttp) REVERT: E 310 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8609 (tm-30) REVERT: F 69 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8983 (pt) REVERT: F 227 MET cc_start: 0.8801 (pmm) cc_final: 0.8540 (pmm) REVERT: F 231 PHE cc_start: 0.9344 (t80) cc_final: 0.9113 (t80) REVERT: F 260 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7461 (ptm-80) REVERT: F 287 LYS cc_start: 0.9220 (tmmt) cc_final: 0.8929 (pptt) REVERT: F 426 ASP cc_start: 0.8250 (m-30) cc_final: 0.8046 (m-30) outliers start: 135 outliers final: 79 residues processed: 548 average time/residue: 0.4163 time to fit residues: 360.8591 Evaluate side-chains 499 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 414 time to evaluate : 5.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 292 SER Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain D residue 479 ASN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 260 ARG Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 470 LYS Chi-restraints excluded: chain F residue 471 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 235 optimal weight: 8.9990 chunk 284 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 197 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 ASN A 272 HIS ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 HIS ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 GLN ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.106189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078481 restraints weight = 71813.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080779 restraints weight = 37771.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082342 restraints weight = 24522.819| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22674 Z= 0.144 Angle : 0.789 12.543 30715 Z= 0.376 Chirality : 0.044 0.269 3561 Planarity : 0.005 0.073 3968 Dihedral : 8.332 107.937 3170 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.54 % Favored : 92.83 % Rotamer: Outliers : 3.99 % Allowed : 22.74 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2861 helix: 0.32 (0.15), residues: 1272 sheet: 0.19 (0.24), residues: 495 loop : -0.83 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 262 HIS 0.011 0.001 HIS C 402 PHE 0.026 0.001 PHE E 339 TYR 0.021 0.002 TYR E 187 ARG 0.009 0.001 ARG A 268 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 993) hydrogen bonds : angle 5.22429 ( 2808) covalent geometry : bond 0.00327 (22673) covalent geometry : angle 0.78859 (30715) Misc. bond : bond 0.00221 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 446 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8718 (pt) REVERT: A 105 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8605 (mt-10) REVERT: A 171 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.8995 (p) REVERT: A 417 MET cc_start: 0.8872 (tpp) cc_final: 0.8647 (mmt) REVERT: A 485 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8396 (mm) REVERT: A 489 LEU cc_start: 0.9288 (mt) cc_final: 0.9002 (mt) REVERT: B 105 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8002 (mt-10) REVERT: B 250 ASN cc_start: 0.9409 (m-40) cc_final: 0.9209 (m110) REVERT: B 406 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: B 417 MET cc_start: 0.9478 (mmt) cc_final: 0.8836 (mmt) REVERT: B 443 LEU cc_start: 0.8499 (tp) cc_final: 0.8267 (tp) REVERT: B 459 LYS cc_start: 0.9377 (mmtt) cc_final: 0.8122 (pptt) REVERT: B 466 HIS cc_start: 0.8297 (OUTLIER) cc_final: 0.7191 (t70) REVERT: B 496 LYS cc_start: 0.8967 (tppp) cc_final: 0.8695 (tptp) REVERT: C 226 MET cc_start: 0.7450 (tpt) cc_final: 0.7101 (tpt) REVERT: C 313 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7706 (mp0) REVERT: C 381 ARG cc_start: 0.9200 (mmm-85) cc_final: 0.8556 (ttp-170) REVERT: C 450 PHE cc_start: 0.9373 (t80) cc_final: 0.9006 (t80) REVERT: D 182 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7821 (mp) REVERT: D 226 MET cc_start: 0.8753 (mtm) cc_final: 0.8353 (mtm) REVERT: D 253 ARG cc_start: 0.9344 (mtp180) cc_final: 0.8962 (ttp-170) REVERT: D 325 CYS cc_start: 0.8977 (m) cc_final: 0.8650 (m) REVERT: D 335 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7500 (m-10) REVERT: D 463 ARG cc_start: 0.8475 (mmm160) cc_final: 0.8190 (mmm160) REVERT: D 489 LEU cc_start: 0.9330 (tt) cc_final: 0.9067 (pp) REVERT: E 17 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8777 (mm-40) REVERT: E 215 LEU cc_start: 0.9170 (tt) cc_final: 0.8951 (tp) REVERT: E 229 LYS cc_start: 0.9279 (ptmt) cc_final: 0.9026 (pttp) REVERT: E 310 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8433 (tm-30) REVERT: E 431 ASN cc_start: 0.8920 (t0) cc_final: 0.8717 (t0) REVERT: F 69 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8892 (pt) REVERT: F 227 MET cc_start: 0.8798 (pmm) cc_final: 0.8475 (pmm) REVERT: F 260 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7504 (ptm-80) REVERT: F 453 GLU cc_start: 0.9303 (tp30) cc_final: 0.9061 (tp30) REVERT: F 465 TYR cc_start: 0.8229 (t80) cc_final: 0.7856 (t80) REVERT: F 477 ASP cc_start: 0.9054 (m-30) cc_final: 0.8511 (m-30) REVERT: F 491 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8413 (mm-40) outliers start: 97 outliers final: 46 residues processed: 511 average time/residue: 0.3266 time to fit residues: 260.6670 Evaluate side-chains 470 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 415 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 272 HIS Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 260 ARG Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 490 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 198 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 0.0000 chunk 122 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 overall best weight: 2.