Starting phenix.real_space_refine on Mon Aug 25 07:48:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c2t_45160/08_2025/9c2t_45160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c2t_45160/08_2025/9c2t_45160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c2t_45160/08_2025/9c2t_45160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c2t_45160/08_2025/9c2t_45160.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c2t_45160/08_2025/9c2t_45160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c2t_45160/08_2025/9c2t_45160.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 4 Type Number sf(0) Gaussians S 103 5.16 5 C 17240 2.51 5 N 4540 2.21 5 O 5087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26970 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4021 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 472} Chain breaks: 4 Chain: "B" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4021 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 472} Chain breaks: 4 Chain: "C" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4021 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 472} Chain breaks: 4 Chain: "D" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4021 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 472} Chain breaks: 4 Chain: "E" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4021 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 472} Chain breaks: 4 Chain: "F" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4021 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 472} Chain breaks: 4 Chain: "S" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2844 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 12, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 6.56, per 1000 atoms: 0.24 Number of scatterers: 26970 At special positions: 0 Unit cell: (234.36, 177.12, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 103 16.00 O 5087 8.00 N 4540 7.00 C 17240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6308 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 63 sheets defined 11.9% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.527A pdb=" N LEU A 97 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.893A pdb=" N ILE A 283 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 284 " --> pdb=" O HIS A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 284' Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.628A pdb=" N ARG A 535 " --> pdb=" O GLN A 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.523A pdb=" N LEU B 97 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 196 through 199 removed outlier: 3.783A pdb=" N GLY B 199 " --> pdb=" O GLY B 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 196 through 199' Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.838A pdb=" N ILE B 283 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 524 through 528 Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.714A pdb=" N ARG B 535 " --> pdb=" O GLN B 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'C' and resid 213 through 217 removed outlier: 3.662A pdb=" N SER C 217 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 524 through 528 Processing helix chain 'C' and resid 532 through 536 removed outlier: 4.243A pdb=" N ARG C 535 " --> pdb=" O GLN C 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 377 through 382 Processing helix chain 'D' and resid 524 through 528 Processing helix chain 'D' and resid 532 through 536 removed outlier: 3.821A pdb=" N ARG D 535 " --> pdb=" O GLN D 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 94 through 98 Processing helix chain 'E' and resid 100 through 111 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 213 through 217 removed outlier: 3.532A pdb=" N SER E 217 " --> pdb=" O LEU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 284 removed outlier: 3.680A pdb=" N ILE E 283 " --> pdb=" O ASP E 280 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN E 284 " --> pdb=" O HIS E 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 280 through 284' Processing helix chain 'E' and resid 377 through 382 Processing helix chain 'E' and resid 524 through 528 Processing helix chain 'E' and resid 532 through 536 removed outlier: 3.622A pdb=" N ARG E 535 " --> pdb=" O GLN E 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 7 Processing helix chain 'F' and resid 94 through 98 Processing helix chain 'F' and resid 100 through 111 Processing helix chain 'F' and resid 196 through 199 Processing helix chain 'F' and resid 213 through 217 Processing helix chain 'F' and resid 280 through 284 removed outlier: 3.736A pdb=" N ILE F 283 " --> pdb=" O ASP F 280 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN F 284 " --> pdb=" O HIS F 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 280 through 284' Processing helix chain 'F' and resid 377 through 382 Processing helix chain 'F' and resid 524 through 528 Processing helix chain 'F' and resid 532 through 536 Processing helix chain 'S' and resid 49 through 68 Processing helix chain 'S' and resid 76 through 90 removed outlier: 3.731A pdb=" N GLY S 90 " --> pdb=" O PHE S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 93 through 102 removed outlier: 3.866A pdb=" N THR S 97 " --> pdb=" O ASN S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 111 through 128 Processing helix chain 'S' and resid 150 through 160 Processing helix chain 'S' and resid 172 through 188 Processing helix chain 'S' and resid 222 through 226 Processing helix chain 'S' and resid 283 through 290 Processing helix chain 'S' and resid 292 through 302 removed outlier: 3.580A pdb=" N ARG S 298 " --> pdb=" O GLU S 294 " (cutoff:3.500A) Processing helix chain 'S' and resid 324 through 332 Processing helix chain 'S' and resid 334 through 338 removed outlier: 3.559A pdb=" N THR S 338 " --> pdb=" O GLU S 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 12 through 13 current: chain 'B' and resid 35 through 46 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 35 through 46 current: chain 'B' and resid 139 through 143 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 25 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 22 through 25 current: chain 'B' and resid 82 through 89 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 35 through 46 current: chain 'A' and resid 139 through 143 Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 195 removed outlier: 4.514A pdb=" N ASP A 200 " --> pdb=" O GLN A 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 245 removed outlier: 6.770A pdb=" N GLY A 244 " --> pdb=" O HIS A 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.690A pdb=" N LYS A 272 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 289 through 290 removed outlier: 5.987A pdb=" N MET A 289 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AB1, first strand: chain 'A' and resid 338 through 340 Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.762A pdb=" N LYS E 272 " --> pdb=" O ASP E 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 374 through 375 removed outlier: 6.813A pdb=" N PHE A 374 " --> pdb=" O LEU A 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 403 through 404 removed outlier: 6.498A pdb=" N THR D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.043A pdb=" N SER A 428 " --> pdb=" O LEU A 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 435 through 437 removed outlier: 6.355A pdb=" N MET E 289 " --> pdb=" O VAL E 414 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 