Starting phenix.real_space_refine on Fri Sep 19 02:19:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rxt_19579/09_2025/8rxt_19579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rxt_19579/09_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_19579/09_2025/8rxt_19579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rxt_19579/09_2025/8rxt_19579.map" model { file = "/net/cci-nas-00/data/ceres_data/8rxt_19579/09_2025/8rxt_19579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rxt_19579/09_2025/8rxt_19579.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 6.23, per 1000 atoms: 0.28 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: 1.96 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.77 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: 4.05 Time building geometry restraints manager: 2.64 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: 12.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.160 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.280 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG F 48 TYR 0.020 0.002 TYR C 166 PHE 0.032 0.001 PHE C 231 TRP 0.013 0.002 TRP B 191 HIS 0.015 0.001 HIS C 295 Details of bonding type rmsd covalent geometry : bond 0.00514 (22673) covalent geometry : angle 0.91590 (30715) hydrogen bonds : bond 0.17862 ( 993) hydrogen bonds : angle 6.90763 ( 2808) 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 : 0.964 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: 0.1596 time to fit residues: 161.1512 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 : 0.896 ------------------------------------------------------------------------------- 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 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0470 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.6086 ------------------------------------------------------------------------------- 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 100 ASN ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 HIS ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 GLN C 310 GLN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 431 ASN D 55 ASN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 130 HIS E 199 HIS ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 HIS ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.108583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080538 restraints weight = 70571.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082857 restraints weight = 37424.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084425 restraints weight = 24477.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085449 restraints weight = 18341.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.086107 restraints weight = 15078.175| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22674 Z= 0.164 Angle : 0.818 13.291 30715 Z= 0.392 Chirality : 0.045 0.284 3561 Planarity : 0.006 0.080 3968 Dihedral : 9.067 111.699 3176 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.40 % Favored : 93.01 % Rotamer: Outliers : 3.78 % Allowed : 21.22 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2861 helix: 0.20 (0.15), residues: 1295 sheet: 0.53 (0.25), residues: 483 loop : -0.63 (0.21), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 309 TYR 0.024 0.002 TYR C 465 PHE 0.018 0.002 PHE A 450 TRP 0.019 0.002 TRP F 262 HIS 0.009 0.001 HIS C 271 Details of bonding type rmsd covalent geometry : bond 0.00374 (22673) covalent geometry : angle 0.81806 (30715) hydrogen bonds : bond 0.03965 ( 993) hydrogen bonds : angle 5.48545 ( 2808) Misc. bond : bond 0.00004 ( 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 571 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 479 time to evaluate : 0.782 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 229 LYS cc_start: 0.9149 (pttp) cc_final: 0.8922 (pttt) REVERT: A 287 LYS cc_start: 0.9087 (mmtm) cc_final: 0.8851 (mmtm) REVERT: A 320 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8985 (mp0) REVERT: A 450 PHE cc_start: 0.8873 (t80) cc_final: 0.8508 (t80) REVERT: A 467 ARG cc_start: 0.9229 (mtm180) cc_final: 0.9025 (ptp-170) REVERT: A 489 LEU cc_start: 0.9340 (mt) cc_final: 0.9086 (mp) REVERT: B 105 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7968 (mt-10) REVERT: B 306 GLU cc_start: 0.8955 (tp30) cc_final: 0.8292 (tp30) REVERT: B 381 ARG cc_start: 0.7372 (ptm160) cc_final: 0.6972 (mtp180) REVERT: B 417 MET cc_start: 0.9258 (mmt) cc_final: 0.8878 (mmt) REVERT: B 443 LEU cc_start: 0.8318 (tp) cc_final: 0.8073 (tp) REVERT: B 459 LYS cc_start: 0.9238 (mmtt) cc_final: 0.8102 (pptt) REVERT: B 466 HIS cc_start: 0.8316 (OUTLIER) cc_final: 0.7201 (t70) REVERT: C 226 MET cc_start: 0.7466 (tpt) cc_final: 0.7090 (tpt) REVERT: C 234 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8225 (mp) REVERT: C 313 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7666 (mp0) REVERT: C 380 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8716 (t70) REVERT: C 381 ARG cc_start: 0.9312 (mmm-85) cc_final: 0.8883 (ttp-170) REVERT: C 450 PHE cc_start: 0.9354 (t80) cc_final: 0.8999 (t80) REVERT: D 14 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9205 (pt) REVERT: D 17 GLN cc_start: 0.8166 (mp10) cc_final: 0.7860 (mp10) REVERT: D 90 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9021 (mm) REVERT: D 120 SER cc_start: 0.9232 (m) cc_final: 0.9012 (p) REVERT: D 212 HIS cc_start: 0.8590 (m-70) cc_final: 0.8111 (m90) REVERT: D 226 MET cc_start: 0.8674 (mtm) cc_final: 0.8186 (mtm) REVERT: D 325 CYS cc_start: 0.8994 (m) cc_final: 0.8580 (m) REVERT: D 335 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7705 (m-10) REVERT: E 3 LEU cc_start: 0.9239 (pt) cc_final: 0.8888 (tp) REVERT: E 229 LYS cc_start: 0.9229 (ptmt) cc_final: 0.8946 (pttp) REVERT: E 262 TRP cc_start: 0.8907 (OUTLIER) cc_final: 0.8628 (p-90) REVERT: E 306 GLU cc_start: 0.7401 (mp0) cc_final: 0.7123 (mp0) REVERT: E 310 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8594 (tm-30) REVERT: E 316 ARG cc_start: 0.8220 (ttp80) cc_final: 0.8019 (tmm-80) REVERT: E 474 THR cc_start: 0.8803 (m) cc_final: 0.8593 (p) REVERT: F 82 ASP cc_start: 0.8432 (m-30) cc_final: 0.8201 (m-30) REVERT: F 227 MET cc_start: 0.8716 (pmm) cc_final: 0.8476 (pmm) REVERT: F 260 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7488 (ppt170) REVERT: F 287 LYS cc_start: 0.9149 (tmmt) cc_final: 0.8899 (pptt) outliers start: 92 outliers final: 50 residues processed: 537 average time/residue: 0.1539 time to fit residues: 130.1563 Evaluate side-chains 480 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 422 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 387 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 396 LEU 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 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 234 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 380 ASP Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 90 LEU 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 301 LEU Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 387 THR Chi-restraints excluded: chain E residue 15 VAL 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 163 VAL Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 262 TRP Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain F residue 96 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 202 optimal weight: 0.2980 chunk 273 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 68 optimal weight: 0.0970 chunk 29 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.107519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079507 restraints weight = 71334.