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 HIS A 431 ASN C 151 HIS C 431 ASN D 55 ASN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.104116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.076127 restraints weight = 72231.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.078314 restraints weight = 39203.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.079841 restraints weight = 25952.509| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22674 Z= 0.183 Angle : 0.773 12.303 30715 Z= 0.370 Chirality : 0.044 0.320 3561 Planarity : 0.005 0.074 3968 Dihedral : 7.961 109.404 3170 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.10 % Favored : 92.28 % Rotamer: Outliers : 4.93 % Allowed : 22.49 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2861 helix: 0.42 (0.15), residues: 1274 sheet: 0.11 (0.24), residues: 493 loop : -0.91 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 262 HIS 0.011 0.001 HIS C 402 PHE 0.030 0.002 PHE C 231 TYR 0.020 0.002 TYR A 465 ARG 0.008 0.001 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 993) hydrogen bonds : angle 5.13802 ( 2808) covalent geometry : bond 0.00409 (22673) covalent geometry : angle 0.77319 (30715) Misc. bond : bond 0.00105 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 429 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8773 (pt) REVERT: A 384 MET cc_start: 0.7464 (tpt) cc_final: 0.7193 (tpt) REVERT: A 417 MET cc_start: 0.9078 (tpp) cc_final: 0.8564 (mmt) REVERT: A 455 MET cc_start: 0.8600 (mmm) cc_final: 0.8302 (mmm) REVERT: A 485 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8304 (mm) REVERT: A 489 LEU cc_start: 0.9338 (mt) cc_final: 0.9095 (mp) REVERT: B 406 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: B 417 MET cc_start: 0.9506 (mmt) cc_final: 0.9026 (mmt) REVERT: B 443 LEU cc_start: 0.8553 (tp) cc_final: 0.8322 (tp) REVERT: B 466 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.7235 (t70) REVERT: B 496 LYS cc_start: 0.8891 (tppp) cc_final: 0.8541 (tptm) REVERT: C 226 MET cc_start: 0.7514 (tpt) cc_final: 0.7185 (tpt) REVERT: C 259 PHE cc_start: 0.8507 (t80) cc_final: 0.8111 (t80) REVERT: C 313 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7794 (mm-30) REVERT: C 439 MET cc_start: 0.9110 (mmm) cc_final: 0.8891 (mmt) REVERT: D 17 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8617 (mp10) REVERT: D 226 MET cc_start: 0.8725 (mtm) cc_final: 0.8387 (mtm) REVERT: D 253 ARG cc_start: 0.9345 (mtp180) cc_final: 0.8982 (ttp-170) REVERT: D 325 CYS cc_start: 0.8963 (m) cc_final: 0.8674 (m) REVERT: D 335 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7532 (m-10) REVERT: D 385 GLN cc_start: 0.8144 (tp-100) cc_final: 0.7941 (tp-100) REVERT: D 440 VAL cc_start: 0.7551 (OUTLIER) cc_final: 0.7263 (m) REVERT: D 489 LEU cc_start: 0.9397 (tt) cc_final: 0.9104 (pp) REVERT: E 95 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: E 215 LEU cc_start: 0.9184 (tt) cc_final: 0.8960 (tp) REVERT: E 229 LYS cc_start: 0.9270 (ptmt) cc_final: 0.9033 (pttp) REVERT: E 264 LEU cc_start: 0.9414 (mm) cc_final: 0.9018 (tt) REVERT: E 310 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8511 (tm-30) REVERT: E 431 ASN cc_start: 0.9044 (t0) cc_final: 0.8779 (t0) REVERT: F 260 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7537 (ptm-80) REVERT: F 412 GLU cc_start: 0.9182 (mp0) cc_final: 0.8776 (pm20) REVERT: F 416 LYS cc_start: 0.9452 (mttt) cc_final: 0.9188 (pttm) REVERT: F 432 LEU cc_start: 0.8696 (mt) cc_final: 0.8459 (mt) REVERT: F 453 GLU cc_start: 0.9230 (tp30) cc_final: 0.8875 (tp30) REVERT: F 465 TYR cc_start: 0.8213 (t80) cc_final: 0.7881 (t80) REVERT: F 477 ASP cc_start: 0.9113 (m-30) cc_final: 0.8568 (m-30) REVERT: F 482 LYS cc_start: 0.9113 (tptt) cc_final: 0.8910 (tptp) outliers start: 120 outliers final: 79 residues processed: 511 average time/residue: 0.3281 time to fit residues: 262.1927 Evaluate side-chains 483 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 396 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 272 HIS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 496 LYS Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 406 GLN Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 262 TRP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 260 ARG Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 490 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 132 optimal weight: 0.0670 chunk 18 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 201 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN B 159 ASN C 186 ASN C 448 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.103975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076760 restraints weight = 72835.