191 through 194 Processing sheet with id=AB8, first strand: chain 'B' and resid 244 through 245 removed outlier: 6.681A pdb=" N GLY B 244 " --> pdb=" O HIS B 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 272 through 275 removed outlier: 6.789A pdb=" N LYS B 272 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 289 through 290 removed outlier: 6.277A pdb=" N MET B 289 " --> pdb=" O VAL B 414 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.641A pdb=" N SER B 317 " --> pdb=" O TYR C 392 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 338 through 341 Processing sheet with id=AC4, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.753A pdb=" N LYS C 272 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AC6, first strand: chain 'B' and resid 403 through 404 Processing sheet with id=AC7, first strand: chain 'B' and resid 427 through 429 removed outlier: 5.944A pdb=" N SER B 428 " --> pdb=" O LEU B 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 435 through 437 removed outlier: 5.909A pdb=" N MET C 289 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 12 through 13 current: chain 'D' and resid 35 through 46 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 35 through 46 current: chain 'D' and resid 139 through 143 No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 22 through 25 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 22 through 25 current: chain 'D' and resid 81 through 89 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 31 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 35 through 46 current: chain 'C' and resid 139 through 143 Processing sheet with id=AD3, first strand: chain 'C' and resid 55 through 57 Processing sheet with id=AD4, first strand: chain 'C' and resid 191 through 194 Processing sheet with id=AD5, first strand: chain 'C' and resid 244 through 245 removed outlier: 6.643A pdb=" N GLY C 244 " --> pdb=" O HIS C 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 325 through 327 Processing sheet with id=AD7, first strand: chain 'C' and resid 338 through 340 Processing sheet with id=AD8, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.704A pdb=" N LYS F 272 " --> pdb=" O ASP F 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AE1, first strand: chain 'C' and resid 427 through 429 removed outlier: 6.044A pdb=" N SER C 428 " --> pdb=" O LEU C 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 435 through 437 removed outlier: 6.320A pdb=" N MET F 289 " --> pdb=" O VAL F 414 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 190 through 194 Processing sheet with id=AE4, first strand: chain 'D' and resid 244 through 245 removed outlier: 6.608A pdb=" N GLY D 244 " --> pdb=" O HIS D 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 272 through 274 removed outlier: 6.582A pdb=" N LYS D 272 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 289 through 290 removed outlier: 6.108A pdb=" N MET D 289 " --> pdb=" O VAL D 414 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 338 through 340 Processing sheet with id=AE8, first strand: chain 'D' and resid 356 through 357 Processing sheet with id=AE9, first strand: chain 'D' and resid 403 through 404 Processing sheet with id=AF1, first strand: chain 'D' and resid 427 through 429 removed outlier: 5.995A pdb=" N SER D 428 " --> pdb=" O LEU D 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 28 through 31 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 35 through 46 current: chain 'E' and resid 139 through 143 Processing sheet with id=AF3, first strand: chain 'E' and resid 55 through 57 Processing sheet with id=AF4, first strand: chain 'E' and resid 191 through 194 Processing sheet with id=AF5, first strand: chain 'E' and resid 244 through 245 removed outlier: 6.755A pdb=" N GLY E 244 " --> pdb=" O HIS E 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 338 through 340 Processing sheet with id=AF7, first strand: chain 'E' and resid 356 through 357 removed outlier: 3.513A pdb=" N VAL E 371 " --> pdb=" O THR E 357 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 374 through 375 removed outlier: 6.986A pdb=" N PHE E 374 " --> pdb=" O LEU E 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'E' and resid 427 through 429 removed outlier: 5.941A pdb=" N SER E 428 " --> pdb=" O LEU E 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'F' and resid 28 through 31 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 35 through 46 current: chain 'F' and resid 139 through 143 Processing sheet with id=AG2, first strand: chain 'F' and resid 55 through 57 Processing sheet with id=AG3, first strand: chain 'F' and resid 191 through 194 Processing sheet with id=AG4, first strand: chain 'F' and resid 244 through 245 removed outlier: 6.633A pdb=" N GLY F 244 " --> pdb=" O HIS F 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'F' and resid 338 through 341 Processing sheet with id=AG6, first strand: chain 'F' and resid 356 through 357 Processing sheet with id=AG7, first strand: chain 'F' and resid 427 through 429 removed outlier: 5.928A pdb=" N SER F 428 " --> pdb=" O LEU F 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'S' and resid 73 through 75 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 73 through 75 current: chain 'S' and resid 238 through 256 removed outlier: 11.578A pdb=" N THR S 250 " --> pdb=" O LYS S 267 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LYS S 267 " --> pdb=" O THR S 250 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 272 through 279 current: chain 'S' and resid 391 through 394 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 391 through 394 current: chain 'S' and resid 413 through 417 Processing sheet with id=AG9, first strand: chain 'S' and resid 133 through 137 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 133 through 137 current: chain 'S' and resid 166 through 168 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 166 through 168 current: chain 'S' and resid 356 through 365 No H-bonds generated for sheet with id=AG9 390 hydrogen bonds defined for protein. 852 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: 5.24 Time building geometry restraints manager: 3.32 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: 4827 1.33 - 1.45: 7496 1.45 - 1.57: 15260 1.57 - 1.69: 0 1.69 - 1.81: 181 Bond restraints: 27764 Sorted by residual: bond pdb=" CD GLN S 120 " pdb=" OE1 GLN S 120 " ideal model delta sigma weight residual 1.231 1.203 0.028 1.90e-02 2.77e+03 2.11e+00 bond pdb=" N ALA E 547 " pdb=" CA ALA E 547 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.92e+00 bond pdb=" CA VAL B 237 " pdb=" CB VAL B 237 " ideal model delta sigma weight residual 1.546 1.537 0.010 8.80e-03 1.29e+04 1.21e+00 bond pdb=" CB ASN S 351 " pdb=" CG ASN S 351 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.16e+00 bond pdb=" CB GLU S 112 " pdb=" CG GLU S 112 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 27759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 37197 1.71 - 3.41: 582 3.41 - 5.12: 34 5.12 - 6.83: 16 6.83 - 8.53: 3 Bond angle restraints: 37832 Sorted by residual: angle pdb=" CA MET S 290 " pdb=" CB MET S 290 " pdb=" CG MET S 290 " ideal model delta sigma weight residual 114.10 120.29 -6.19 2.00e+00 2.50e-01 9.58e+00 angle pdb=" C VAL S 241 " pdb=" CA VAL S 241 " pdb=" CB VAL S 241 " ideal model delta sigma weight residual 109.33 112.06 -2.73 9.80e-01 1.04e+00 7.75e+00 angle pdb=" CA VAL S 241 " pdb=" C VAL S 241 " pdb=" N PRO S 242 " ideal model delta