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.081812 restraints weight = 37635.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083378 restraints weight = 24521.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.084435 restraints weight = 18266.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.085099 restraints weight = 14907.618| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22674 Z= 0.154 Angle : 0.756 11.381 30715 Z= 0.364 Chirality : 0.043 0.327 3561 Planarity : 0.005 0.073 3968 Dihedral : 8.144 105.737 3170 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.19 % Favored : 93.18 % Rotamer: Outliers : 3.87 % Allowed : 21.67 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2861 helix: 0.38 (0.15), residues: 1285 sheet: 0.44 (0.24), residues: 478 loop : -0.77 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 463 TYR 0.023 0.002 TYR A 465 PHE 0.015 0.001 PHE E 300 TRP 0.029 0.002 TRP F 262 HIS 0.012 0.001 HIS C 272 Details of bonding type rmsd covalent geometry : bond 0.00350 (22673) covalent geometry : angle 0.75633 (30715) hydrogen bonds : bond 0.03680 ( 993) hydrogen bonds : angle 5.20032 ( 2808) Misc. bond : bond 0.00191 ( 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 529 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 435 time to evaluate : 0.855 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 69 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8734 (pt) REVERT: A 287 LYS cc_start: 0.9125 (mmtm) cc_final: 0.8875 (mmtm) REVERT: A 455 MET cc_start: 0.8583 (mmm) cc_final: 0.8281 (mmm) REVERT: A 485 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8389 (mm) REVERT: A 489 LEU cc_start: 0.9297 (mt) cc_final: 0.9006 (mp) REVERT: B 105 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 417 MET cc_start: 0.9305 (mmt) cc_final: 0.8977 (mmt) REVERT: B 443 LEU cc_start: 0.8390 (tp) cc_final: 0.8125 (tp) REVERT: B 459 LYS cc_start: 0.9298 (mmtt) cc_final: 0.8112 (pptt) REVERT: B 466 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.7206 (t70) REVERT: C 226 MET cc_start: 0.7442 (tpt) cc_final: 0.7023 (tpt) REVERT: C 234 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8187 (mp) REVERT: C 313 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7643 (mp0) REVERT: C 380 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8734 (t70) REVERT: C 450 PHE cc_start: 0.9351 (t80) cc_final: 0.8991 (t80) REVERT: D 193 ASP cc_start: 0.9066 (m-30) cc_final: 0.8135 (t70) REVERT: D 226 MET cc_start: 0.8648 (mtm) cc_final: 0.8125 (mtm) REVERT: D 325 CYS cc_start: 0.9027 (m) cc_final: 0.8662 (m) REVERT: D 370 TYR cc_start: 0.8314 (t80) cc_final: 0.8037 (t80) REVERT: D 440 VAL cc_start: 0.7590 (OUTLIER) cc_final: 0.7269 (t) REVERT: D 489 LEU cc_start: 0.9306 (tt) cc_final: 0.9062 (pp) REVERT: E 229 LYS cc_start: 0.9268 (ptmt) cc_final: 0.9004 (pttp) REVERT: E 306 GLU cc_start: 0.7477 (mp0) cc_final: 0.7053 (mp0) REVERT: E 310 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8459 (tm-30) REVERT: E 474 THR cc_start: 0.8867 (m) cc_final: 0.8530 (p) REVERT: F 69 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8882 (pt) REVERT: F 227 MET cc_start: 0.8739 (pmm) cc_final: 0.8471 (pmm) REVERT: F 260 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7302 (ptm-80) REVERT: F 262 TRP cc_start: 0.6845 (m-90) cc_final: 0.6585 (m-10) REVERT: F 412 GLU cc_start: 0.9216 (mp0) cc_final: 0.8906 (pm20) REVERT: F 465 TYR cc_start: 0.8237 (t80) cc_final: 0.7836 (t80) outliers start: 94 outliers final: 51 residues processed: 504 average time/residue: 0.1514 time to fit residues: 120.7884 Evaluate side-chains 462 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 403 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 209 CYS 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 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 11 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 291 ILE 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 396 LEU 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 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 234 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 380 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 113 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 235 LEU 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 98 LEU Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 133 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 96 ILE 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 248 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 168 optimal weight: 0.3980 chunk 101 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 199 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 0.0770 chunk 112 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 overall best weight: 1.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 ASN B 272 HIS ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 HIS C 272 HIS C 431 ASN D 55 ASN ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 ASN ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.106397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.078450 restraints weight = 71862.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.080683 restraints weight = 38691.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.082207 restraints weight = 25422.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.083201 restraints weight = 19083.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083854 restraints weight = 15722.319| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22674 Z= 0.161 Angle : 0.756 11.355 30715 Z= 0.360 Chirality : 0.043 0.341 3561 Planarity : 0.005 0.075 3968 Dihedral : 7.815 106.685 3170 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.47 % Favored : 92.87 % Rotamer: Outliers : 4.44 % Allowed : 21.