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.078925 restraints weight = 39108.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.080401 restraints weight = 25689.658| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22674 Z= 0.177 Angle : 0.779 14.262 30715 Z= 0.371 Chirality : 0.043 0.317 3561 Planarity : 0.005 0.072 3968 Dihedral : 7.860 109.245 3170 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.17 % Favored : 92.21 % Rotamer: Outliers : 5.55 % Allowed : 23.27 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2861 helix: 0.42 (0.15), residues: 1280 sheet: 0.11 (0.24), residues: 489 loop : -0.95 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 262 HIS 0.015 0.001 HIS A 272 PHE 0.033 0.002 PHE E 339 TYR 0.032 0.002 TYR D 465 ARG 0.009 0.001 ARG D 463 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 993) hydrogen bonds : angle 5.11376 ( 2808) covalent geometry : bond 0.00399 (22673) covalent geometry : angle 0.77945 (30715) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 424 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8747 (pt) REVERT: A 204 MET cc_start: 0.8987 (mtm) cc_final: 0.8448 (mtm) REVERT: A 290 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: A 455 MET cc_start: 0.8717 (mmm) cc_final: 0.8231 (mmm) REVERT: A 478 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8812 (mtp) REVERT: A 485 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8316 (mm) REVERT: A 489 LEU cc_start: 0.9323 (mt) cc_final: 0.9081 (mp) REVERT: B 1 MET cc_start: 0.8751 (mmm) cc_final: 0.8512 (mmm) REVERT: B 69 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8396 (pt) REVERT: B 105 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7989 (mt-10) REVERT: B 159 ASN cc_start: 0.9452 (OUTLIER) cc_final: 0.9175 (p0) REVERT: B 272 HIS cc_start: 0.9020 (p90) cc_final: 0.8626 (p90) REVERT: B 381 ARG cc_start: 0.7429 (ptm160) cc_final: 0.7091 (mtp180) REVERT: B 417 MET cc_start: 0.9524 (mmt) cc_final: 0.9049 (mmt) REVERT: B 443 LEU cc_start: 0.8564 (tp) cc_final: 0.8356 (tp) REVERT: B 459 LYS cc_start: 0.9338 (mmpt) cc_final: 0.8192 (pptt) REVERT: B 466 HIS cc_start: 0.8362 (OUTLIER) cc_final: 0.7254 (t70) REVERT: B 496 LYS cc_start: 0.8836 (tppp) cc_final: 0.8533 (tptm) REVERT: C 226 MET cc_start: 0.7580 (tpt) cc_final: 0.7247 (tpt) REVERT: C 259 PHE cc_start: 0.8577 (t80) cc_final: 0.8141 (t80) REVERT: C 448 GLN cc_start: 0.9315 (mt0) cc_final: 0.8929 (tm-30) REVERT: D 17 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8612 (mp10) REVERT: D 90 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.9002 (mm) REVERT: D 226 MET cc_start: 0.8736 (mtm) cc_final: 0.8399 (mtm) REVERT: D 246 CYS cc_start: 0.9320 (OUTLIER) cc_final: 0.9088 (m) REVERT: D 253 ARG cc_start: 0.9352 (mtp180) cc_final: 0.9000 (ttp-170) REVERT: D 325 CYS cc_start: 0.8963 (m) cc_final: 0.8695 (m) REVERT: D 335 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7668 (m-10) REVERT: D 385 GLN cc_start: 0.8149 (tp-100) cc_final: 0.7902 (tp-100) REVERT: D 440 VAL cc_start: 0.7566 (OUTLIER) cc_final: 0.7293 (m) REVERT: E 17 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8610 (mm-40) REVERT: E 95 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7921 (mp10) REVERT: E 215 LEU cc_start: 0.9163 (tt) cc_final: 0.8936 (tp) REVERT: E 229 LYS cc_start: 0.9264 (ptmt) cc_final: 0.9036 (pttp) REVERT: E 264 LEU cc_start: 0.9415 (mm) cc_final: 0.9016 (tt) REVERT: E 310 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8492 (tm-30) REVERT: F 260 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7459 (ptm-80) REVERT: F 262 TRP cc_start: 0.7327 (m-90) cc_final: 0.6767 (m-10) REVERT: F 412 GLU cc_start: 0.9233 (mp0) cc_final: 0.8856 (pm20) REVERT: F 432 LEU cc_start: 0.8721 (mt) cc_final: 0.8471 (mt) REVERT: F 453 GLU cc_start: 0.9151 (tp30) cc_final: 0.8547 (tp30) REVERT: F 457 LYS cc_start: 0.9233 (mttm) cc_final: 0.8788 (mttm) REVERT: F 465 TYR cc_start: 0.8209 (t80) cc_final: 0.7909 (t80) REVERT: F 477 ASP cc_start: 0.9126 (m-30) cc_final: 0.8499 (m-30) outliers start: 135 outliers final: 84 residues processed: 518 average time/residue: 0.3490 time to fit residues: 284.6541 Evaluate side-chains 493 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 396 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 262 TRP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 260 ARG Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 490 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 8.9990 chunk 245 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 431 ASN B 130 HIS B 159 ASN B 169 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.099441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.071883 restraints weight = 73060.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.073986 restraints weight = 39421.