Starting phenix.real_space_refine on Sun Jun 22 19:17:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c2t_45160/06_2025/9c2t_45160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c2t_45160/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c2t_45160/06_2025/9c2t_45160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c2t_45160/06_2025/9c2t_45160.map" model { file = "/net/cci-nas-00/data/ceres_data/9c2t_45160/06_2025/9c2t_45160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c2t_45160/06_2025/9c2t_45160.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 18.71, per 1000 atoms: 0.69 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: 7.06 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 3.73 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: 9.58 Time building geometry restraints manager: 8.35 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: 9.800 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: 0.040 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 65.330 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.150 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.910 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (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 TRP 0.015 0.001 TRP S 299 HIS 0.006 0.001 HIS A 53 PHE 0.022 0.002 PHE S 86 TYR 0.024 0.001 TYR S 161 ARG 0.007 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.19871 ( 390) hydrogen bonds : angle 6.63225 ( 852) covalent geometry : bond 0.00300 (27764) covalent geometry : angle 0.52648 (37832) *********************** 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 : 2.901 Fit side-chains revert: symmetry clash REVERT: A 417 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8031 (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: 0.6431 (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: 0.3641 time to fit residues: 251.4792 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 : 3.276 ------------------------------------------------------------------------------- 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 287 optimal weight: 6.9990 chunk 258 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 103 optimal weight: 0.0070 chunk 162 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 309 optimal weight: 7.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- 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 ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 351 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.114198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.082555 restraints weight = 36258.313| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 1.70 r_work: 0.2622 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 27764 Z= 0.282 Angle : 0.577 9.160 37832 Z= 0.293 Chirality : 0.043 0.172 4091 Planarity : 0.005 0.039 4910 Dihedral : 6.098 67.563 3761 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.26 % Allowed : 12.62 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 3397 helix: -0.43 (0.31), residues: 264 sheet: -0.28 (0.18), residues: 752 loop : -0.48 (0.12), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 25 HIS 0.009 0.001 HIS A 53 PHE 0.019 0.002 PHE A 44 TYR 0.013 0.002 TYR E 111 ARG 0.005 0.001 ARG S 320 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 390) hydrogen bonds : angle 5.71983 ( 852) covalent geometry : bond 0.00675 (27764) covalent geometry : angle 0.57651 (37832) *********************** 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 509 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 413 time to evaluate : 3.681 Fit side-chains REVERT: A 53 HIS cc_start: 0.8483 (m-70) cc_final: 0.8131 (m-70) REVERT: A 417 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8112 (mtt90) REVERT: B 125 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8643 (mm-30) REVERT: B 344 LYS cc_start: 0.7961 (ttmm) cc_final: 0.7665 (mtmm) REVERT: B 417 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7815 (mtt90) REVERT: B 534 HIS cc_start: 0.7775 (m-70) cc_final: 0.6665 (p90) REVERT: C 107 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8970 (tp) REVERT: C 201 SER cc_start: 0.8935 (m) cc_final: 0.8409 (p) REVERT: D 53 HIS cc_start: 0.6965 (OUTLIER) cc_final: 0.6664 (p90) REVERT: D 133 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8651 (m-30) REVERT: D 344 LYS cc_start: 0.7785 (tptt) cc_final: 0.7242 (ptpt) REVERT: E 208 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8270 (mt-10) REVERT: E 280 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8479 (p0) REVERT: E 489 THR cc_start: 0.9127 (m) cc_final: 0.8876 (m) REVERT: E 554 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7682 (mp) REVERT: F 27 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8518 (mm-30) REVERT: F 107 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.8936 (tp) REVERT: F 109 GLU cc_start: 0.8181 (tt0) cc_final: 0.7856 (pt0) REVERT: F 215 GLU cc_start: 0.8986 (mp0) cc_final: 0.8392 (mp0) REVERT: F 554 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7327 (mp) REVERT: S 207 LEU cc_start: 0.8220 (tp) cc_final: 0.7998 (tp) REVERT: S 209 ASN cc_start: 0.7030 (t0) cc_final: 0.6394 (t0) REVERT: S 258 GLU cc_start: 0.7373 (pm20) cc_final: 0.7046 (pm20) REVERT: S 285 GLU cc_start: 0.7366 (pm20) cc_final: 0.6822 (pm20) REVERT: S 286 GLU cc_start: 0.7774 (mp0) cc_final: 0.6533 (mp0) outliers start: 96 outliers final: 76 residues processed: 475 average time/residue: 0.4728 time to fit residues: 365.7970 Evaluate side-chains 475 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 391 time to evaluate : 3.985 ------------------------------------------------------------------------------- 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 75 CYS 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 414 VAL Chi-restraints excluded: chain A residue 432 ASN 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 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 402 THR 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 107 LEU 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 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 23 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 167 GLN 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 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 277 THR Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 342 THR 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 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 107 LEU Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 139 VAL 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 475 ILE Chi-restraints excluded: chain F residue 498 LYS Chi-restraints excluded: chain F residue 528 THR Chi-restraints excluded: chain F residue 546 THR Chi-restraints excluded: chain F residue 554 LEU Chi-restraints excluded: chain S residue 110 THR 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 194 ASP 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 287 VAL Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain S residue 391 THR 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 131 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 224 optimal weight: 0.8980 chunk 289 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS A 295 ASN ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS E 193 ASN E 356 GLN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 5 ASN S 281 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.117228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.085728 restraints weight = 36266.831| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 1.73 r_work: 0.2671 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0841 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= 0.124 Angle : 0.491 9.501 37832 Z= 0.249 Chirality : 0.040 0.147 4091 Planarity : 0.004 0.038 4910 Dihedral : 5.164 58.178 3724 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.54 % Allowed : 13.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 3397 helix: -0.14 (0.32), residues: 263 sheet: -0.33 (0.18), residues: 740 loop : -0.42 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 25 HIS 0.009 0.001 HIS A 53 PHE 0.014 0.002 PHE A 393 TYR 0.010 0.001 TYR S 210 ARG 0.005 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 390) hydrogen bonds : angle 5.46296 ( 852) covalent geometry : bond 0.00293 (27764) covalent geometry : angle 0.49080 (37832) *********************** 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 507 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 432 time to evaluate : 3.182 Fit side-chains revert: symmetry clash REVERT: A 53 HIS cc_start: 0.8443 (m170) cc_final: 0.8233 (m-70) REVERT: A 407 ARG cc_start: 0.9350 (OUTLIER) cc_final: 0.9051 (ttm170) REVERT: A 539 GLU cc_start: 0.8700 (tt0) cc_final: 0.8356 (mt-10) REVERT: A 554 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7230 (mp) REVERT: B 107 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9090 (tp) REVERT: B 344 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7741 (mtmm) REVERT: B 374 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: B 417 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7697 (mtt90) REVERT: B 534 HIS cc_start: 0.7747 (m-70) cc_final: 0.6748 (p90) REVERT: C 201 SER cc_start: 0.8904 (m) cc_final: 0.8312 (p) REVERT: C 542 GLU cc_start: 0.8563 (pt0) cc_final: 0.8312 (pt0) REVERT: D 35 SER cc_start: 0.9389 (OUTLIER) cc_final: 0.9172 (t) REVERT: D 53 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.6701 (p90) REVERT: D 133 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8619 (m-30) REVERT: D 257 TYR cc_start: 0.9026 (m-80) cc_final: 0.8488 (m-80) REVERT: D 279 GLU cc_start: 0.7490 (mp0) cc_final: 0.7014 (mp0) REVERT: D 344 LYS cc_start: 0.7823 (tptt) cc_final: 0.7305 (ptpt) REVERT: E 107 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8883 (tp) REVERT: E 208 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8382 (mm-30) REVERT: E 280 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8421 (p0) REVERT: E 489 THR cc_start: 0.9107 (m) cc_final: 