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.16), residues: 2861 helix: 0.51 (0.15), residues: 1285 sheet: 0.33 (0.24), residues: 490 loop : -0.81 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 463 TYR 0.019 0.002 TYR A 465 PHE 0.027 0.002 PHE E 339 TRP 0.016 0.001 TRP F 262 HIS 0.012 0.001 HIS C 402 Details of bonding type rmsd covalent geometry : bond 0.00358 (22673) covalent geometry : angle 0.75630 (30715) hydrogen bonds : bond 0.03395 ( 993) hydrogen bonds : angle 5.08500 ( 2808) Misc. bond : bond 0.00121 ( 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 537 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 429 time to evaluate : 0.926 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 69 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8747 (pt) REVERT: A 287 LYS cc_start: 0.9144 (mmtm) cc_final: 0.8884 (mmtm) REVERT: A 290 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8439 (tt0) REVERT: A 384 MET cc_start: 0.7316 (tpt) cc_final: 0.6906 (tpt) REVERT: A 455 MET cc_start: 0.8628 (mmm) cc_final: 0.8205 (mmm) REVERT: A 463 ARG cc_start: 0.8763 (mmm160) cc_final: 0.8560 (mmm160) REVERT: A 467 ARG cc_start: 0.9279 (mtm180) cc_final: 0.9009 (ptp-170) REVERT: A 485 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8449 (mm) REVERT: A 489 LEU cc_start: 0.9336 (mt) cc_final: 0.9121 (mt) REVERT: B 417 MET cc_start: 0.9360 (mmt) cc_final: 0.9074 (mmt) REVERT: B 443 LEU cc_start: 0.8378 (tp) cc_final: 0.8122 (tp) REVERT: B 459 LYS cc_start: 0.9337 (mmtt) cc_final: 0.8156 (pptt) REVERT: B 466 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.7222 (t70) REVERT: C 226 MET cc_start: 0.7518 (tpt) cc_final: 0.7105 (tpt) REVERT: C 259 PHE cc_start: 0.8120 (t80) cc_final: 0.7763 (t80) REVERT: C 313 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7721 (mm-30) REVERT: C 371 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7526 (pp) REVERT: C 439 MET cc_start: 0.9074 (mmm) cc_final: 0.8839 (mmt) REVERT: C 450 PHE cc_start: 0.9318 (t80) cc_final: 0.8932 (t80) REVERT: D 17 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8492 (mp10) REVERT: D 182 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7911 (mp) REVERT: D 193 ASP cc_start: 0.9064 (m-30) cc_final: 0.8205 (t70) REVERT: D 226 MET cc_start: 0.8680 (mtm) cc_final: 0.8113 (mtm) REVERT: D 253 ARG cc_start: 0.9286 (mtp180) cc_final: 0.8938 (ttp80) REVERT: D 325 CYS cc_start: 0.8972 (m) cc_final: 0.8623 (m) REVERT: D 335 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7395 (m-10) REVERT: D 440 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7303 (m) REVERT: D 489 LEU cc_start: 0.9355 (tt) cc_final: 0.9129 (pp) REVERT: E 17 GLN cc_start: 0.8882 (mm110) cc_final: 0.8569 (mm-40) REVERT: E 95 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: E 132 ASP cc_start: 0.9087 (t0) cc_final: 0.8492 (t70) REVERT: E 229 LYS cc_start: 0.9284 (ptmt) cc_final: 0.9008 (pttp) REVERT: E 306 GLU cc_start: 0.7508 (mp0) cc_final: 0.7174 (mp0) REVERT: E 310 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8435 (tm-30) REVERT: F 165 ASP cc_start: 0.8600 (m-30) cc_final: 0.8018 (p0) REVERT: F 227 MET cc_start: 0.8741 (pmm) cc_final: 0.8424 (pmm) REVERT: F 260 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7308 (ptm-80) REVERT: F 262 TRP cc_start: 0.6856 (m-90) cc_final: 0.6594 (m-10) REVERT: F 316 ARG cc_start: 0.9072 (ttm110) cc_final: 0.8828 (ttm110) REVERT: F 432 LEU cc_start: 0.8676 (mt) cc_final: 0.8423 (mt) REVERT: F 443 LEU cc_start: 0.8868 (tp) cc_final: 0.8607 (tp) REVERT: F 453 GLU cc_start: 0.9206 (tp30) cc_final: 0.8960 (tp30) REVERT: F 465 TYR cc_start: 0.8205 (t80) cc_final: 0.7947 (t80) REVERT: F 477 ASP cc_start: 0.9071 (m-30) cc_final: 0.8571 (m-30) outliers start: 108 outliers final: 63 residues processed: 502 average time/residue: 0.1532 time to fit residues: 122.4233 Evaluate side-chains 492 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 419 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 239 SER 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 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 14 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 304 LEU Chi-restraints excluded: chain B residue 396 LEU 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 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 272 HIS Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 371 LEU 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 160 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 235 LEU 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 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 47 ASP 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 193 ASP 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 486 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 66 THR 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 378 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 43 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 258 optimal weight: 7.9990 chunk 268 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 264 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 249 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 151 HIS ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** 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 = 0.3743 r_free = 0.3743 target = 0.105808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.078036 restraints weight = 72684.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.080326 restraints weight = 38612.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081862 restraints weight = 25213.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.082886 restraints weight = 18808.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.083582 restraints weight = 15393.432| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22674 Z= 0.162 Angle : 0.759 13.720 30715 Z= 0.359 Chirality : 0.043 0.325 3561 Planarity : 0.005 0.073 3968 Dihedral : 7.613 106.729 3168 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.78 % Favored : 92.56 % Rotamer: Outliers : 4.28 % Allowed : 22.86 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2861 helix: 0.52 (0.15), residues: 1273 sheet: 0.23 (0.24), residues: 490 loop : -0.85 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 463 TYR 0.030 0.002 TYR D 465 PHE 0.022 0.001 PHE E 300 TRP 0.011 0.001 TRP F 262 HIS 0.014 0.001 HIS C 272 Details of bonding type rmsd covalent geometry : bond 0.00365 (22673) covalent geometry : angle 0.75924 (30715) hydrogen bonds : bond 0.03279 ( 993) hydrogen bonds : angle 5.01742 ( 2808) Misc. bond : bond 0.00087 ( 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 540 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 436 time to evaluate : 0.823 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 47 ASP cc_start: 0.8490 (m-30) cc_final: 0.8281 (m-30) REVERT: A 204 MET cc_start: 0.8963 (mtm) cc_final: 0.8415 (mtm) REVERT: A 209 CYS cc_start: 0.7560 (p) cc_final: 0.7093 (p) REVERT: A 290 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: A 417 MET cc_start: 0.9051 (tpp) cc_final: 0.8610 (mmt) REVERT: A 455 MET cc_start: 0.8832 (mmm) cc_final: 0.8342 (mmm) REVERT: A 467 ARG cc_start: 0.9290 (mtm180) cc_final: 0.8582 (mtp180) REVERT: A 478 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8743 (mtp) REVERT: A 485 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8303 (mm) REVERT: A 489 LEU cc_start: 0.9352 (mt) cc_final: 0.9118 (mp) REVERT: B 1 MET cc_start: 0.8732 (mmm) cc_final: 0.8526 (mmm) REVERT: B 105 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8053 (mt-10) REVERT: B 159 ASN cc_start: 0.9465 (OUTLIER) cc_final: 0.9177 (p0) REVERT: B 250 ASN cc_start: 0.9374 (m-40) cc_final: 0.9160 (m110) REVERT: B 417 MET cc_start: 0.9370 (mmt) cc_final: 0.9027 (mmt) REVERT: B 443 LEU cc_start: 0.8488 (tp) cc_final: 0.8236 (tp) REVERT: B 459 LYS cc_start: 0.9366 (mmtt) cc_final: 0.8161 (pptt) REVERT: B 466 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7254 (t70) REVERT: C 112 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8736 (tp) REVERT: C 226 MET cc_start: 0.7489 (tpt) cc_final: 0.7130 (tpt) REVERT: C 313 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7789 (mm-30) REVERT: C 371 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7503 (pp) REVERT: C 380 ASP cc_start: 0.8632 (t70) cc_final: 0.8235 (t70) REVERT: C 439 MET cc_start: 0.9105 (mmm) cc_final: 0.8880 (mmt) REVERT: D 17 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8741 (mp10) REVERT: D 182 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7807 (mp) REVERT: D 193 ASP cc_start: 0.9092 (m-30) cc_final: 0.8226 (t0) REVERT: D 226 MET cc_start: 0.8684 (mtm) cc_final: 0.8124 (mtm) REVERT: D 335 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7488 (m-10) REVERT: D 440 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.7203 (m) REVERT: D 450 PHE cc_start: 0.9148 (t80) cc_final: 0.8803 (t80) REVERT: D 478 MET cc_start: 0.9228 (tpp) cc_final: 0.8941 (mmm) REVERT: E 17 GLN cc_start: 0.8933 (mm110) cc_final: 0.8615 (mm-40) REVERT: E 95 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7890 (mp10) REVERT: E 132 ASP cc_start: 0.9143 (t0) cc_final: 0.8557 (t70) REVERT: E 229 LYS cc_start: 0.9260 (ptmt) cc_final: 0.9006 (pttp) REVERT: E 231 PHE cc_start: 0.9378 (t80) cc_final: 0.9172 (t80) REVERT: E 310 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8414 (tm-30) REVERT: E 496 LYS cc_start: 0.8879 (tppt) cc_final: 0.8452 (tppt) REVERT: F 227 MET cc_start: 0.8763 (pmm) cc_final: 0.8443 (pmm) REVERT: F 260 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7239 (ptm-80) REVERT: F 316 ARG cc_start: 0.9081 (ttm110) cc_final: 0.8852 (ttm110) REVERT: F 338 LYS cc_start: 0.9443 (tmtt) cc_final: 0.9165 (ttpp) REVERT: F 412 GLU cc_start: 0.9124 (mp0) cc_final: 0.8767 (pm20) REVERT: F 416 LYS cc_start: 0.9452 (mttt) cc_final: 0.9239 (pttm) REVERT: F 417 MET cc_start: 0.8711 (tpp) cc_final: 0.8483 (tpp) REVERT: F 432 LEU cc_start: 0.8693 (mt) cc_final: 0.8432 (mt) REVERT: F 453 GLU cc_start: 0.9196 (tp30) cc_final: 0.8987 (tm-30) REVERT: F 465 TYR cc_start: 0.8247 (t80) cc_final: 0.7963 (t80) REVERT: F 477 ASP cc_start: 0.9100 (m-30) cc_final: 0.8558 (m-30) outliers start: 104 outliers final: 65 residues processed: 507 average time/residue: 0.1506 time to fit residues: 120.2991 Evaluate side-chains 473 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 396 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 82 ASP Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 239 SER 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 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 159 ASN Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 271 HIS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 466 HIS Chi-restraints excluded: chain C residue 3 LEU 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 112 LEU 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 272 HIS Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 69 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 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 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 133 ASN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 256 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 124 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 GLN ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 479 ASN ** E 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 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 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 = 0.3746 r_free = 0.3746 target = 0.105972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.078315 restraints weight = 73204.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.080617 restraints weight = 38560.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.082177 restraints weight = 25058.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.083206 restraints weight = 18601.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083886 restraints weight = 15216.046| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22674 Z= 0.139 Angle : 0.757 13.889 30715 Z= 0.356 Chirality : 0.043 0.242 3561 Planarity : 0.005 0.071 3968 Dihedral : 7.519 106.278 3168 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.85 % Favored : 92.49 % Rotamer: Outliers : 3.87 % Allowed : 24.18 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.16), residues: 2861 helix: 0.60 (0.15), residues: 1266 sheet: 0.28 (0.24), residues: 490 loop : -0.83 (0.20), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 463 TYR 0.020 0.002 TYR B 465 PHE 0.013 0.001 PHE E 300 TRP 0.027 0.001 TRP F 262 HIS 0.010 0.001 HIS C 402 Details of bonding type rmsd covalent geometry : bond 0.00319 (22673) covalent geometry : angle 0.75750 (30715) hydrogen bonds : bond 0.03115 ( 993) hydrogen bonds : angle 4.94731 ( 2808) Misc. bond : bond 0.00081 ( 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 514 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 420 time to evaluate : 0.829 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 7 LYS cc_start: 0.8621 (tptt) cc_final: 0.8368 (tptt) REVERT: A 204 MET cc_start: 0.8936 (mtm) cc_final: 0.8394 (mtm) REVERT: A 290 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8443 (tt0) REVERT: A 417 MET cc_start: 0.9047 (tpp) cc_final: 0.8623 (mmt) REVERT: A 455 MET cc_start: 0.8899 (mmm) cc_final: 0.8510 (mmm) REVERT: A 467 ARG cc_start: 0.9295 (mtm180) cc_final: 0.8612 (mtp180) REVERT: A 485 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8299 (mm) REVERT: A 489 LEU cc_start: 0.9357 (mt) cc_final: 0.9141 (mp) REVERT: B 69 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8339 (pt) REVERT: B 105 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8026 (mt-10) REVERT: B 159 ASN cc_start: 0.9502 (OUTLIER) cc_final: 0.9023 (p0) REVERT: B 250 ASN cc_start: 0.9368 (m-40) cc_final: 0.9152 (m110) REVERT: B 272 HIS cc_start: 0.9057 (p-80) cc_final: 0.8612 (p90) REVERT: B 417 MET cc_start: 0.9445 (mmt) cc_final: 0.8959 (mmt) REVERT: B 443 LEU cc_start: 0.8446 (tp) cc_final: 0.8154 (tp) REVERT: B 459 LYS cc_start: 0.9361 (mmtt) cc_final: 0.8161 (pptt) REVERT: B 466 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.7269 (t70) REVERT: C 112 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8731 (tp) REVERT: C 226 MET cc_start: 0.7552 (tpt) cc_final: 0.7212 (tpt) REVERT: C 271 HIS cc_start: 0.8168 (t70) cc_final: 0.7822 (t70) REVERT: C 313 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7794 (mm-30) REVERT: C 371 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7517 (pp) REVERT: C 380 ASP cc_start: 0.8618 (t70) cc_final: 0.8306 (t70) REVERT: C 381 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8208 (ttp-170) REVERT: C 439 MET cc_start: 0.9114 (mmm) cc_final: 0.8901 (mmt) REVERT: C 448 GLN cc_start: 0.9321 (mt0) cc_final: 0.8924 (tm-30) REVERT: D 182 