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.075432 restraints weight = 26266.075| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22674 Z= 0.246 Angle : 0.812 13.317 30715 Z= 0.390 Chirality : 0.044 0.277 3561 Planarity : 0.005 0.069 3968 Dihedral : 7.959 109.427 3170 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.72 % Favored : 91.65 % Rotamer: Outliers : 5.35 % Allowed : 24.10 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2861 helix: 0.34 (0.15), residues: 1279 sheet: -0.01 (0.24), residues: 469 loop : -1.04 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 262 HIS 0.014 0.001 HIS A 272 PHE 0.024 0.002 PHE E 339 TYR 0.022 0.002 TYR D 465 ARG 0.012 0.001 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 993) hydrogen bonds : angle 5.21983 ( 2808) covalent geometry : bond 0.00540 (22673) covalent geometry : angle 0.81186 (30715) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 405 time to evaluate : 3.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8773 (pt) REVERT: A 204 MET cc_start: 0.9023 (mtm) cc_final: 0.8471 (mtm) REVERT: A 290 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8513 (tt0) REVERT: A 309 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7791 (mmp-170) REVERT: A 345 MET cc_start: 0.7681 (tmm) cc_final: 0.7467 (tmm) REVERT: A 384 MET cc_start: 0.7516 (tpt) cc_final: 0.7144 (tpt) REVERT: A 417 MET cc_start: 0.9057 (tpp) cc_final: 0.8678 (mmt) REVERT: A 455 MET cc_start: 0.8861 (mmm) cc_final: 0.8470 (mmm) REVERT: A 478 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8776 (mtp) REVERT: A 485 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8260 (mm) REVERT: A 489 LEU cc_start: 0.9316 (mt) cc_final: 0.9094 (mp) REVERT: B 69 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8441 (pt) REVERT: B 159 ASN cc_start: 0.9437 (OUTLIER) cc_final: 0.8990 (p0) REVERT: B 272 HIS cc_start: 0.9089 (p90) cc_final: 0.8837 (p90) REVERT: B 417 MET cc_start: 0.9538 (mmt) cc_final: 0.9119 (mmt) REVERT: B 443 LEU cc_start: 0.8691 (tp) cc_final: 0.8483 (tp) REVERT: B 466 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.7265 (t70) REVERT: C 1 MET cc_start: 0.7364 (tmm) cc_final: 0.7083 (tmm) REVERT: C 226 MET cc_start: 0.7597 (tpt) cc_final: 0.7289 (tpt) REVERT: C 259 PHE cc_start: 0.8642 (t80) cc_final: 0.8216 (t80) REVERT: D 17 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8605 (mp10) REVERT: D 226 MET cc_start: 0.8759 (mtm) cc_final: 0.8478 (mtm) REVERT: D 253 ARG cc_start: 0.9359 (mtp180) cc_final: 0.9043 (ttp-170) REVERT: D 325 CYS cc_start: 0.8936 (m) cc_final: 0.8721 (m) REVERT: D 335 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7449 (m-10) REVERT: D 440 VAL cc_start: 0.7543 (OUTLIER) cc_final: 0.7299 (m) REVERT: E 17 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8784 (mm-40) REVERT: E 95 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7900 (mp10) REVERT: E 186 ASN cc_start: 0.8460 (m-40) cc_final: 0.7956 (m-40) REVERT: E 215 LEU cc_start: 0.9161 (tt) cc_final: 0.8924 (tp) REVERT: E 229 LYS cc_start: 0.9259 (ptmt) cc_final: 0.9034 (pttp) REVERT: E 231 PHE cc_start: 0.9426 (t80) cc_final: 0.9134 (t80) REVERT: E 310 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8479 (tm-30) REVERT: F 260 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7506 (ptm-80) REVERT: F 262 TRP cc_start: 0.7398 (m-90) cc_final: 0.6903 (m-10) REVERT: F 432 LEU cc_start: 0.8741 (mt) cc_final: 0.8485 (mt) REVERT: F 443 LEU cc_start: 0.9008 (tp) cc_final: 0.8791 (tp) REVERT: F 455 MET cc_start: 0.8963 (mtm) cc_final: 0.8641 (mtm) REVERT: F 477 ASP cc_start: 0.9172 (m-30) cc_final: 0.8647 (m-30) outliers start: 130 outliers final: 98 residues processed: 497 average time/residue: 0.3951 time to fit residues: 310.4854 Evaluate side-chains 499 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 389 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 68 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain B residue 469 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 262 TRP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 135 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 260 ARG Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 490 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 280 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 239 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 219 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 270 optimal weight: 8.9990 chunk 279 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN B 159 ASN B 250 ASN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 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 = 0.3648 r_free = 0.3648 target = 0.100181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.073450 restraints weight = 73793.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.075596 restraints weight = 38897.