sigma weight residual 116.57 119.23 -2.66 9.80e-01 1.04e+00 7.38e+00 angle pdb=" N ILE B 176 " pdb=" CA ILE B 176 " pdb=" C ILE B 176 " ideal model delta sigma weight residual 112.83 110.25 2.58 9.90e-01 1.02e+00 6.80e+00 angle pdb=" CB MET S 205 " pdb=" CG MET S 205 " pdb=" SD MET S 205 " ideal model delta sigma weight residual 112.70 120.35 -7.65 3.00e+00 1.11e-01 6.50e+00 ... (remaining 37827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 14664 17.98 - 35.97: 1238 35.97 - 53.95: 328 53.95 - 71.94: 68 71.94 - 89.92: 29 Dihedral angle restraints: 16327 sinusoidal: 6431 harmonic: 9896 Sorted by residual: dihedral pdb=" CA LYS S 101 " pdb=" C LYS S 101 " pdb=" N GLY S 102 " pdb=" CA GLY S 102 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU S 100 " pdb=" C LEU S 100 " pdb=" N LYS S 101 " pdb=" CA LYS S 101 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA HIS D 53 " pdb=" C HIS D 53 " pdb=" N TYR D 54 " pdb=" CA TYR D 54 " ideal model delta harmonic sigma weight residual 180.00 162.05 17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 16324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3304 0.047 - 0.094: 601 0.094 - 0.141: 180 0.141 - 0.188: 4 0.188 - 0.235: 2 Chirality restraints: 4091 Sorted by residual: chirality pdb=" CB ILE S 115 " pdb=" CA ILE S 115 " pdb=" CG1 ILE S 115 " pdb=" CG2 ILE S 115 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE S 196 " pdb=" CA ILE S 196 " pdb=" CG1 ILE S 196 " pdb=" CG2 ILE S 196 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB THR S 82 " pdb=" CA THR S 82 " pdb=" OG1 THR S 82 " pdb=" CG2 THR S 82 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 4088 not shown) Planarity restraints: 4910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS S 116 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C HIS S 116 " 0.035 2.00e-02 2.50e+03 pdb=" O HIS S 116 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN S 117 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN S 120 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" CD GLN S 120 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN S 120 " -0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN S 120 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 452 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 453 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " -0.023 5.00e-02 4.00e+02 ... (remaining 4907 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 792 2.68 - 3.24: 25264 3.24 - 3.79: 45503 3.79 - 4.35: 62543 4.35 - 4.90: 102392 Nonbonded interactions: 236494 Sorted by model distance: nonbonded pdb=" OG SER D 353 " pdb=" O GLY D 355 " model vdw 2.126 3.040 nonbonded pdb=" OG SER F 353 " pdb=" O GLY F 355 " model vdw 2.134 3.040 nonbonded pdb=" ND2 ASN A 287 " pdb=" O GLY D 164 " model vdw 2.173 3.120 nonbonded pdb=" OG SER C 353 " pdb=" O GLY C 355 " model vdw 2.174 3.040 nonbonded pdb=" OD2 ASP A 91 " pdb=" OG1 THR A 169 " model vdw 2.187 3.040 ... (remaining 236489 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 individual isotropic 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: 8.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.180 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 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 : 0.003 0.031 27764 Z= 0.132 Angle : 0.526 8.534 37832 Z= 0.273 Chirality : 0.040 0.235 4091 Planarity : 0.004 0.041 4910 Dihedral : 15.092 89.920 10019 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.43 % Allowed : 14.01 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.55 (0.13), residues: 3397 helix: -0.35 (0.32), residues: 264 sheet: -0.14 (0.19), residues: 692 loop : -0.40 (0.11), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 274 TYR 0.024 0.001 TYR S 161 PHE 0.022 0.002 PHE S 86 TRP 0.015 0.001 TRP S 299 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00300 (27764) covalent geometry : angle 0.52648 (37832) hydrogen bonds : bond 0.19871 ( 390) hydrogen bonds : angle 6.63225 ( 852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 414 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 417 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8032 (mtt90) REVERT: B 215 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: B 344 LYS cc_start: 0.7920 (ttmm) cc_final: 0.7661 (mtmm) REVERT: B 407 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8351 (ttm-80) REVERT: B 417 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7724 (mtt90) REVERT: C 201 SER cc_start: 0.8967 (m) cc_final: 0.8515 (p) REVERT: D 193 ASN cc_start: 0.7904 (m-40) cc_final: 0.7701 (t0) REVERT: D 344 LYS cc_start: 0.7765 (tptt) cc_final: 0.7154 (ptpp) REVERT: D 404 GLN cc_start: 0.8340 (pt0) cc_final: 0.8108 (pt0) REVERT: E 125 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7552 (tm-30) REVERT: E 410 MET cc_start: 0.9246 (mtm) cc_final: 0.8955 (mtm) REVERT: E 432 ASN cc_start: 0.8796 (p0) cc_final: 0.8416 (p0) REVERT: F 27 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8566 (mm-30) REVERT: F 125 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8348 (mm-30) REVERT: F 554 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7292 (mp) REVERT: S 209 ASN cc_start: 0.6952 (t0) cc_final: 0.6430 (t0) REVERT: S 258 GLU cc_start: 0.7246 (pm20) cc_final: 0.6520 (pm20) REVERT: S 286 GLU cc_start: 0.7898 (mp0) cc_final: 0.7260 (mp0) REVERT: S 333 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8076 (mm) outliers start: 42 outliers final: 32 residues processed: 431 average time/residue: 0.1898 time to fit residues: 131.6081 Evaluate side-chains 441 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 405 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 407 ARG Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 432 ASN Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain E residue 278 HIS Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 358 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.0030 overall best weight: 1.4452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 GLN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN D 167 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS E 193 ASN E 356 GLN F 5 ASN S 351 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.117613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.086058 restraints weight = 36479.346| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 1.74 r_work: 0.2659 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27764 Z= 0.139 Angle : 0.507 9.349 37832 Z= 0.258 Chirality : 0.040 0.157 4091 Planarity : 0.004 0.037 4910 Dihedral : 5.796 67.163 3761 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.17 % Allowed : 13.10 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.54 (0.13), residues: 3397 helix: -0.26 (0.31), residues: 264 sheet: -0.21 (0.18), residues: 740 loop : -0.38 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 373 TYR 0.011 0.001 TYR S 210 PHE 0.019 0.002 PHE A 393 TRP 0.008 0.001 TRP A 25 HIS 0.008 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00328 (27764) covalent geometry : angle 0.50664 (37832) hydrogen bonds : bond 0.03877 ( 390) hydrogen bonds : angle 5.51791 ( 852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 440 time to evaluate : 0.829 Fit side-chains REVERT: A 53 HIS cc_start: 0.8388 (m-70) cc_final: 0.8134 (m-70) REVERT: A 405 ILE cc_start: 0.9252 (mm) cc_final: 0.9022 (mm) REVERT: A 417 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.8055 (mtt90) REVERT: A 539 GLU cc_start: 0.8691 (tt0) cc_final: 0.8365 (mt-10) REVERT: A 554 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7425 (mp) REVERT: B 170 LEU cc_start: 0.9014 (mt) cc_final: 0.8780 (mt) REVERT: B 344 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7775 (mtmm) REVERT: B 417 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7746 (mtt90) REVERT: C 201 SER cc_start: 0.8923 (m) cc_final: 0.8391 (p) REVERT: C 542 GLU cc_start: 0.8555 (pt0) cc_final: 0.8302 (pt0) REVERT: D 53 HIS cc_start: 0.6958 (OUTLIER) cc_final: 0.6668 (p90) REVERT: D 133 ASP cc_start: 0.8901 (OUTLIER) cc_final: 0.8649 (m-30) REVERT: D 279 GLU cc_start: 0.7514 (mp0) cc_final: 0.7034 (mp0) REVERT: D 344 LYS cc_start: 0.7868 (tptt) cc_final: 0.7377 (ptpt) REVERT: E 107 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8910 (tp) REVERT: E 280 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8456 (p0) REVERT: E 489 THR cc_start: 0.9103 (m) cc_final: 0.8845 (m) REVERT: E 554 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7655 (mp) REVERT: F 27 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8575 (mm-30) REVERT: F 107 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8890 (tp) REVERT: F 109 GLU cc_start: 0.8073 (tt0) cc_final: 0.7869 (pt0) REVERT: F 257 TYR cc_start: 0.9218 (m-80) cc_final: 0.8819 (m-80) REVERT: F 554 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7260 (mp) REVERT: S 207 LEU cc_start: 0.8223 (tp) cc_final: 0.7992 (tp) REVERT: S 208 VAL cc_start: 0.8671 (t) cc_final: 0.8375 (p) REVERT: S 209 ASN cc_start: 0.7021 (t0) cc_final: 0.6439 (t0) REVERT: S 258 GLU cc_start: 0.7337 (pm20) cc_final: 0.6971 (pm20) REVERT: S 285 GLU cc_start: 0.7399 (pm20) cc_final: 0.6910 (pm20) REVERT: S 286 GLU cc_start: 0.7714 (mp0) cc_final: 0.6569 (mp0) REVERT: S 409 GLN cc_start: 0.6067 (pp30) cc_final: 0.5853 (pp30) outliers start: 64 outliers final: 42 residues processed: 484 average time/residue: 0.1671 time to fit residues: 131.2523 Evaluate side-chains 460 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 409 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 528 THR Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 177 LYS Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain S residue 247 HIS Chi-restraints excluded: chain S residue 261 CYS Chi-restraints excluded: chain S residue 400 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 36 optimal weight: 0.8980 chunk 259 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 158 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 295 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS E 110 ASN E 193 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 281 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.117694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.086132 restraints weight = 36462.952| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 1.74 r_work: 0.2672 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27764 Z= 0.138 Angle : 0.489 9.210 37832 Z= 0.247 Chirality : 0.040 0.144 4091 Planarity : 0.004 0.037 4910 Dihedral : 4.946 59.714 3715 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.82 % Allowed : 13.20 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.54 (0.13), residues: 3397 helix: -0.11 (0.32), residues: 263 sheet: -0.26 (0.18), residues: 738 loop : -0.39 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 274 TYR 0.011 0.001 TYR B 111 PHE 0.014 0.001 PHE A 393 TRP 0.007 0.001 TRP A 25 HIS 0.007 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00330 (27764) covalent geometry : angle 0.48865 (37832) hydrogen bonds : bond 0.03515 ( 390) hydrogen bonds : angle 5.37233 ( 852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 421 time to evaluate : 1.087 Fit side-chains REVERT: A 53 HIS cc_start: 0.8292 (m-70) cc_final: 0.7918 (m-70) REVERT: A 407 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.9026 (ttm170) REVERT: A 417 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.7753 (mtt90) REVERT: A 539 GLU cc_start: 0.8665 (tt0) cc_final: 0.8462 (tt0) REVERT: A 554 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7184 (mp) REVERT: B 107 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9087 (tp) REVERT: B 344 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7736 (mtmm) REVERT: B 374 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: B 378 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8507 (pttt) REVERT: B 417 ARG cc_start: 0.8162 (mtm-85) cc_final: 0.7774 (mtt90) REVERT: B 534 HIS cc_start: 0.7746 (m-70) cc_final: 0.6707 (p90) REVERT: C 201 SER cc_start: 0.8892 (m) cc_final: 0.8293 (p) REVERT: C 289 MET cc_start: 0.9502 (mmt) cc_final: 0.9281 (mmt) REVERT: D 35 SER cc_start: 0.9378 (OUTLIER) cc_final: 0.9136 (t) REVERT: D 107 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8843 (tp) REVERT: D 133 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8636 (m-30) REVERT: D 279 GLU cc_start: 0.7519 (mp0) cc_final: 0.7038 (mp0) REVERT: E 208 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8319 (mm-30) REVERT: E 489 THR cc_start: 0.9104 (m) cc_final: 0.8849 (m) REVERT: E 554 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7689 (mp) REVERT: F 27 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8543 (mm-30) REVERT: F 107 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8877 (tp) REVERT: F 257 TYR cc_start: 0.9173 (m-80) cc_final: 0.8694 (m-80) REVERT: F 554 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7297 (mp) REVERT: S 145 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6978 (pm20) REVERT: S 207 LEU cc_start: 0.8198 (tp) cc_final: 0.7961 (tp) REVERT: S 208 VAL cc_start: 0.8664 (t) cc_final: 0.8328 (p) REVERT: S 209 ASN cc_start: 0.7003 (t0) cc_final: 0.6372 (t0) REVERT: S 285 GLU cc_start: 0.7397 (pm20) cc_final: 0.6715 (pm20) REVERT: S 286 GLU cc_start: 0.7702 (mp0) cc_final: 0.6327 (mp0) REVERT: S 290 MET cc_start: 0.7462 (tpp) cc_final: 0.7139 (tpp) outliers start: 83 outliers final: 54 residues processed: 476 average time/residue: 0.1705 time to fit residues: 131.3615 Evaluate side-chains 464 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 397 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 432 ASN Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 528 THR Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain S residue 145 GLU Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 177 LYS Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain S residue 247 HIS Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 400 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 98 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 332 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 257 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 110 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN D 167 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS E 193 ASN E 380 GLN F 5 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 281 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.118739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.087286 restraints weight = 36140.011| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 1.73 r_work: 0.2682 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27764 Z= 0.117 Angle : 0.475 9.173 37832 Z= 0.240 Chirality : 0.040 0.143 4091 Planarity : 0.004 0.038 4910 Dihedral : 4.865 58.596 3715 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.65 % Allowed : 13.61 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.51 (0.13), residues: 3397 helix: 0.00 (0.32), residues: 263 sheet: -0.30 (0.18), residues: 740 loop : -0.35 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 274 TYR 0.009 0.001 TYR E 111 PHE 0.013 0.001 PHE S 412 TRP 0.007 0.001 TRP C 25 HIS 0.008 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00278 (27764) covalent geometry : angle 0.47513 (37832) hydrogen bonds : bond 0.03173 ( 390) hydrogen bonds : angle 5.26098 ( 852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 432 time to evaluate : 1.136 Fit side-chains REVERT: A 53 HIS cc_start: 0.8362 (m170) cc_final: 0.8148 (m-70) REVERT: A 407 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.9007 (ttm170) REVERT: A 539 GLU cc_start: 0.8599 (tt0) cc_final: 0.8300 (mt-10) REVERT: A 554 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7422 (mp) REVERT: B 107 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9040 (tp) REVERT: B 344 LYS cc_start: 0.7978 (ttmm) cc_final: 0.7721 (mtmm) REVERT: B 374 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: B 393 PHE cc_start: 0.8823 (m-80) cc_final: 0.8558 (m-80) REVERT: B 417 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7715 (mtt90) REVERT: B 534 HIS cc_start: 0.7748 (m-70) cc_final: 0.6695 (p90) REVERT: C 201 SER cc_start: 0.8880 (m) cc_final: 0.8231 (p) REVERT: C 289 MET cc_start: 0.9485 (mmt) cc_final: 0.9162 (mmt) REVERT: D 35 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.9152 (t) REVERT: D 125 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8636 (mm-30) REVERT: D 133 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8586 (m-30) REVERT: D 279 GLU cc_start: 0.7500 (mp0) cc_final: 0.7008 (mp0) REVERT: E 107 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8851 (tp) REVERT: E 208 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8500 (mm-30) REVERT: E 404 GLN cc_start: 0.8501 (pm20) cc_final: 0.7662 (pm20) REVERT: E 489 THR cc_start: 0.9105 (m) cc_final: 0.8851 (m) REVERT: E 554 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7664 (mp) REVERT: F 27 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8547 (mm-30) REVERT: F 107 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8889 (tp) REVERT: F 109 GLU cc_start: 0.7980 (tt0) cc_final: 0.7743 (pt0) REVERT: F 257 TYR cc_start: 0.9145 (m-80) cc_final: 0.8673 (m-80) REVERT: S 207 LEU cc_start: 0.8211 (tp) cc_final: 0.7963 (tp) REVERT: S 208 VAL cc_start: 0.8628 (t) cc_final: 0.8270 (p) REVERT: S 209 ASN cc_start: 0.6950 (t0) cc_final: 0.6328 (t0) REVERT: S 285 GLU cc_start: 0.7462 (pm20) cc_final: 0.6806 (pm20) REVERT: S 286 GLU cc_start: 0.7770 (mp0) cc_final: 0.6245 (mp0) REVERT: S 290 MET cc_start: 0.7725 (tpp) cc_final: 0.7419 (tpp) REVERT: S 391 THR cc_start: 0.8452 (t) cc_final: 0.8164 (p) outliers start: 78 outliers final: 45 residues processed: 482 average time/residue: 0.1708 time to fit residues: 133.9923 Evaluate side-chains 453 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 398 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 432 ASN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain S residue 137 MET Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 177 LYS Chi-restraints excluded: chain S residue 262 THR Chi-restraints excluded: chain S residue 400 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 62 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 312 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN C 517 HIS ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN F 5 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 281 GLN S 330 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.114954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.083336 restraints weight = 36378.252| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 1.71 r_work: 0.2629 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 27764 Z= 0.245 Angle : 0.539 8.893 37832 Z= 0.272 Chirality : 0.042 0.147 4091 Planarity : 0.004 0.039 4910 Dihedral : 4.988 54.355 3712 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.66 % Allowed : 13.30 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.63 (0.13), residues: 3397 helix: -0.15 (0.32), residues: 263 sheet: -0.32 (0.18), residues: 735 loop : -0.45 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 397 TYR 0.014 0.002 TYR A 337 PHE 0.020 0.002 PHE A 44 TRP 0.010 0.001 TRP B 545 HIS 0.005 0.001 HIS S 116 Details of bonding type rmsd covalent geometry : bond 0.00588 (27764) covalent geometry : angle 0.53902 (37832) hydrogen bonds : bond 0.03482 ( 390) hydrogen bonds : angle 5.47446 ( 852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 401 time to evaluate : 1.048 Fit side-chains REVERT: A 195 GLN cc_start: 0.7908 (mp10) cc_final: 0.7463 (mp10) REVERT: A 407 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.9033 (ttp-170) REVERT: A 554 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7424 (mp) REVERT: B 107 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9036 (tp) REVERT: B 344 LYS cc_start: 0.8067 (ttmm) cc_final: 0.7762 (mtmm) REVERT: B 378 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8534 (pttt) REVERT: B 417 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7826 (mtt90) REVERT: B 534 HIS cc_start: 0.7752 (m-70) cc_final: 0.6620 (p90) REVERT: C 201 SER cc_start: 0.8952 (m) cc_final: 0.8326 (p) REVERT: D 55 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8812 (mttp) REVERT: D 107 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8849 (tp) REVERT: D 133 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8608 (m-30) REVERT: D 407 ARG cc_start: 0.9403 (OUTLIER) cc_final: 0.8698 (ttm-80) REVERT: E 107 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8884 (tp) REVERT: E 193 ASN cc_start: 0.7763 (m-40) cc_final: 0.7484 (m110) REVERT: E 208 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8392 (mt-10) REVERT: E 404 GLN cc_start: 0.8458 (pm20) cc_final: 0.7631 (pm20) REVERT: E 489 THR cc_start: 0.9127 (m) cc_final: 0.8879 (m) REVERT: E 554 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7670 (mp) REVERT: F 27 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8506 (mm-30) REVERT: F 107 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8899 (tp) REVERT: F 257 TYR cc_start: 0.9217 (m-80) cc_final: 0.8721 (m-80) REVERT: F 344 LYS cc_start: 0.8088 (ptpp) cc_final: 0.7792 (pttp) REVERT: S 145 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: S 208 VAL cc_start: 0.8608 (t) cc_final: 0.8233 (p) REVERT: S 209 ASN cc_start: 0.7067 (t0) cc_final: 0.6456 (t0) REVERT: S 258 GLU cc_start: 0.7442 (pm20) cc_final: 0.7090 (pm20) REVERT: S 285 GLU cc_start: 0.7468 (pm20) cc_final: 0.6821 (pm20) REVERT: S 286 GLU cc_start: 0.7892 (mp0) cc_final: 0.6212 (mp0) REVERT: S 415 SER cc_start: 0.8827 (t) cc_final: 0.8441 (p) outliers start: 108 outliers final: 83 residues processed: 474 average time/residue: 0.1652 time to fit residues: 126.8304 Evaluate side-chains 482 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 386 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 53 HIS Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 55 LYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 278 HIS Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain S residue 110 THR Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 137 MET Chi-restraints excluded: chain S residue 145 GLU Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 177 LYS Chi-restraints excluded: chain S residue 247 HIS Chi-restraints excluded: chain S residue 262 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 354 VAL Chi-restraints excluded: chain S residue 400 