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7761 (mp) REVERT: D 193 ASP cc_start: 0.9088 (m-30) cc_final: 0.8239 (t0) REVERT: D 226 MET cc_start: 0.8670 (mtm) cc_final: 0.8143 (mtm) REVERT: D 335 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7448 (m-10) REVERT: D 450 PHE cc_start: 0.9158 (t80) cc_final: 0.8842 (t80) REVERT: D 478 MET cc_start: 0.9233 (tpp) cc_final: 0.8968 (mmm) REVERT: E 95 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: E 132 ASP cc_start: 0.9143 (t0) cc_final: 0.8529 (t70) REVERT: E 229 LYS cc_start: 0.9280 (ptmt) cc_final: 0.9036 (pttp) REVERT: E 310 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8479 (tm-30) REVERT: F 227 MET cc_start: 0.8754 (pmm) cc_final: 0.8467 (pmm) REVERT: F 260 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7354 (ptm-80) REVERT: F 262 TRP cc_start: 0.7117 (m-90) cc_final: 0.6610 (m-10) REVERT: F 338 LYS cc_start: 0.9429 (tmtt) cc_final: 0.9169 (ttpp) REVERT: F 412 GLU cc_start: 0.9152 (mp0) cc_final: 0.8779 (pm20) REVERT: F 416 LYS cc_start: 0.9446 (mttt) cc_final: 0.9241 (pttm) REVERT: F 432 LEU cc_start: 0.8686 (mt) cc_final: 0.8423 (mt) REVERT: F 465 TYR cc_start: 0.8227 (t80) cc_final: 0.7979 (t80) REVERT: F 477 ASP cc_start: 0.9142 (m-30) cc_final: 0.8570 (m-30) outliers start: 94 outliers final: 62 residues processed: 488 average time/residue: 0.1422 time to fit residues: 110.3492 Evaluate side-chains 471 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 398 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 82 ASP Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 239 SER 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 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 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 37 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 112 LEU 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 371 LEU 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 69 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 235 LEU 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 479 ASN Chi-restraints excluded: chain E residue 43 LYS 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 436 THR Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain F residue 96 ILE 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 490 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 46 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 251 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 220 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 488 HIS B 159 ASN B 418 HIS ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN ** 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** F 497 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.101343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.073826 restraints weight = 75014.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.075889 restraints weight = 41168.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.077302 restraints weight = 27581.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.078240 restraints weight = 20940.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.078856 restraints weight = 17349.067| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 22674 Z= 0.323 Angle : 0.859 13.358 30715 Z= 0.420 Chirality : 0.046 0.219 3561 Planarity : 0.006 0.068 3968 Dihedral : 7.914 107.308 3168 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.97 % Favored : 91.44 % Rotamer: Outliers : 4.89 % Allowed : 24.26 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.16), residues: 2861 helix: 0.23 (0.14), residues: 1275 sheet: -0.15 (0.24), residues: 480 loop : -1.08 (0.20), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 316 TYR 0.017 0.002 TYR B 465 PHE 0.023 0.002 PHE D 81 TRP 0.022 0.002 TRP F 262 HIS 0.012 0.002 HIS C 272 Details of bonding type rmsd covalent geometry : bond 0.00697 (22673) covalent geometry : angle 0.85896 (30715) hydrogen bonds : bond 0.03901 ( 993) hydrogen bonds : angle 5.30642 ( 2808) Misc. bond : bond 0.00012 ( 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 524 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 405 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.9028 (mtm) cc_final: 0.8474 (mtm) REVERT: A 213 SER cc_start: 0.9106 (m) cc_final: 0.8835 (p) REVERT: A 309 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7659 (mmp-170) REVERT: A 345 MET cc_start: 0.7913 (tmm) cc_final: 0.7682 (tmm) REVERT: A 417 MET cc_start: 0.9023 (tpp) cc_final: 0.8609 (mmt) REVERT: A 455 MET cc_start: 0.8982 (mmm) cc_final: 0.8616 (mmm) REVERT: A 467 ARG cc_start: 0.9338 (mtm180) cc_final: 0.8655 (mtp180) REVERT: A 478 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8812 (mtp) REVERT: A 485 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8277 (mm) REVERT: A 489 LEU cc_start: 0.9350 (mt) cc_final: 0.9148 (mp) REVERT: B 69 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8535 (pt) REVERT: B 159 ASN cc_start: 0.9555 (OUTLIER) cc_final: 0.9055 (p0) REVERT: B 250 ASN cc_start: 0.9399 (m-40) cc_final: 0.9194 (m-40) REVERT: B 272 HIS cc_start: 0.9131 (p-80) cc_final: 0.8621 (p90) REVERT: B 417 MET cc_start: 0.9510 (mmt) cc_final: 0.9022 (mmt) REVERT: B 443 LEU cc_start: 0.8715 (tp) cc_final: 0.8463 (tp) REVERT: B 466 HIS cc_start: 0.8396 (OUTLIER) cc_final: 0.7227 (t70) REVERT: B 496 LYS cc_start: 0.8901 (tppp) cc_final: 0.8617 (tptm) REVERT: C 226 MET cc_start: 0.7559 (tpt) cc_final: 0.7249 (tpt) REVERT: C 271 HIS cc_start: 0.8032 (t70) cc_final: 0.7674 (t70) REVERT: D 90 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9059 (mm) REVERT: D 226 MET cc_start: 0.8720 (mtm) cc_final: 0.8354 (mtm) REVERT: D 325 CYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8919 (m) REVERT: D 335 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7677 (m-10) REVERT: D 345 MET cc_start: 0.8264 (tmm) cc_final: 0.7987 (tmm) REVERT: D 440 VAL cc_start: 0.7387 (OUTLIER) cc_final: 0.7183 (m) REVERT: D 450 PHE cc_start: 0.9207 (t80) cc_final: 0.8950 (t80) REVERT: E 95 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: E 132 ASP cc_start: 0.9156 (t0) cc_final: 0.8587 (t70) REVERT: E 229 LYS cc_start: 0.9242 (ptmt) cc_final: 0.8999 (pttp) REVERT: E 306 GLU cc_start: 0.7609 (mp0) cc_final: 0.7401 (mp0) REVERT: E 310 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8462 (tm-30) REVERT: E 380 ASP cc_start: 0.8959 (m-30) cc_final: 0.8597 (m-30) REVERT: F 34 MET cc_start: 0.8514 (ppp) cc_final: 0.8211 (tmm) REVERT: F 227 MET cc_start: 0.8743 (pmm) cc_final: 0.8523 (pmm) REVERT: F 260 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7410 (ptm-80) REVERT: F 262 TRP cc_start: 0.7301 (m-90) cc_final: 0.6819 (m-10) REVERT: F 338 LYS cc_start: 0.9476 (tmtt) cc_final: 0.9196 (ttpp) REVERT: F 432 LEU cc_start: 0.8781 (mt) cc_final: 0.8495 (mt) REVERT: F 465 TYR cc_start: 0.8333 (t80) cc_final: 0.8073 (t80) REVERT: F 477 ASP cc_start: 0.9132 (m-30) cc_final: 0.8898 (t0) outliers start: 119 outliers final: 78 residues processed: 487 average time/residue: 0.1424 time to fit residues: 110.8974 Evaluate side-chains 473 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 