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.077059 restraints weight = 25379.520| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22674 Z= 0.183 Angle : 0.802 13.877 30715 Z= 0.379 Chirality : 0.043 0.220 3561 Planarity : 0.005 0.069 3968 Dihedral : 7.840 110.821 3168 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.48 % Favored : 91.93 % Rotamer: Outliers : 4.85 % Allowed : 25.12 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.16), residues: 2861 helix: 0.38 (0.15), residues: 1280 sheet: -0.10 (0.24), residues: 475 loop : -0.99 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 262 HIS 0.009 0.001 HIS C 402 PHE 0.032 0.002 PHE E 339 TYR 0.023 0.002 TYR B 465 ARG 0.013 0.001 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 993) hydrogen bonds : angle 5.12412 ( 2808) covalent geometry : bond 0.00413 (22673) covalent geometry : angle 0.80172 (30715) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 407 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8727 (pt) REVERT: A 204 MET cc_start: 0.9017 (mtm) cc_final: 0.8443 (mtm) REVERT: A 309 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7770 (mmp-170) REVERT: A 339 PHE cc_start: 0.9401 (p90) cc_final: 0.9142 (p90) REVERT: A 384 MET cc_start: 0.7583 (tpt) cc_final: 0.7286 (tpt) REVERT: A 417 MET cc_start: 0.9050 (tpp) cc_final: 0.8707 (mmt) REVERT: A 455 MET cc_start: 0.8868 (mmm) cc_final: 0.8470 (mmm) REVERT: A 467 ARG cc_start: 0.9152 (ptp-170) cc_final: 0.8675 (mtt180) REVERT: A 478 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8756 (mtp) REVERT: A 485 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8293 (mm) REVERT: A 489 LEU cc_start: 0.9319 (mt) cc_final: 0.9100 (mp) REVERT: B 69 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8400 (pt) REVERT: B 159 ASN cc_start: 0.9546 (OUTLIER) cc_final: 0.9048 (p0) REVERT: B 272 HIS cc_start: 0.9057 (p90) cc_final: 0.8574 (p90) REVERT: B 417 MET cc_start: 0.9528 (mmt) cc_final: 0.9095 (mmt) REVERT: B 459 LYS cc_start: 0.9447 (mmpt) cc_final: 0.8056 (pptt) REVERT: B 466 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.7307 (t70) REVERT: C 1 MET cc_start: 0.7464 (tmm) cc_final: 0.7227 (tmm) REVERT: C 226 MET cc_start: 0.7603 (tpt) cc_final: 0.7292 (tpt) REVERT: C 259 PHE cc_start: 0.8649 (t80) cc_final: 0.8197 (t80) REVERT: C 381 ARG cc_start: 0.9161 (mmm-85) cc_final: 0.8231 (ttp-170) REVERT: C 448 GLN cc_start: 0.9290 (mt0) cc_final: 0.8904 (tm-30) REVERT: D 17 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8584 (mp10) REVERT: D 226 MET cc_start: 0.8796 (mtm) cc_final: 0.8576 (mtp) REVERT: D 246 CYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9123 (m) REVERT: D 253 ARG cc_start: 0.9345 (mtp180) cc_final: 0.9053 (ttp-170) REVERT: D 325 CYS cc_start: 0.8947 (m) cc_final: 0.8723 (m) REVERT: D 335 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7501 (m-10) REVERT: D 440 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7358 (m) REVERT: E 17 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8809 (mm-40) REVERT: E 95 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: E 186 ASN cc_start: 0.8444 (m-40) cc_final: 0.7970 (m-40) REVERT: E 215 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8907 (tp) REVERT: E 229 LYS cc_start: 0.9256 (ptmt) cc_final: 0.9041 (pttp) REVERT: E 310 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8563 (tp40) REVERT: E 496 LYS cc_start: 0.8933 (tppt) cc_final: 0.8377 (tppt) REVERT: F 262 TRP cc_start: 0.7347 (m-90) cc_final: 0.6883 (m-10) REVERT: F 338 LYS cc_start: 0.9425 (tmtt) cc_final: 0.9092 (ttpp) REVERT: F 412 GLU cc_start: 0.9088 (mp0) cc_final: 0.8834 (pm20) REVERT: F 416 LYS cc_start: 0.9537 (mtmt) cc_final: 0.9305 (pttm) REVERT: F 432 LEU cc_start: 0.8777 (mt) cc_final: 0.8512 (mt) REVERT: F 477 ASP cc_start: 0.9179 (m-30) cc_final: 0.8610 (m-30) outliers start: 118 outliers final: 82 residues processed: 483 average time/residue: 0.3320 time to fit residues: 253.2204 Evaluate side-chains 484 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 390 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 262 TRP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 135 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 133 ASN Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 238 LEU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 490 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 20 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 246 optimal weight: 0.8980 chunk 272 optimal weight: 0.6980 chunk 281 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN B 159 ASN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 271 HIS ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.101159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.073538 restraints weight = 71899.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.075719 restraints weight = 37791.