0.8844 (m) REVERT: E 554 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7655 (mp) REVERT: F 27 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8567 (mm-30) REVERT: F 107 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8887 (tp) REVERT: F 109 GLU cc_start: 0.8037 (tt0) cc_final: 0.7794 (pt0) REVERT: F 257 TYR cc_start: 0.9047 (m-80) cc_final: 0.8759 (m-80) REVERT: F 554 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7277 (mp) REVERT: S 207 LEU cc_start: 0.8218 (tp) cc_final: 0.8000 (tp) REVERT: S 208 VAL cc_start: 0.8644 (t) cc_final: 0.8309 (p) REVERT: S 209 ASN cc_start: 0.7076 (t0) cc_final: 0.6445 (t0) REVERT: S 285 GLU cc_start: 0.7380 (pm20) cc_final: 0.6702 (pm20) REVERT: S 286 GLU cc_start: 0.7739 (mp0) cc_final: 0.6329 (mp0) REVERT: S 290 MET cc_start: 0.7501 (tpp) cc_final: 0.7201 (tpp) outliers start: 75 outliers final: 43 residues processed: 481 average time/residue: 0.3717 time to fit residues: 287.7425 Evaluate side-chains 453 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 397 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 130 ASP 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 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 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 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 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 53 HIS Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 341 ASP 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 347 THR Chi-restraints excluded: chain E residue 420 LEU 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 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 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 354 VAL Chi-restraints excluded: chain S residue 363 LEU 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 49 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 339 optimal weight: 8.9990 chunk 290 optimal weight: 8.9990 chunk 184 optimal weight: 0.0770 chunk 206 optimal weight: 8.9990 chunk 254 optimal weight: 0.0070 chunk 87 optimal weight: 5.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN 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 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 HIS ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.117048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.085481 restraints weight = 36571.572| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 1.73 r_work: 0.2669 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27764 Z= 0.145 Angle : 0.492 9.206 37832 Z= 0.248 Chirality : 0.040 0.144 4091 Planarity : 0.004 0.039 4910 Dihedral : 4.984 57.866 3716 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.19 % Allowed : 13.74 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 3397 helix: -0.11 (0.32), residues: 263 sheet: -0.35 (0.18), residues: 740 loop : -0.41 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 25 HIS 0.004 0.001 HIS B 281 PHE 0.012 0.002 PHE A 393 TYR 0.011 0.001 TYR E 111 ARG 0.006 0.000 ARG C 274 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 390) hydrogen bonds : angle 5.38818 ( 852) covalent geometry : bond 0.00347 (27764) covalent geometry : angle 0.49186 (37832) *********************** 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 506 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 412 time to evaluate : 2.882 Fit side-chains revert: symmetry clash REVERT: A 53 HIS cc_start: 0.8053 (m170) cc_final: 0.7802 (m-70) REVERT: A 407 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.9033 (ttm170) REVERT: A 539 GLU cc_start: 0.8678 (tt0) cc_final: 0.8365 (mt-10) REVERT: A 554 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7462 (mp) REVERT: B 107 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9026 (tp) REVERT: B 125 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8589 (mm-30) REVERT: B 344 LYS cc_start: 0.8025 (ttmm) cc_final: 0.7752 (mtmm) REVERT: B 374 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: B 378 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8513 (pttt) REVERT: B 417 ARG cc_start: 0.8110 (mtm-85) cc_final: 0.7739 (mtt90) REVERT: B 534 HIS cc_start: 0.7728 (m-70) cc_final: 0.6708 (p90) REVERT: C 201 SER cc_start: 0.8904 (m) cc_final: 0.8271 (p) REVERT: C 289 MET cc_start: 0.9530 (mmt) cc_final: 0.9268 (mmt) REVERT: D 35 SER cc_start: 0.9389 (OUTLIER) cc_final: 0.9167 (t) REVERT: D 53 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6642 (p90) REVERT: D 107 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8818 (tp) REVERT: D 133 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8568 (m-30) REVERT: D 407 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8684 (ttm-80) REVERT: E 107 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8873 (tp) REVERT: E 208 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8475 (mt-10) REVERT: E 404 GLN cc_start: 0.8491 (pm20) cc_final: 0.7617 (pm20) REVERT: E 489 THR cc_start: 0.9124 (m) cc_final: 0.8866 (m) REVERT: E 554 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7697 (mp) REVERT: F 27 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8544 (mm-30) REVERT: F 107 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8891 (tp) REVERT: F 109 GLU cc_start: 0.8066 (tt0) cc_final: 0.7819 (pt0) REVERT: F 257 TYR cc_start: 0.9066 (m-80) cc_final: 0.8692 (m-80) REVERT: F 344 LYS cc_start: 0.8089 (ptpp) cc_final: 0.7811 (pttp) REVERT: F 554 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7310 (mp) REVERT: S 207 LEU cc_start: 0.8141 (tp) cc_final: 0.7882 (tp) REVERT: S 208 VAL cc_start: 0.8635 (t) cc_final: 0.8235 (p) REVERT: S 209 ASN cc_start: 0.7076 (t0) cc_final: 0.6462 (t0) REVERT: S 285 GLU cc_start: 0.7466 (pm20) cc_final: 0.6814 (pm20) REVERT: S 286 GLU cc_start: 0.7822 (mp0) cc_final: 0.6185 (mp0) outliers start: 94 outliers final: 64 residues processed: 479 average time/residue: 0.3526 time to fit residues: 272.0120 Evaluate side-chains 471 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 392 time to evaluate : 2.856 ------------------------------------------------------------------------------- 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 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 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 220 GLN 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 378 LYS 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 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 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 53 HIS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 407 ARG 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 283 ILE 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 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 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 528 THR Chi-restraints excluded: chain F residue 554 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 247 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 212 optimal weight: 4.9990 chunk 275 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 43 optimal weight: 0.0060 chunk 183 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 overall best weight: 3.5802 ------------------------------------------------------------------------------- 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** A 432 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3150 r_free = 0.3150 target = 0.114183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.082618 restraints weight = 36521.283| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 1.72 r_work: 0.2610 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 27764 Z= 0.257 Angle : 0.549 9.131 37832 Z= 0.277 Chirality : 0.042 0.146 4091 Planarity : 0.004 0.041 4910 Dihedral : 5.224 56.699 3716 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.63 % Allowed : 14.05 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 3397 helix: -0.20 (0.32), residues: 263 sheet: -0.38 (0.18), residues: 735 loop : -0.52 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 25 HIS 0.005 0.001 HIS A 248 PHE 0.018 0.002 PHE A 44 TYR 0.015 0.002 TYR D 257 ARG 0.013 0.001 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 390) hydrogen bonds : angle 5.58305 ( 852) covalent geometry : bond 0.00620 (27764) covalent geometry : angle 0.54880 (37832) *********************** 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 504 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 397 time to evaluate : 2.969 Fit side-chains revert: symmetry clash REVERT: A 195 GLN cc_start: 0.7912 (mp10) cc_final: 0.7462 (mp10) REVERT: A 407 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.9066 (ttm170) REVERT: A 554 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7453 (mp) REVERT: B 344 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7723 (mtmm) REVERT: B 417 ARG cc_start: 0.8229 (mtm-85) cc_final: 0.7828 (mtt90) REVERT: B 534 HIS cc_start: 0.7818 (m-70) cc_final: 0.6686 (p90) REVERT: C 55 LYS cc_start: 0.9057 (mtmt) cc_final: 0.8842 (mtmm) REVERT: C 129 LYS cc_start: 0.9280 (mttt) cc_final: 0.9064 (mttt) REVERT: C 201 SER cc_start: 0.8977 (m) cc_final: 0.8371 (p) REVERT: D 53 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.6653 (p90) REVERT: D 107 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8886 (tp) REVERT: D 133 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8592 (m-30) REVERT: D 279 GLU cc_start: 0.7549 (mp0) cc_final: 0.7027 (mp0) REVERT: E 107 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8913 (tp) REVERT: E 193 ASN cc_start: 0.7776 (m-40) cc_final: 0.7502 (m110) REVERT: E 208 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8446 (mt-10) REVERT: E 404 GLN cc_start: 0.8467 (pm20) cc_final: 0.7547 (pm20) REVERT: E 432 ASN cc_start: 0.8853 (p0) cc_final: 0.8503 (p0) REVERT: E 489 THR cc_start: 0.9141 (m) cc_final: 0.8894 (m) REVERT: E 554 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7690 (mp) REVERT: F 27 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8555 (mm-30) REVERT: F 107 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8910 (tp) REVERT: F 109 