383 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 82 ASP Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 239 SER 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 90 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 304 LEU 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 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 235 LEU Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 272 HIS 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 468 LEU 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 262 TRP Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 325 CYS 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 26 SER Chi-restraints excluded: chain E residue 43 LYS 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 163 VAL Chi-restraints excluded: chain E residue 186 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 216 LEU 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 431 ASN 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 238 LEU Chi-restraints excluded: chain F residue 260 ARG Chi-restraints excluded: chain F residue 272 HIS 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 490 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 253 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 7 optimal weight: 0.0060 chunk 278 optimal weight: 5.9990 chunk 251 optimal weight: 3.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 479 ASN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 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 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 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 = 0.3702 r_free = 0.3702 target = 0.102831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.075466 restraints weight = 73257.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.077631 restraints weight = 39224.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079105 restraints weight = 25894.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080001 restraints weight = 19435.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080719 restraints weight = 16047.449| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22674 Z= 0.189 Angle : 0.819 15.771 30715 Z= 0.386 Chirality : 0.044 0.188 3561 Planarity : 0.005 0.067 3968 Dihedral : 7.755 109.869 3168 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.34 % Favored : 92.07 % Rotamer: Outliers : 3.78 % Allowed : 25.78 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.16), residues: 2861 helix: 0.35 (0.15), residues: 1287 sheet: -0.18 (0.24), residues: 476 loop : -0.97 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 316 TYR 0.022 0.002 TYR B 465 PHE 0.019 0.002 PHE E 450 TRP 0.018 0.002 TRP F 262 HIS 0.009 0.001 HIS C 402 Details of bonding type rmsd covalent geometry : bond 0.00426 (22673) covalent geometry : angle 0.81852 (30715) hydrogen bonds : bond 0.03371 ( 993) hydrogen bonds : angle 5.09417 ( 2808) Misc. bond : bond 0.00042 ( 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 495 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 403 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.8978 (mtm) cc_final: 0.8392 (mtm) REVERT: A 213 SER cc_start: 0.9114 (m) cc_final: 0.8807 (p) REVERT: A 317 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8731 (tm-30) REVERT: A 417 MET cc_start: 0.9025 (tpp) cc_final: 0.8626 (mmt) REVERT: A 455 MET cc_start: 0.8963 (mmm) cc_final: 0.8607 (mmm) REVERT: A 467 ARG cc_start: 0.9309 (mtm180) cc_final: 0.9045 (ptp-170) REVERT: A 478 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8750 (mtp) REVERT: A 485 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8291 (mm) REVERT: A 489 LEU cc_start: 0.9352 (mt) cc_final: 0.9147 (mp) REVERT: B 69 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8421 (pt) REVERT: B 105 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8107 (mt-10) REVERT: B 250 ASN cc_start: 0.9383 (m-40) cc_final: 0.9180 (m110) REVERT: B 272 HIS cc_start: 0.9092 (p-80) cc_final: 0.8638 (p90) REVERT: B 417 MET cc_start: 0.9495 (mmt) cc_final: 0.8998 (mmt) REVERT: B 443 LEU cc_start: 0.8601 (tp) cc_final: 0.8380 (tp) REVERT: B 459 LYS cc_start: 0.9274 (mmpt) cc_final: 0.8254 (pptt) REVERT: B 466 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7931 (t70) REVERT: C 226 MET cc_start: 0.7570 (tpt) cc_final: 0.7270 (tpt) REVERT: C 271 HIS cc_start: 0.8051 (t70) cc_final: 0.7644 (t70) REVERT: C 448 GLN cc_start: 0.9307 (mt0) cc_final: 0.8890 (tm-30) REVERT: D 90 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9020 (mm) REVERT: D 193 ASP cc_start: 0.9182 (m-30) cc_final: 0.8131 (t0) REVERT: D 226 MET cc_start: 0.8778 (mtm) cc_final: 0.8256 (mtm) REVERT: D 253 ARG cc_start: 0.9335 (mtp180) cc_final: 0.9033 (ttp-170) REVERT: D 325 CYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8881 (m) REVERT: D 335 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7600 (m-10) REVERT: D 450 PHE cc_start: 0.9210 (t80) cc_final: 0.8941 (t80) REVERT: E 95 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: E 132 ASP cc_start: 0.9136 (t0) cc_final: 0.8559 (t70) REVERT: E 204 MET cc_start: 0.9138 (mmm) cc_final: 0.8798 (ttt) REVERT: E 226 MET cc_start: 0.9230 (ttp) cc_final: 0.8887 (mtm) REVERT: E 229 LYS cc_start: 0.9246 (ptmt) cc_final: 0.9022 (pttp) REVERT: E 306 GLU cc_start: 0.7728 (mp0) cc_final: 0.7475 (mp0) REVERT: E 310 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8459 (tm-30) REVERT: F 69 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8863 (pt) REVERT: F 227 MET cc_start: 0.8719 (pmm) cc_final: 0.8477 (pmm) REVERT: F 260 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7587 (ptm-80) REVERT: F 262 TRP cc_start: 0.7229 (m-90) cc_final: 0.6819 (m-10) REVERT: F 382 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8415 (tp) REVERT: F 412 GLU cc_start: 0.9040 (mp0) cc_final: 0.8808 (pm20) REVERT: F 432 LEU cc_start: 0.8800 (mt) cc_final: 0.8532 (mt) REVERT: F 465 TYR cc_start: 0.8281 (t80) cc_final: 0.8040 (t80) REVERT: F 477 ASP cc_start: 0.9116 (m-30) cc_final: 0.8584 (m-30) outliers start: 92 outliers final: 73 residues processed: 470 average time/residue: 0.1365 time to fit residues: 103.4172 Evaluate side-chains 479 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 395 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 82 ASP Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 324 ILE 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 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 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 272 HIS 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 468 LEU 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 262 TRP Chi-restraints excluded: chain D residue 325 CYS 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 441 CYS Chi-restraints excluded: chain D residue 465 TYR Chi-restraints excluded: chain E residue 43 LYS 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 186 ASN Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 275 SER 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 66 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 96 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 67 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 196 optimal weight: 0.2980 chunk 41 optimal weight: 10.0000 chunk 122 optimal weight: 0.0470 chunk 143 optimal weight: 0.0270 chunk 233 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 overall best weight: 1.2740 ------------------------------------------------------------------------------- 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 ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN E 55 ASN ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.104318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.076884 restraints weight = 72930.