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 208 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 307 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 269 optimal weight: 0.0040 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN C 53 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 281 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.117788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.086372 restraints weight = 36326.459| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 1.73 r_work: 0.2667 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27764 Z= 0.116 Angle : 0.481 8.815 37832 Z= 0.242 Chirality : 0.040 0.146 4091 Planarity : 0.004 0.039 4910 Dihedral : 4.742 49.894 3712 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.02 % Allowed : 14.46 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.56 (0.13), residues: 3397 helix: -0.07 (0.32), residues: 263 sheet: -0.33 (0.18), residues: 735 loop : -0.38 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 397 TYR 0.009 0.001 TYR A 337 PHE 0.015 0.001 PHE S 56 TRP 0.007 0.001 TRP C 25 HIS 0.009 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00272 (27764) covalent geometry : angle 0.48132 (37832) hydrogen bonds : bond 0.03032 ( 390) hydrogen bonds : angle 5.34508 ( 852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 416 time to evaluate : 0.719 Fit side-chains REVERT: A 535 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7659 (mmm160) REVERT: A 554 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7431 (mp) REVERT: B 107 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8991 (tp) REVERT: B 280 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8146 (p0) REVERT: B 344 LYS cc_start: 0.8054 (ttmm) cc_final: 0.7783 (mtmm) REVERT: B 374 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.7640 (m-80) REVERT: B 378 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8554 (pttt) REVERT: B 417 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7792 (mtt90) REVERT: B 534 HIS cc_start: 0.7726 (m-70) cc_final: 0.6648 (p90) REVERT: C 201 SER cc_start: 0.8874 (m) cc_final: 0.8215 (p) REVERT: D 55 LYS cc_start: 0.9117 (mttt) cc_final: 0.8908 (mttt) REVERT: D 107 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8782 (tp) REVERT: D 133 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8615 (m-30) REVERT: D 279 GLU cc_start: 0.7501 (mp0) cc_final: 0.6998 (mp0) REVERT: E 107 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8893 (tp) REVERT: E 125 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7613 (tm-30) REVERT: E 208 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8534 (mt-10) REVERT: E 280 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8416 (p0) REVERT: E 404 GLN cc_start: 0.8450 (pm20) cc_final: 0.7699 (pm20) REVERT: E 489 THR cc_start: 0.9111 (m) cc_final: 0.8862 (m) REVERT: E 554 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7563 (mp) REVERT: F 27 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8564 (mm-30) REVERT: F 107 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8899 (tp) REVERT: F 257 TYR cc_start: 0.9154 (m-80) cc_final: 0.8756 (m-80) REVERT: S 208 VAL cc_start: 0.8584 (t) cc_final: 0.8128 (p) REVERT: S 209 ASN cc_start: 0.7090 (t0) cc_final: 0.6527 (t0) REVERT: S 258 GLU cc_start: 0.7487 (pm20) cc_final: 0.7144 (pm20) REVERT: S 285 GLU cc_start: 0.7478 (pm20) cc_final: 0.6874 (pm20) REVERT: S 286 GLU cc_start: 0.7913 (mp0) cc_final: 0.6209 (mp0) REVERT: S 290 MET cc_start: 0.7710 (tpp) cc_final: 0.7467 (tpp) REVERT: S 391 THR cc_start: 0.8502 (t) cc_final: 0.8149 (p) REVERT: S 415 SER cc_start: 0.8845 (t) cc_final: 0.8410 (p) outliers start: 89 outliers final: 59 residues processed: 476 average time/residue: 0.1544 time to fit residues: 120.4548 Evaluate side-chains 462 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 391 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 280 ASP Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 137 MET Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 177 LYS Chi-restraints excluded: chain S residue 262 THR Chi-restraints excluded: chain S residue 400 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 326 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 295 optimal weight: 8.9990 chunk 334 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 320 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 53 HIS A 110 ASN ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN C 53 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS ** E 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN F 5 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 281 GLN S 351 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.112943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.081456 restraints weight = 36400.228| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 1.69 r_work: 0.2595 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.116 27764 Z= 0.362 Angle : 0.608 9.226 37832 Z= 0.305 Chirality : 0.045 0.141 4091 Planarity : 0.005 0.040 4910 Dihedral : 5.178 51.491 3710 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.50 % Allowed : 14.46 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.71 (0.13), residues: 3397 helix: -0.37 (0.31), residues: 263 sheet: -0.20 (0.19), residues: 705 loop : -0.56 (0.12), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 417 TYR 0.016 0.002 TYR F 111 PHE 0.022 0.002 PHE F 44 TRP 0.014 0.002 TRP B 545 HIS 0.010 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00877 (27764) covalent geometry : angle 0.60762 (37832) hydrogen bonds : bond 0.03720 ( 390) hydrogen bonds : angle 5.64168 ( 852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 388 time to evaluate : 0.923 Fit side-chains REVERT: A 195 GLN cc_start: 0.7924 (mp10) cc_final: 0.7476 (mp10) REVERT: A 554 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 107 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9039 (tp) REVERT: B 344 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7743 (mtmm) REVERT: B 417 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7737 (mtt90) REVERT: B 534 HIS cc_start: 0.7771 (m-70) cc_final: 0.6629 (p90) REVERT: C 201 SER cc_start: 0.9035 (m) cc_final: 0.8447 (p) REVERT: D 55 LYS cc_start: 0.9101 (mttt) cc_final: 0.8891 (mttm) REVERT: D 107 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8937 (tp) REVERT: D 133 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8592 (m-30) REVERT: E 107 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.8906 (tp) REVERT: E 208 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8450 (mt-10) REVERT: E 280 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8479 (p0) REVERT: E 404 GLN cc_start: 0.8497 (pm20) cc_final: 0.7606 (pm20) REVERT: E 432 ASN cc_start: 0.8867 (p0) cc_final: 0.8438 (p0) REVERT: E 489 THR cc_start: 0.9127 (m) cc_final: 0.8888 (m) REVERT: E 554 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7660 (mp) REVERT: F 27 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8571 (mm-30) REVERT: F 107 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.8907 (tp) REVERT: F 322 GLN cc_start: 0.8726 (mm110) cc_final: 0.8413 (mm110) REVERT: F 344 LYS cc_start: 0.8066 (ptpp) cc_final: 0.7780 (pttp) REVERT: S 86 PHE cc_start: 0.8115 (t80) cc_final: 0.7910 (t80) REVERT: S 208 VAL cc_start: 0.8576 (t) cc_final: 0.8118 (p) REVERT: S 209 ASN cc_start: 0.7138 (t0) cc_final: 0.6572 (t0) REVERT: S 285 GLU cc_start: 0.7471 (pm20) cc_final: 0.6870 (pm20) REVERT: S 286 