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.077211 restraints weight = 24749.965| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22674 Z= 0.136 Angle : 0.801 14.402 30715 Z= 0.372 Chirality : 0.043 0.181 3561 Planarity : 0.005 0.069 3968 Dihedral : 7.629 112.008 3168 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.13 % Favored : 92.35 % Rotamer: Outliers : 3.74 % Allowed : 26.40 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2861 helix: 0.47 (0.15), residues: 1286 sheet: 0.01 (0.24), residues: 486 loop : -0.91 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 262 HIS 0.009 0.001 HIS C 402 PHE 0.032 0.001 PHE E 339 TYR 0.022 0.002 TYR B 465 ARG 0.012 0.001 ARG D 463 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 993) hydrogen bonds : angle 4.98205 ( 2808) covalent geometry : bond 0.00319 (22673) covalent geometry : angle 0.80089 (30715) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 417 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8647 (pt) REVERT: A 82 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8013 (m-30) REVERT: A 204 MET cc_start: 0.8988 (mtm) cc_final: 0.8405 (mtm) REVERT: A 213 SER cc_start: 0.9041 (m) cc_final: 0.8773 (p) REVERT: A 339 PHE cc_start: 0.9356 (p90) cc_final: 0.9089 (p90) REVERT: A 384 MET cc_start: 0.7719 (tpt) cc_final: 0.7413 (tpt) REVERT: A 417 MET cc_start: 0.9029 (tpp) cc_final: 0.8636 (mmt) REVERT: A 455 MET cc_start: 0.8889 (mmm) cc_final: 0.8501 (mmm) REVERT: A 467 ARG cc_start: 0.9130 (ptp-170) cc_final: 0.8552 (mtt180) REVERT: A 478 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8738 (mtp) REVERT: A 485 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8271 (mm) REVERT: A 489 LEU cc_start: 0.9322 (mt) cc_final: 0.9107 (mp) REVERT: B 69 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8349 (pt) REVERT: B 159 ASN cc_start: 0.9473 (OUTLIER) cc_final: 0.9017 (p0) REVERT: B 272 HIS cc_start: 0.8974 (p90) cc_final: 0.8518 (p90) REVERT: B 417 MET cc_start: 0.9518 (mmt) cc_final: 0.9129 (mmt) REVERT: B 459 LYS cc_start: 0.9419 (mmpt) cc_final: 0.8155 (pttp) REVERT: B 466 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.7296 (t70) REVERT: C 226 MET cc_start: 0.7682 (tpt) cc_final: 0.7365 (tpt) REVERT: C 259 PHE cc_start: 0.8631 (t80) cc_final: 0.8157 (t80) REVERT: C 313 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7640 (mp0) REVERT: C 380 ASP cc_start: 0.8692 (t70) cc_final: 0.8343 (t70) REVERT: C 381 ARG cc_start: 0.9109 (mmm-85) cc_final: 0.8288 (ttp-170) REVERT: C 448 GLN cc_start: 0.9283 (mt0) cc_final: 0.8910 (tm-30) REVERT: D 246 CYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9126 (m) REVERT: D 253 ARG cc_start: 0.9322 (mtp180) cc_final: 0.9016 (ttp-170) REVERT: D 325 CYS cc_start: 0.8954 (m) cc_final: 0.8140 (m) REVERT: D 335 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7375 (m-10) REVERT: D 345 MET cc_start: 0.8336 (tmm) cc_final: 0.8083 (tmm) REVERT: E 17 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8783 (mm-40) REVERT: E 95 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: E 186 ASN cc_start: 0.8451 (m-40) cc_final: 0.8003 (m-40) REVERT: E 215 LEU cc_start: 0.9113 (tt) cc_final: 0.8753 (tp) REVERT: E 264 LEU cc_start: 0.9405 (mm) cc_final: 0.9013 (tt) REVERT: E 310 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8556 (tp40) REVERT: E 314 THR cc_start: 0.9042 (p) cc_final: 0.8775 (p) REVERT: E 422 MET cc_start: 0.9256 (mmp) cc_final: 0.9012 (ptm) REVERT: F 262 TRP cc_start: 0.7179 (m-90) cc_final: 0.6764 (m-10) REVERT: F 412 GLU cc_start: 0.9091 (mp0) cc_final: 0.8795 (pm20) REVERT: F 416 LYS cc_start: 0.9531 (mtmt) cc_final: 0.9286 (pttm) REVERT: F 432 LEU cc_start: 0.8770 (mt) cc_final: 0.8507 (mt) REVERT: F 477 ASP cc_start: 0.9213 (m-30) cc_final: 0.8638 (m-30) outliers start: 91 outliers final: 69 residues processed: 479 average time/residue: 0.3177 time to fit residues: 240.3887 Evaluate side-chains 472 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 393 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain D residue 262 TRP Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 441 CYS Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 135 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 260 ARG Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 490 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 0 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 213 optimal weight: 10.0000 chunk 85 optimal weight: 0.3980 chunk 144 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 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 = 0.3651 r_free = 0.3651 target = 0.100173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.073149 restraints weight = 74532.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.075263 restraints weight = 39525.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.076696 restraints weight = 26013.909| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22674 Z= 0.222 Angle : 0.844 15.932 30715 Z= 0.398 Chirality : 0.044 0.170 3561 Planarity : 0.005 0.067 3968 Dihedral : 7.815 112.149 3168 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.97 % Favored : 91.58 % Rotamer: Outliers : 3.74 % Allowed : 26.77 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2861 helix: 0.41 (0.15), residues: 1288 sheet: -0.12 (0.24), residues: 472 loop : -1.04 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 262 HIS 0.009 0.001 HIS C 402 PHE 0.031 0.002 PHE E 339 TYR 0.033 0.003 TYR D 370 ARG 0.016 0.001 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 993) hydrogen bonds : angle 5.13481 ( 2808) covalent geometry : bond 0.00496 (22673) covalent geometry : angle 0.84442 (30715) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 395 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.8855 (tptt) cc_final: 0.8578 (tptt) REVERT: A 69 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8740 (pt) REVERT: A 204 MET cc_start: 0.9035 (mtm) cc_final: 0.8453 (mtm) REVERT: A 213 SER cc_start: 0.9050 (m) cc_final: 0.8782 (p) REVERT: A 290 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8672 (tt0) REVERT: A 309 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7817 (mmp-170) REVERT: A 339 PHE cc_start: 0.9389 (p90) cc_final: 0.9141 (p90) REVERT: A 455 MET cc_start: 0.8929 (mmm) cc_final: 0.8229 (mmm) REVERT: A 465 TYR cc_start: 0.8486 (t80) cc_final: 0.8142 (t80) REVERT: A 467 ARG cc_start: 0.9144 (ptp-170) cc_final: 0.8565 (mtt180) REVERT: A 478 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8756 (mtp) REVERT: A 485 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8330 (mm) REVERT: B 69 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8402 (pt) REVERT: B 159 ASN cc_start: 0.9525 (OUTLIER) cc_final: 0.9046 (p0) REVERT: B 272 HIS cc_start: 0.9032 (p90) cc_final: 0.8556 (p90) REVERT: B 417 MET cc_start: 0.9530 (mmt) cc_final: 0.9138 (mmt) REVERT: B 466 HIS cc_start: 0.8430 (OUTLIER) cc_final: 0.7369 (t70) REVERT: C 226 MET cc_start: 0.7590 (tpt) cc_final: 0.7277 (tpt) REVERT: C 259 PHE cc_start: 0.8708 (t80) cc_final: 0.8262 (t80) REVERT: C 381 ARG cc_start: 0.9166 (mmm-85) cc_final: 0.8011 (ttp-170) REVERT: C 448 GLN cc_start: 0.9287 (mt0) cc_final: 0.8897 (tm-30) REVERT: D 204 MET cc_start: 0.9007 (tpp) cc_final: 0.8796 (tpp) REVERT: D 253 ARG cc_start: 0.9343 (mtp180) cc_final: 0.9046 (ttp-170) REVERT: D 325 CYS cc_start: 0.8820 (m) cc_final: 0.8602 (m) REVERT: E 17 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8798 (mm-40) REVERT: E 95 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7965 (mp10) REVERT: E 186 ASN cc_start: 0.8488 (m-40) cc_final: 0.8072 (m-40) REVERT: E 204 MET cc_start: 0.9249 (mmm) cc_final: 0.8898 (ttt) REVERT: E 310 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8549 (tp40) REVERT: E 496 LYS cc_start: 0.8922 (tppt) cc_final: 0.8714 (tppt) REVERT: F 262 TRP cc_start: 0.7214 (m-90) cc_final: 0.6794 (m-10) REVERT: F 338 LYS cc_start: 0.9448 (tmtt) cc_final: 0.9126 (ttpp) REVERT: F 412 GLU cc_start: 0.9083 (mp0) cc_final: 0.8773 (pm20) REVERT: F 416 LYS cc_start: 0.9527 (mtmt) cc_final: 0.9283 (pttm) REVERT: F 432 LEU cc_start: 0.8783 (mt) cc_final: 0.8520 (mt) REVERT: F 477 ASP cc_start: 0.9218 (m-30) cc_final: 0.8649 (m-30) outliers start: 91 outliers final: 72 residues processed: 460 average time/residue: 0.3210 time to fit residues: 234.4772 Evaluate side-chains 467 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 386 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 212 HIS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 262 TRP Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 135 HIS Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 348 CYS Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 490 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 60 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 81 optimal weight: 0.0010 chunk 196 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 272 optimal weight: 0.0670 overall best weight: 0.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 ASN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 103 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 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 = 0.3743 r_free = 0.3743 target = 0.105348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.077587 restraints weight = 72815.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.079870 restraints weight = 38889.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.081403 restraints weight = 25419.595| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 22674 Z= 0.137 Angle : 0.859 16.903 30715 Z= 0.393 Chirality : 0.043 0.187 3561 Planarity : 0.005 0.069 3968 Dihedral : 7.408 112.413 3168 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.06 % Favored : 92.56 % Rotamer: Outliers : 2.59 % Allowed : 27.51 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2861 helix: 0.49 (0.15), residues: 1276 sheet: 0.01 (0.24), residues: 485 loop : -0.96 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 262 HIS 0.009 0.001 HIS C 402 PHE 0.030 0.001 PHE E 339 TYR 0.036 0.003 TYR D 370 ARG 0.012 0.001 ARG A 381 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 993) hydrogen bonds : angle 4.94881 ( 2808) covalent geometry : bond 0.00320 (22673) covalent geometry : angle 0.85942 (30715) Misc. bond : bond 0.00044 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5722 Ramachandran restraints generated. 