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.079132 restraints weight = 38620.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080640 restraints weight = 25216.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.081646 restraints weight = 18781.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.082310 restraints weight = 15363.048| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22674 Z= 0.144 Angle : 0.816 16.098 30715 Z= 0.380 Chirality : 0.043 0.268 3561 Planarity : 0.005 0.067 3968 Dihedral : 7.515 108.013 3168 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.27 % Favored : 92.10 % Rotamer: Outliers : 3.29 % Allowed : 26.32 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.16), residues: 2861 helix: 0.47 (0.15), residues: 1289 sheet: -0.14 (0.23), residues: 500 loop : -0.93 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 463 TYR 0.024 0.002 TYR B 465 PHE 0.027 0.001 PHE E 339 TRP 0.014 0.001 TRP F 262 HIS 0.009 0.001 HIS C 402 Details of bonding type rmsd covalent geometry : bond 0.00334 (22673) covalent geometry : angle 0.81647 (30715) hydrogen bonds : bond 0.03166 ( 993) hydrogen bonds : angle 4.97602 ( 2808) Misc. bond : bond 0.00050 ( 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 496 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 416 time to evaluate : 0.979 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 7 LYS cc_start: 0.8739 (tptt) cc_final: 0.8447 (tptt) REVERT: A 204 MET cc_start: 0.8938 (mtm) cc_final: 0.8367 (mtm) REVERT: A 213 SER cc_start: 0.9094 (m) cc_final: 0.8767 (p) REVERT: A 299 LEU cc_start: 0.9075 (tt) cc_final: 0.8865 (tt) REVERT: A 309 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7545 (mmp-170) REVERT: A 384 MET cc_start: 0.7477 (tpt) cc_final: 0.7145 (tpt) REVERT: A 417 MET cc_start: 0.9029 (tpp) cc_final: 0.8572 (mmt) REVERT: A 455 MET cc_start: 0.8917 (mmm) cc_final: 0.8552 (mmm) REVERT: A 467 ARG cc_start: 0.9289 (mtm180) cc_final: 0.8533 (mtp180) REVERT: A 478 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8714 (mtp) REVERT: A 485 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8427 (mm) REVERT: B 69 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8371 (pt) REVERT: B 105 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7962 (mt-10) REVERT: B 159 ASN cc_start: 0.9547 (OUTLIER) cc_final: 0.9227 (p0) REVERT: B 272 HIS cc_start: 0.8973 (p-80) cc_final: 0.8579 (p90) REVERT: B 417 MET cc_start: 0.9497 (mmt) cc_final: 0.9046 (mmt) REVERT: B 443 LEU cc_start: 0.8525 (tp) cc_final: 0.8301 (tp) REVERT: B 459 LYS cc_start: 0.9229 (mmpt) cc_final: 0.8135 (pptt) REVERT: B 466 HIS cc_start: 0.8314 (OUTLIER) cc_final: 0.7893 (t70) REVERT: C 226 MET cc_start: 0.7668 (tpt) cc_final: 0.7366 (tpt) REVERT: C 271 HIS cc_start: 0.8046 (t70) cc_final: 0.7624 (t70) REVERT: C 334 GLU cc_start: 0.9570 (mp0) cc_final: 0.8942 (mm-30) REVERT: C 380 ASP cc_start: 0.8583 (t70) cc_final: 0.8284 (t70) REVERT: C 439 MET cc_start: 0.8949 (mmm) cc_final: 0.8741 (mmt) REVERT: C 448 GLN cc_start: 0.9292 (mt0) cc_final: 0.8878 (tm-30) REVERT: D 90 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9014 (mm) REVERT: D 193 ASP cc_start: 0.9142 (m-30) cc_final: 0.8104 (t0) REVERT: D 226 MET cc_start: 0.8793 (mtm) cc_final: 0.8262 (mtm) REVERT: D 253 ARG cc_start: 0.9299 (mtp-110) cc_final: 0.8998 (ttp-170) REVERT: D 325 CYS cc_start: 0.9183 (m) cc_final: 0.8779 (t) REVERT: D 335 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7598 (m-10) REVERT: D 450 PHE cc_start: 0.9185 (t80) cc_final: 0.8936 (t80) REVERT: E 95 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8037 (mp10) REVERT: E 132 ASP cc_start: 0.9098 (t0) cc_final: 0.8553 (t70) REVERT: E 204 MET cc_start: 0.9110 (mmm) cc_final: 0.8822 (ttt) REVERT: E 306 GLU cc_start: 0.7742 (mp0) cc_final: 0.7478 (mp0) REVERT: E 310 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8544 (tp40) REVERT: E 422 MET cc_start: 0.9239 (mmp) cc_final: 0.8979 (ptm) REVERT: F 262 TRP cc_start: 0.7042 (m-90) cc_final: 0.6666 (m-10) REVERT: F 382 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8363 (tp) REVERT: F 412 GLU cc_start: 0.8981 (mp0) cc_final: 0.8766 (pm20) REVERT: F 432 LEU cc_start: 0.8787 (mt) cc_final: 0.8515 (mt) REVERT: F 465 TYR cc_start: 0.8221 (t80) cc_final: 0.8009 (t80) REVERT: F 477 ASP cc_start: 0.9081 (m-30) cc_final: 0.8556 (m-30) outliers start: 80 outliers final: 62 residues processed: 472 average time/residue: 0.1545 time to fit residues: 116.0191 Evaluate side-chains 468 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 396 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 371 LEU 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 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 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 272 HIS 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 468 LEU 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 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 E residue 43 LYS 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 186 ASN 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 383 ASP Chi-restraints excluded: chain E residue 431 ASN 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 238 LEU Chi-restraints excluded: chain F residue 291 ILE 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 490 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 113 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 144 optimal weight: 0.2980 chunk 240 optimal weight: 10.0000 chunk 272 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 265 optimal weight: 0.4980 chunk 279 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 B 169 GLN ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 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 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.100978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.074041 restraints weight = 73855.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.076191 restraints weight = 38685.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077651 restraints weight = 25286.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.078628 restraints weight = 18877.