GLU cc_start: 0.7957 (mp0) cc_final: 0.6129 (mp0) REVERT: S 290 MET cc_start: 0.7681 (tpp) cc_final: 0.7364 (tpp) REVERT: S 415 SER cc_start: 0.8900 (t) cc_final: 0.8450 (p) outliers start: 103 outliers final: 82 residues processed: 453 average time/residue: 0.1653 time to fit residues: 123.3115 Evaluate side-chains 472 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 381 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 432 ASN Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 342 THR Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 420 LEU Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain S residue 89 LEU Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 177 LYS Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain S residue 262 THR Chi-restraints excluded: chain S residue 338 THR Chi-restraints excluded: chain S residue 354 VAL Chi-restraints excluded: chain S residue 400 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 203 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 321 optimal weight: 20.0000 chunk 229 optimal weight: 0.0070 chunk 9 optimal weight: 0.6980 chunk 205 optimal weight: 4.9990 chunk 324 optimal weight: 10.0000 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS C 380 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS E 193 ASN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 281 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.116843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.085522 restraints weight = 36286.759| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 1.70 r_work: 0.2657 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27764 Z= 0.119 Angle : 0.505 8.734 37832 Z= 0.254 Chirality : 0.040 0.145 4091 Planarity : 0.004 0.039 4910 Dihedral : 4.831 46.951 3710 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.92 % Allowed : 14.90 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.67 (0.13), residues: 3397 helix: -0.30 (0.32), residues: 269 sheet: -0.44 (0.18), residues: 735 loop : -0.44 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 417 TYR 0.014 0.001 TYR F 257 PHE 0.013 0.001 PHE S 56 TRP 0.009 0.001 TRP S 299 HIS 0.003 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00281 (27764) covalent geometry : angle 0.50494 (37832) hydrogen bonds : bond 0.03074 ( 390) hydrogen bonds : angle 5.35877 ( 852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 408 time to evaluate : 1.107 Fit side-chains REVERT: A 497 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8188 (mtm180) REVERT: A 554 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7552 (mp) REVERT: B 107 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8999 (tp) REVERT: B 344 LYS cc_start: 0.8084 (ttmm) cc_final: 0.7765 (mtmm) REVERT: B 374 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: B 417 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7615 (mtt90) REVERT: B 534 HIS cc_start: 0.7718 (m-70) cc_final: 0.6644 (p90) REVERT: C 201 SER cc_start: 0.8914 (m) cc_final: 0.8274 (p) REVERT: D 107 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8845 (tp) REVERT: D 133 ASP cc_start: 0.8877 (OUTLIER) cc_final: 0.8532 (m-30) REVERT: D 344 LYS cc_start: 0.7625 (tptt) cc_final: 0.7072 (ptpt) REVERT: E 107 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8916 (tp) REVERT: E 125 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7833 (tm-30) REVERT: E 208 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8455 (mt-10) REVERT: E 280 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8441 (p0) REVERT: E 404 GLN cc_start: 0.8440 (pm20) cc_final: 0.7741 (pm20) REVERT: E 489 THR cc_start: 0.9112 (m) cc_final: 0.8872 (m) REVERT: E 554 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7545 (mp) REVERT: F 27 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8589 (mm-30) REVERT: F 107 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8859 (tp) REVERT: F 257 TYR cc_start: 0.9066 (m-80) cc_final: 0.8845 (m-80) REVERT: F 539 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8742 (mt-10) REVERT: S 204 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6528 (ptm) REVERT: S 208 VAL cc_start: 0.8448 (t) cc_final: 0.7988 (p) REVERT: S 209 ASN cc_start: 0.7131 (t0) cc_final: 0.6634 (t0) REVERT: S 285 GLU cc_start: 0.7377 (pm20) cc_final: 0.6862 (pm20) REVERT: S 286 GLU cc_start: 0.7971 (mp0) cc_final: 0.6233 (mp0) REVERT: S 290 MET cc_start: 0.7504 (tpp) cc_final: 0.7217 (tpp) REVERT: S 391 THR cc_start: 0.8526 (t) cc_final: 0.8158 (p) REVERT: S 415 SER cc_start: 0.8942 (t) cc_final: 0.8467 (p) outliers start: 86 outliers final: 62 residues processed: 467 average time/residue: 0.1698 time to fit residues: 130.4575 Evaluate side-chains 476 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 403 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 374 PHE Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 137 MET Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 177 LYS Chi-restraints excluded: chain S residue 194 ASP Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain S residue 262 THR Chi-restraints excluded: chain S residue 354 VAL Chi-restraints excluded: chain S residue 400 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 69 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 324 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 110 ASN ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN E 425 GLN F 5 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 281 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.116617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.085260 restraints weight = 36304.284| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 1.70 r_work: 0.2652 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27764 Z= 0.152 Angle : 0.513 8.633 37832 Z= 0.256 Chirality : 0.040 0.144 4091 Planarity : 0.004 0.040 4910 Dihedral : 4.768 46.593 3709 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.68 % Allowed : 15.24 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.65 (0.13), residues: 3397 helix: -0.18 (0.32), residues: 264 sheet: -0.41 (0.18), residues: 734 loop : -0.44 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 417 TYR 0.014 0.001 TYR F 257 PHE 0.015 0.002 PHE S 412 TRP 0.010 0.001 TRP S 299 HIS 0.007 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00366 (27764) covalent geometry : angle 0.51283 (37832) hydrogen bonds : bond 0.03128 ( 390) hydrogen bonds : angle 5.29991 ( 852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 403 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8620 (t80) cc_final: 0.8351 (t80) REVERT: A 554 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7698 (mp) REVERT: B 107 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8987 (tp) REVERT: B 344 LYS cc_start: 0.8117 (ttmm) cc_final: 0.7837 (mtmm) REVERT: B 417 ARG cc_start: 0.8020 (mtm-85) cc_final: 0.7643 (mtt90) REVERT: B 534 HIS cc_start: 0.7714 (m-70) cc_final: 0.6656 (p90) REVERT: C 201 SER cc_start: 0.8911 (m) cc_final: 0.8252 (p) REVERT: D 107 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8834 (tp) REVERT: D 133 ASP cc_start: 0.8902 (OUTLIER) cc_final: 0.8580 (m-30) REVERT: E 107 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8873 (tp) REVERT: E 125 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7795 (tm-30) REVERT: E 183 GLN cc_start: 0.8951 (tt0) cc_final: 0.8718 (tt0) REVERT: E 208 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8461 (mt-10) REVERT: E 404 GLN cc_start: 0.8448 (pm20) cc_final: 0.7654 (pm20) REVERT: E 489 THR cc_start: 0.9126 (m) cc_final: 0.8893 (m) REVERT: E 554 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7544 (mp) REVERT: F 27 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8569 (mm-30) REVERT: F 107 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8892 (tp) REVERT: F 257 TYR cc_start: 0.8970 (m-80) cc_final: 0.8634 (m-80) REVERT: F 344 LYS cc_start: 0.8143 (ptpp) cc_final: 0.7893 (pttp) REVERT: F 539 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8763 (mt-10) REVERT: S 204 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6557 (ptm) REVERT: S 208 VAL cc_start: 0.8422 (t) cc_final: 0.7980 (p) REVERT: S 209 ASN cc_start: 0.7143 (t0) cc_final: 0.6670 (t0) REVERT: S 265 GLU cc_start: 0.7504 (tt0) cc_final: 0.7154 (tm-30) REVERT: S 285 GLU cc_start: 0.7385 (pm20) cc_final: 0.6858 (pm20) REVERT: S 286 GLU cc_start: 0.7974 (mp0) cc_final: 0.6177 (mp0) REVERT: S 290 MET cc_start: 0.7536 (tpp) cc_final: 0.7251 (tpp) REVERT: S 391 THR cc_start: 0.8545 (t) cc_final: 0.8164 (p) REVERT: S 415 SER cc_start: 0.8953 (t) cc_final: 0.8476 (p) outliers start: 79 outliers final: 68 residues processed: 457 average time/residue: 0.1799 time to fit residues: 135.1756 Evaluate side-chains 472 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 395 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 278 HIS Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 137 MET Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 177 LYS Chi-restraints excluded: chain S residue 194 ASP Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain S residue 262 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 316 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 290 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 291 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 337 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 218 optimal weight: 0.0370 overall best weight: 2.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN F 5 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.116127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.084786 restraints weight = 36355.127| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 1.70 r_work: 0.2645 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27764 Z= 0.176 Angle : 0.523 8.670 37832 Z= 0.261 Chirality : 0.041 0.143 4091 Planarity : 0.004 0.040 4910 Dihedral : 4.795 46.441 3709 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.71 % Allowed : 15.27 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.67 (0.13), residues: 3397 helix: -0.19 (0.32), residues: 264 sheet: -0.42 (0.18), residues: 734 loop : -0.45 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 417 TYR 0.014 0.001 TYR F 257 PHE 0.015 0.002 PHE S 86 TRP 0.014 0.001 TRP S 299 HIS 0.005 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00424 (27764) covalent geometry : angle 0.52265 (37832) hydrogen bonds : bond 0.03161 ( 390) hydrogen bonds : angle 5.34494 ( 852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6794 Ramachandran restraints generated. 3397 Oldfield, 0 Emsley, 3397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 391 time to evaluate : 1.119 Fit side-chains revert: symmetry clash REVERT: A 57 PHE cc_start: 0.8604 (t80) cc_final: 0.8371 (t80) REVERT: A 554 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7649 (mp) REVERT: B 107 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8993 (tp) REVERT: B 344 LYS cc_start: 0.8124 (ttmm) cc_final: 0.7842 (mtmm) REVERT: B 374 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: B 417 ARG cc_start: 0.8035 (mtm-85) cc_final: 0.7681 (mtt90) REVERT: B 534 HIS cc_start: 0.7861 (m-70) cc_final: 0.6645 (p90) REVERT: C 201 SER cc_start: 0.8918 (m) cc_final: 0.8259 (p) REVERT: D 107 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8847 (tp) REVERT: D 133 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8574 (m-30) REVERT: E 107 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8890 (tp) REVERT: E 125 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7828 (tm-30) REVERT: E 208 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8439 (mt-10) REVERT: E 404 GLN cc_start: 0.8451 (pm20) cc_final: 0.7657 (pm20) REVERT: E 489 THR cc_start: 0.9126 (m) cc_final: 0.8889 (m) REVERT: E 554 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7601 (mp) REVERT: F 27 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8587 (mm-30) REVERT: F 107 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8876 (tp) REVERT: F 257 TYR cc_start: 0.9034 (m-80) cc_final: 0.8661 (m-80) REVERT: F 344 LYS cc_start: 0.8163 (ptpp) cc_final: 0.7905 (pttp) REVERT: F 539 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8767 (mt-10) REVERT: S 204 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6582 (ptm) REVERT: S 208 VAL cc_start: 0.8416 (t) cc_final: 0.7963 (p) REVERT: S 209 ASN cc_start: 0.7151 (t0) cc_final: 0.6708 (t0) REVERT: S 265 GLU cc_start: 0.7571 (tt0) cc_final: 0.7200 (tm-30) REVERT: S 285 GLU cc_start: 0.7373 (pm20) cc_final: 0.6848 (pm20) REVERT: S 286 GLU cc_start: 0.7925 (mp0) cc_final: 0.6125 (mp0) REVERT: S 290 MET cc_start: 0.7549 (tpp) cc_final: 0.7261 (tpp) REVERT: S 415 SER cc_start: 0.8965 (t) cc_final: 0.8475 (p) outliers start: 80 outliers final: 67 residues processed: 447 average time/residue: 0.1822 time to fit residues: 133.4440 Evaluate side-chains 463 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 386 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 477 THR Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 27 GLU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 230 MET Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain S residue 130 SER Chi-restraints excluded: chain S residue 137 MET Chi-restraints excluded: chain S residue 154 THR Chi-restraints excluded: chain S residue 177 LYS Chi-restraints excluded: chain S residue 204 MET Chi-restraints excluded: chain S residue 262 THR Chi-restraints excluded: chain S residue 287 VAL Chi-restraints excluded: chain S residue 354 VAL Chi-restraints excluded: chain S residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 277 optimal weight: 0.0470 chunk 294 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN C 53 HIS C 167 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN F 5 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 351 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.118985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.087816 restraints weight = 36016.980| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.71 r_work: 0.2694 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27764 Z= 0.105 Angle : 0.489 8.298 37832 Z= 0.243 Chirality : 0.040 0.167 4091 Planarity : 0.004 0.048 4910 Dihedral : 4.576 45.003 3709 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.58 % Allowed : 15.41 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -0.59 (0.13), residues: 3397 helix: -0.25 (0.32), residues: 270 sheet: -0.41 (0.18), residues: 734 loop : -0.36 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 417 TYR 0.012 0.001 TYR F 257 PHE 0.017 0.001 PHE S 86 TRP 0.012 0.001 TRP S 299 HIS 0.004 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00250 (27764) covalent geometry : angle 0.48852 (37832) hydrogen bonds : bond 0.02922 ( 390) hydrogen bonds : angle 5.19739 ( 852) =============================================================================== Job complete usr+sys time: 7841.87 seconds wall clock time: 135 minutes 20.70 seconds (8120.70 seconds total)