2861 Oldfield, 0 Emsley, 2861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 413 time to evaluate : 2.692 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 7 LYS cc_start: 0.8796 (tptt) cc_final: 0.8473 (tptt) REVERT: A 69 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8611 (pt) REVERT: A 82 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: A 204 MET cc_start: 0.9005 (mtm) cc_final: 0.8388 (mtm) REVERT: A 213 SER cc_start: 0.8990 (m) cc_final: 0.8726 (p) REVERT: A 290 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8685 (tt0) REVERT: A 339 PHE cc_start: 0.9338 (p90) cc_final: 0.9100 (p90) REVERT: A 345 MET cc_start: 0.7915 (tmm) cc_final: 0.7699 (tmm) REVERT: A 384 MET cc_start: 0.7330 (tpt) cc_final: 0.6923 (tpt) REVERT: A 439 MET cc_start: 0.8846 (ppp) cc_final: 0.8467 (ppp) REVERT: A 455 MET cc_start: 0.8901 (mmm) cc_final: 0.8210 (mmm) REVERT: A 465 TYR cc_start: 0.8440 (t80) cc_final: 0.8095 (t80) REVERT: A 467 ARG cc_start: 0.9127 (ptp-170) cc_final: 0.8625 (mtt180) REVERT: A 478 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8876 (mtp) REVERT: B 69 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8289 (pt) REVERT: B 250 ASN cc_start: 0.8890 (m110) cc_final: 0.8682 (p0) REVERT: B 272 HIS cc_start: 0.9014 (p90) cc_final: 0.8628 (p90) REVERT: B 417 MET cc_start: 0.9515 (mmt) cc_final: 0.9152 (mmt) REVERT: B 459 LYS cc_start: 0.9301 (mmpt) cc_final: 0.8058 (pptt) REVERT: B 466 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.7978 (t70) REVERT: C 226 MET cc_start: 0.7597 (tpt) cc_final: 0.7283 (tpt) REVERT: C 259 PHE cc_start: 0.8649 (t80) cc_final: 0.8195 (t80) REVERT: C 334 GLU cc_start: 0.9642 (mp0) cc_final: 0.8981 (mm-30) REVERT: C 380 ASP cc_start: 0.8757 (t70) cc_final: 0.8431 (t70) REVERT: C 381 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8428 (ttp-170) REVERT: C 448 GLN cc_start: 0.9285 (mt0) cc_final: 0.8880 (tm-30) REVERT: D 14 ILE cc_start: 0.8353 (pt) cc_final: 0.8121 (pt) REVERT: D 17 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8639 (mm-40) REVERT: D 39 GLU cc_start: 0.6563 (mp0) cc_final: 0.6262 (mp0) REVERT: D 226 MET cc_start: 0.8920 (mtm) cc_final: 0.8519 (ptp) REVERT: D 246 CYS cc_start: 0.9397 (t) cc_final: 0.9154 (m) REVERT: D 253 ARG cc_start: 0.9332 (mtp180) cc_final: 0.9025 (ttp-170) REVERT: D 325 CYS cc_start: 0.8843 (m) cc_final: 0.8631 (m) REVERT: D 422 MET cc_start: 0.9137 (mmm) cc_final: 0.8896 (mmm) REVERT: E 17 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8643 (mm-40) REVERT: E 186 ASN cc_start: 0.8432 (m-40) cc_final: 0.8052 (m-40) REVERT: E 204 MET cc_start: 0.9247 (mmm) cc_final: 0.8891 (ttt) REVERT: E 264 LEU cc_start: 0.9397 (mm) cc_final: 0.8995 (tt) REVERT: E 422 MET cc_start: 0.9263 (mmp) cc_final: 0.9002 (ptm) REVERT: E 496 LYS cc_start: 0.8921 (tppt) cc_final: 0.8702 (tppt) REVERT: F 204 MET cc_start: 0.8881 (ttt) cc_final: 0.8601 (ttp) REVERT: F 262 TRP cc_start: 0.7003 (m-90) cc_final: 0.6644 (m-10) REVERT: F 412 GLU cc_start: 0.9095 (mp0) cc_final: 0.8795 (pm20) REVERT: F 416 LYS cc_start: 0.9539 (mtmt) cc_final: 0.9286 (pttm) REVERT: F 432 LEU cc_start: 0.8769 (mt) cc_final: 0.8506 (mt) REVERT: F 477 ASP cc_start: 0.9244 (m-30) cc_final: 0.8788 (m-30) outliers start: 63 outliers final: 50 residues processed: 459 average time/residue: 0.3279 time to fit residues: 235.3575 Evaluate side-chains 450 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 394 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 483 LYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 262 TRP Chi-restraints excluded: chain D residue 348 CYS Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 224 LYS Chi-restraints excluded: chain F residue 260 ARG Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 411 ARG Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 490 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 157 optimal weight: 6.9990 chunk 270 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 210 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 488 HIS ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 HIS ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 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 = 0.3718 r_free = 0.3718 target = 0.103717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.076042 restraints weight = 73311.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078201 restraints weight = 39939.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.079650 restraints weight = 26621.237| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 22674 Z= 0.170 Angle : 0.855 16.424 30715 Z= 0.396 Chirality : 0.043 0.257 3561 Planarity : 0.005 0.069 3968 Dihedral : 7.367 109.486 3168 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.93 % Favored : 91.72 % Rotamer: Outliers : 2.71 % Allowed : 27.88 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2861 helix: 0.50 (0.15), residues: 1272 sheet: -0.09 (0.24), residues: 472 loop : -1.00 (0.20), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 262 HIS 0.009 0.001 HIS C 402 PHE 0.027 0.002 PHE E 339 TYR 0.035 0.003 TYR D 370 ARG 0.016 0.001 ARG A 463 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 993) hydrogen bonds : angle 5.01879 ( 2808) covalent geometry : bond 0.00396 (22673) covalent geometry : angle 0.85543 (30715) Misc. bond : bond 0.00002 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10112.25 seconds wall clock time: 181 minutes 25.09 seconds (10885.09 seconds total)