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079293 restraints weight = 15438.205| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22674 Z= 0.186 Angle : 0.848 15.935 30715 Z= 0.397 Chirality : 0.044 0.233 3561 Planarity : 0.005 0.087 3968 Dihedral : 7.515 106.311 3168 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.65 % Favored : 91.82 % Rotamer: Outliers : 3.25 % Allowed : 26.56 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.16), residues: 2861 helix: 0.45 (0.15), residues: 1288 sheet: -0.08 (0.24), residues: 482 loop : -0.99 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 381 TYR 0.024 0.002 TYR B 465 PHE 0.028 0.002 PHE E 339 TRP 0.013 0.001 TRP C 262 HIS 0.009 0.001 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00422 (22673) covalent geometry : angle 0.84778 (30715) hydrogen bonds : bond 0.03316 ( 993) hydrogen bonds : angle 5.05551 ( 2808) Misc. bond : bond 0.00013 ( 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 477 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 398 time to evaluate : 0.955 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 204 MET cc_start: 0.8983 (mtm) cc_final: 0.8408 (mtm) REVERT: A 213 SER cc_start: 0.9059 (m) cc_final: 0.8716 (p) REVERT: A 299 LEU cc_start: 0.9025 (tt) cc_final: 0.8649 (tt) REVERT: A 309 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7606 (mmp-170) REVERT: A 339 PHE cc_start: 0.9407 (p90) cc_final: 0.9091 (p90) REVERT: A 417 MET cc_start: 0.9036 (tpp) cc_final: 0.8574 (mmt) REVERT: A 455 MET cc_start: 0.8957 (mmm) cc_final: 0.8602 (mmm) REVERT: A 467 ARG cc_start: 0.9287 (mtm180) cc_final: 0.8650 (mtp180) REVERT: A 478 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8716 (mtp) REVERT: B 69 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8427 (pt) REVERT: B 159 ASN cc_start: 0.9551 (OUTLIER) cc_final: 0.9147 (p0) REVERT: B 272 HIS cc_start: 0.9051 (p-80) cc_final: 0.8639 (p90) REVERT: B 417 MET cc_start: 0.9510 (mmt) cc_final: 0.9069 (mmt) REVERT: B 443 LEU cc_start: 0.8621 (tp) cc_final: 0.8411 (tp) REVERT: B 459 LYS cc_start: 0.9305 (mmpt) cc_final: 0.8300 (pttp) REVERT: B 466 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.7226 (t70) REVERT: C 73 ASN cc_start: 0.8850 (p0) cc_final: 0.8568 (p0) REVERT: C 226 MET cc_start: 0.7561 (tpt) cc_final: 0.7253 (tpt) REVERT: C 271 HIS cc_start: 0.8068 (t70) cc_final: 0.7720 (t70) REVERT: C 334 GLU cc_start: 0.9609 (mp0) cc_final: 0.8938 (mm-30) REVERT: C 380 ASP cc_start: 0.8591 (t70) cc_final: 0.8299 (t70) REVERT: C 448 GLN cc_start: 0.9312 (mt0) cc_final: 0.8900 (tm-30) REVERT: D 90 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9030 (mm) REVERT: D 193 ASP cc_start: 0.9153 (m-30) cc_final: 0.8120 (t0) REVERT: D 226 MET cc_start: 0.8773 (mtm) cc_final: 0.8260 (mtm) REVERT: D 253 ARG cc_start: 0.9332 (mtp-110) cc_final: 0.9019 (ttp-170) REVERT: D 325 CYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8835 (t) REVERT: D 335 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: D 450 PHE cc_start: 0.9189 (t80) cc_final: 0.8916 (t80) REVERT: E 95 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: E 132 ASP cc_start: 0.9169 (t0) cc_final: 0.8601 (t70) REVERT: E 204 MET cc_start: 0.9134 (mmm) cc_final: 0.8823 (ttt) REVERT: E 306 GLU cc_start: 0.7714 (mp0) cc_final: 0.7473 (mp0) REVERT: E 310 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8557 (tp40) REVERT: E 314 THR cc_start: 0.9055 (p) cc_final: 0.8778 (p) REVERT: E 422 MET cc_start: 0.9277 (mmp) cc_final: 0.9024 (ptm) REVERT: E 496 LYS cc_start: 0.8830 (tppt) cc_final: 0.8578 (tppt) REVERT: F 69 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8829 (pt) REVERT: F 262 TRP cc_start: 0.7086 (m-90) cc_final: 0.6703 (m-10) REVERT: F 311 VAL cc_start: 0.8942 (t) cc_final: 0.8521 (p) REVERT: F 382 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8305 (tp) REVERT: F 384 MET cc_start: 0.8207 (mmm) cc_final: 0.7857 (tpt) REVERT: F 412 GLU cc_start: 0.9045 (mp0) cc_final: 0.8728 (pm20) REVERT: F 432 LEU cc_start: 0.8794 (mt) cc_final: 0.8516 (mt) REVERT: F 465 TYR cc_start: 0.8240 (t80) cc_final: 0.8037 (t80) outliers start: 79 outliers final: 63 residues processed: 452 average time/residue: 0.1504 time to fit residues: 107.8195 Evaluate side-chains 467 residues out of total 2435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 393 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 371 LEU 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 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 216 LEU Chi-restraints excluded: chain B residue 304 LEU Chi-restraints excluded: chain B residue 335 PHE 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 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 272 HIS 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 468 LEU 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 262 TRP Chi-restraints excluded: chain D residue 325 CYS 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 E residue 43 LYS 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 186 ASN 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 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 69 LEU Chi-restraints excluded: chain F residue 96 ILE 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 378 LEU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 411 ARG 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 115 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 220 optimal weight: 0.6980 chunk 17 optimal weight: 0.0570 overall best weight: 2.7102 ------------------------------------------------------------------------------- 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** ** C 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN ** E 271 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 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN ** E 466 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.101060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.073929 restraints weight = 74471.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.076092 restraints weight = 39445.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077584 restraints weight = 25964.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.078566 restraints weight = 19361.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.079218 restraints weight = 15879.598| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 22674 Z= 0.219 Angle : 0.954 59.200 30715 Z= 0.480 Chirality : 0.044 0.207 3561 Planarity : 0.005 0.082 3968 Dihedral : 7.509 106.280 3168 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.58 % Favored : 91.89 % Rotamer: Outliers : 3.41 % Allowed : 26.77 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.16), residues: 2861 helix: 0.44 (0.15), residues: 1288 sheet: -0.09 (0.24), residues: 482 loop : -1.00 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 117 TYR 0.022 0.002 TYR B 465 PHE 0.026 0.002 PHE E 339 TRP 0.012 0.001 TRP C 262 HIS 0.009 0.001 HIS C 402 Details of bonding type rmsd covalent geometry : bond 0.00494 (22673) covalent geometry : angle 0.95438 (30715) hydrogen bonds : bond 0.03321 ( 993) hydrogen bonds : angle 5.06682 ( 2808) Misc. bond : bond 0.00030 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4944.22 seconds wall clock time: 86 minutes 11.72 seconds (5171.72 seconds total)