GLU cc_start: 0.8159 (tt0) cc_final: 0.7801 (pt0) REVERT: F 215 GLU cc_start: 0.8966 (mp0) cc_final: 0.8270 (mp0) REVERT: F 257 TYR cc_start: 0.9216 (m-80) cc_final: 0.8846 (m-80) REVERT: S 208 VAL cc_start: 0.8597 (t) cc_final: 0.8214 (p) REVERT: S 209 ASN cc_start: 0.7159 (t0) cc_final: 0.6595 (t0) REVERT: S 258 GLU cc_start: 0.7469 (pm20) cc_final: 0.7123 (pm20) REVERT: S 285 GLU cc_start: 0.7441 (pm20) cc_final: 0.6857 (pm20) REVERT: S 286 GLU cc_start: 0.7911 (mp0) cc_final: 0.6165 (mp0) REVERT: S 391 THR cc_start: 0.8551 (t) cc_final: 0.8172 (p) REVERT: S 409 GLN cc_start: 0.6327 (pm20) cc_final: 0.6122 (pp30) REVERT: S 415 SER cc_start: 0.8879 (t) cc_final: 0.8449 (p) outliers start: 107 outliers final: 84 residues processed: 467 average time/residue: 0.3531 time to fit residues: 267.9426 Evaluate side-chains 485 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 392 time to evaluate : 2.901 ------------------------------------------------------------------------------- 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 207 GLU 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 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 46 ILE Chi-restraints excluded: chain B residue 53 HIS 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 333 VAL 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 56 VAL 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 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 133 ASP 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 84 SER 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 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 402 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 84 SER 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 280 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 528 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 247 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 269 optimal weight: 0.3980 chunk 29 optimal weight: 10.0000 chunk 180 optimal weight: 0.0070 chunk 117 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 320 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS ** 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** B 432 ASN ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS E 380 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.118342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.087082 restraints weight = 36082.302| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.72 r_work: 0.2679 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27764 Z= 0.097 Angle : 0.480 9.717 37832 Z= 0.241 Chirality : 0.040 0.144 4091 Planarity : 0.004 0.040 4910 Dihedral : 4.785 50.067 3714 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.54 % Allowed : 15.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 3397 helix: -0.02 (0.32), residues: 263 sheet: -0.40 (0.18), residues: 735 loop : -0.41 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 299 HIS 0.003 0.001 HIS A 517 PHE 0.012 0.001 PHE S 412 TYR 0.015 0.001 TYR D 257 ARG 0.006 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.02987 ( 390) hydrogen bonds : angle 5.34215 ( 852) covalent geometry : bond 0.00230 (27764) covalent geometry : angle 0.47978 (37832) *********************** 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 506 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 431 time to evaluate : 4.291 Fit side-chains REVERT: A 407 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.9062 (ttm170) REVERT: A 497 ARG cc_start: 0.8739 (mtm-85) cc_final: 0.8064 (mtm180) REVERT: A 535 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7643 (mmm160) REVERT: A 554 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7419 (mp) REVERT: B 107 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8961 (tp) REVERT: B 170 LEU cc_start: 0.9003 (mt) cc_final: 0.8786 (mt) REVERT: B 280 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8165 (p0) REVERT: B 344 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7796 (mtmm) REVERT: B 374 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: B 378 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8536 (pttt) REVERT: B 417 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7732 (mtt90) REVERT: B 534 HIS cc_start: 0.7763 (m-70) cc_final: 0.6720 (p90) REVERT: C 55 LYS cc_start: 0.9065 (mtmt) cc_final: 0.8853 (mtmm) REVERT: C 201 SER cc_start: 0.8871 (m) cc_final: 0.8208 (p) REVERT: D 53 HIS cc_start: 0.6942 (OUTLIER) cc_final: 0.6679 (p90) REVERT: D 107 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8795 (tp) REVERT: D 133 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8567 (m-30) REVERT: D 279 GLU cc_start: 0.7518 (mp0) cc_final: 0.7051 (mp0) REVERT: E 107 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8882 (tp) REVERT: E 125 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7705 (tm-30) REVERT: E 183 GLN cc_start: 0.8964 (tt0) cc_final: 0.8734 (tt0) REVERT: E 208 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8469 (mt-10) REVERT: E 404 GLN cc_start: 0.8437 (pm20) cc_final: 0.7659 (pm20) REVERT: E 489 THR cc_start: 0.9118 (m) cc_final: 0.8870 (m) REVERT: E 554 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7656 (mp) REVERT: F 27 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8565 (mm-30) REVERT: F 107 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8875 (tp) REVERT: F 257 TYR cc_start: 0.9062 (m-80) cc_final: 0.8700 (m-80) REVERT: F 344 LYS cc_start: 0.8125 (ptpp) cc_final: 0.7866 (pttp) REVERT: S 208 VAL cc_start: 0.8539 (t) cc_final: 0.8084 (p) REVERT: S 209 ASN cc_start: 0.7174 (t0) cc_final: 0.6667 (t0) REVERT: S 258 GLU cc_start: 0.7523 (pm20) cc_final: 0.7184 (pm20) REVERT: S 285 GLU cc_start: 0.7390 (pm20) cc_final: 0.6826 (pm20) REVERT: S 286 GLU cc_start: 0.7920 (mp0) cc_final: 0.6193 (mp0) REVERT: S 290 MET cc_start: 0.7653 (tpp) cc_final: 0.7407 (tpp) REVERT: S 391 THR cc_start: 0.8369 (t) cc_final: 0.8073 (p) REVERT: S 397 ARG cc_start: 0.9006 (mtm-85) cc_final: 0.8757 (mtm180) REVERT: S 415 SER cc_start: 0.8918 (t) cc_final: 0.8445 (p) outliers start: 75 outliers final: 41 residues processed: 481 average time/residue: 0.5133 time to fit residues: 403.4385 Evaluate side-chains 457 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 403 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 220 GLN Chi-restraints excluded: chain B residue 280 ASP 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 378 LYS 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 142 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 53 HIS 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 546 THR 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 554 LEU 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 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 402 THR Chi-restraints excluded: chain S residue 89 LEU 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 254 optimal weight: 0.7980 chunk 333 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 269 optimal weight: 0.0980 chunk 117 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 110 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 = 0.3192 r_free = 0.3192 target = 0.117276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.085879 restraints weight = 36300.409| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 1.73 r_work: 0.2672 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27764 Z= 0.140 Angle : 0.496 10.892 37832 Z= 0.248 Chirality : 0.040 0.144 4091 Planarity : 0.004 0.040 4910 Dihedral : 4.705 48.902 3711 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.65 % Allowed : 15.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 3397 helix: -0.07 (0.32), residues: 263 sheet: -0.38 (0.18), residues: 735 loop : -0.39 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 177 HIS 0.009 0.001 HIS A 53 PHE 0.014 0.002 PHE A 98 TYR 0.013 0.001 TYR D 257 ARG 0.014 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03128 ( 390) hydrogen bonds : angle 5.28420 ( 852) covalent geometry : bond 0.00337 (27764) covalent geometry : angle 0.49635 (37832) *********************** 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 485 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 407 time to evaluate : 3.478 Fit side-chains REVERT: A 407 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.9073 (ttp-170) REVERT: A 535 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7619 (mmm160) REVERT: A 554 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7433 (mp) REVERT: B 107 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8930 (tp) REVERT: B 280 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8050 (p0) REVERT: B 344 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7754 (mtmm) REVERT: B 374 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.7581 (m-80) REVERT: B 378 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8517 (pttt) REVERT: B 417 ARG cc_start: 0.8070 (mtm-85) cc_final: 0.7725 (mtt90) REVERT: B 534 HIS cc_start: 0.7733 (m-70) cc_final: 0.6673 (p90) REVERT: C 201 SER cc_start: 0.8889 (m) cc_final: 0.8208 (p) REVERT: D 53 HIS cc_start: 0.6908 (OUTLIER) cc_final: 0.6611 (p90) REVERT: D 107 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8758 (tp) REVERT: D 133 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8610 (m-30) REVERT: E 107 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8850 (tp) REVERT: E 125 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7583 (tm-30) REVERT: E 208 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8492 (mt-10) REVERT: E 404 GLN cc_start: 0.8433 (pm20) cc_final: 0.7557 (pm20) REVERT: E 489 THR cc_start: 0.9128 (m) cc_final: 0.8888 (m) REVERT: E 554 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7631 (mp) REVERT: F 27 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8563 (mm-30) REVERT: F 107 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8901 (tp) REVERT: F 110 ASN cc_start: 0.9213 (m110) cc_final: 0.8972 (m110) REVERT: F 257 TYR cc_start: 0.9087 (m-80) cc_final: 0.8723 (m-80) REVERT: F 344 LYS cc_start: 0.8082 (ptpp) cc_final: 0.7812 (pttp) REVERT: S 86 PHE cc_start: 0.8128 (t80) cc_final: 0.7759 (t80) REVERT: S 204 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6225 (tmm) REVERT: S 208 VAL cc_start: 0.8475 (t) cc_final: 0.8013 (p) REVERT: S 209 ASN cc_start: 0.7200 (t0) cc_final: 0.6702 (t0) REVERT: S 258 GLU cc_start: 0.7500 (pm20) cc_final: 0.7158 (pm20) REVERT: S 285 GLU cc_start: 0.7466 (pm20) cc_final: 0.6935 (pm20) REVERT: S 286 GLU cc_start: 0.7934 (mp0) cc_final: 0.6180 (mp0) REVERT: S 290 MET cc_start: 0.7635 (tpp) cc_final: 0.7341 (tpp) REVERT: S 391 THR cc_start: 0.8371 (t) cc_final: 0.8065 (p) REVERT: S 397 ARG cc_start: 0.9003 (mtm-85) cc_final: 0.8740 (mtm180) REVERT: S 415 SER cc_start: 0.8939 (t) cc_final: 0.8463 (p) outliers start: 78 outliers final: 58 residues processed: 458 average time/residue: 0.3808 time to fit residues: 285.4381 Evaluate side-chains 465 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 393 time to evaluate : 3.343 ------------------------------------------------------------------------------- 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 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 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 220 GLN Chi-restraints excluded: chain B residue 280 ASP 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 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 275 SER Chi-restraints excluded: chain C residue 294 VAL 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 D residue 4 VAL Chi-restraints excluded: chain D residue 53 HIS 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 528 THR Chi-restraints excluded: chain D residue 546 THR 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 283 ILE 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 554 LEU Chi-restraints excluded: chain F residue 23 SER Chi-restraints excluded: chain F residue 27 GLU 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 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 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 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 92 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 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** C 53 HIS ** 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 248 HIS S 281 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.113588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.081974 restraints weight = 36522.807| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 1.73 r_work: 0.2602 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 27764 Z= 0.307 Angle : 0.584 11.446 37832 Z= 0.292 Chirality : 0.044 0.143 4091 Planarity : 0.005 0.040 4910 Dihedral : 5.099 49.840 3711 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.12 % Allowed : 15.07 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 3397 helix: -0.27 (0.32), residues: 263 sheet: -0.27 (0.19), residues: 711 loop : -0.53 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 545 HIS 0.006 0.001 HIS A 248 PHE 0.021 0.002 PHE A 98 TYR 0.014 0.002 TYR E 337 ARG 0.014 0.001 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03576 ( 390) hydrogen bonds : angle 5.57220 ( 852) covalent geometry : bond 0.00742 (27764) covalent geometry : angle 0.58372 (37832) *********************** 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 488 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 396 time to evaluate : 3.234 Fit side-chains REVERT: A 195 GLN cc_start: 0.7955 (mp10) cc_final: 0.7524 (mp10) REVERT: A 407 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.9074 (ttp-170) REVERT: A 497 ARG cc_start: 0.8769 (mtm-85) cc_final: 0.8099 (mtm180) REVERT: A 554 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7658 (mp) REVERT: B 107 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8986 (tp) REVERT: B 344 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7749 (mtmm) REVERT: B 378 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8550 (pttt) REVERT: B 417 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.7831 (mtt90) REVERT: B 534 HIS cc_start: 0.7882 (m-70) cc_final: 0.6590 (p90) REVERT: C 201 SER cc_start: 0.9024 (m) cc_final: 0.8409 (p) REVERT: D 53 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6608 (p90) REVERT: D 107 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8910 (tp) REVERT: D 133 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8586 (m-30) REVERT: D 279 GLU cc_start: 0.7537 (mp0) cc_final: 0.6984 (mp0) REVERT: E 107 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8886 (tp) REVERT: E 208 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8486 (mt-10) REVERT: E 280 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8462 (p0) REVERT: E 404 GLN cc_start: 0.8464 (pm20) cc_final: 0.7630 (pm20) REVERT: E 432 ASN cc_start: 0.8892 (p0) cc_final: 0.8518 (p0) REVERT: E 489 THR cc_start: 0.9138 (m) cc_final: 0.8888 (m) REVERT: E 554 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7641 (mp) REVERT: F 27 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8575 (mm-30) REVERT: F 107 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8920 (tp) REVERT: F 215 GLU cc_start: 0.8967 (mp0) cc_final: 0.8259 (mp0) REVERT: F 257 TYR cc_start: 0.9256 (m-80) cc_final: 0.8847 (m-80) REVERT: F 322 GLN cc_start: 0.8728 (mm110) cc_final: 0.8414 (mm110) REVERT: F 344 LYS cc_start: 0.8060 (ptpp) cc_final: 0.7788 (pttp) REVERT: F 543 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: S 208 VAL cc_start: 0.8527 (t) cc_final: 0.8053 (p) REVERT: S 209 ASN cc_start: 0.7210 (t0) cc_final: 0.6693 (t0) REVERT: S 285 GLU cc_start: 0.7462 (pm20) cc_final: 0.6892 (pm20) REVERT: S 286 GLU cc_start: 0.7947 (mp0) cc_final: 0.6077 (mp0) REVERT: S 290 MET cc_start: 0.7647 (tpp) cc_final: 0.7302 (tpp) REVERT: S 415 SER cc_start: 0.8913 (t) cc_final: 0.8466 (p) outliers start: 92 outliers final: 70 residues processed: 458 average time/residue: 0.3644 time to fit residues: 272.6829 Evaluate side-chains 471 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 388 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 102 LEU 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 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 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 220 GLN 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 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 275 SER Chi-restraints excluded: chain C residue 294 VAL 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 D residue 4 VAL Chi-restraints excluded: chain D residue 53 HIS 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 528 THR Chi-restraints excluded: chain D residue 546 THR 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 278 HIS 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 347 THR Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 476 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 58 SER Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 84 SER 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 266 THR Chi-restraints excluded: chain F residue 280 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 543 GLU Chi-restraints excluded: chain F residue 546 THR 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 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 137 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 322 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 233 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.117957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.086825 restraints weight = 36248.707| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 1.70 r_work: 0.2676 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27764 Z= 0.110 Angle : 0.498 11.722 37832 Z= 0.249 Chirality : 0.040 0.141 4091 Planarity : 0.004 0.042 4910 Dihedral : 4.731 45.091 3711 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.31 % Allowed : 15.88 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3397 helix: -0.15 (0.32), residues: 264 sheet: -0.40 (0.18), residues: 734 loop : -0.42 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 299 HIS 0.005 0.001 HIS E 53 PHE 0.016 0.001 PHE A 98 TYR 0.009 0.001 TYR E 337 ARG 0.013 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 390) hydrogen bonds : angle 5.29804 ( 852) covalent geometry : bond 0.00262 (27764) covalent geometry : angle 0.49841 (37832) *********************** 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 479 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 411 time to evaluate : 3.271 Fit side-chains REVERT: A 407 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.9037 (ttm170) REVERT: A 497 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8150 (mtm180) REVERT: A 535 ARG cc_start: 0.8031 (mmm160) cc_final: 0.7651 (mmm160) REVERT: A 554 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7526 (mp) REVERT: B 110 ASN cc_start: 0.8824 (m-40) cc_final: 0.8596 (m110) REVERT: B 170 LEU cc_start: 0.9004 (mt) cc_final: 0.8783 (mt) REVERT: B 344 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7783 (mtmm) REVERT: B 378 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8568 (pttt) REVERT: B 417 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7781 (mtt90) REVERT: B 534 HIS cc_start: 0.7810 (m-70) cc_final: 0.6601 (p90) REVERT: C 201 SER cc_start: 0.8872 (m) cc_final: 0.8189 (p) REVERT: D 53 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6690 (p90) REVERT: D 107 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8817 (tp) REVERT: D 133 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: D 279 GLU cc_start: 0.7556 (mp0) cc_final: 0.7016 (mp0) REVERT: D 344 LYS cc_start: 0.7609 (tptt) cc_final: 0.7061 (ptpt) REVERT: E 107 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8894 (tp) REVERT: E 125 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7842 (tm-30) REVERT: E 183 GLN cc_start: 0.8927 (tt0) cc_final: 0.8704 (tt0) REVERT: E 208 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8492 (mt-10) REVERT: E 404 GLN cc_start: 0.8427 (pm20) cc_final: 0.7717 (pm20) REVERT: E 489 THR cc_start: 0.9117 (m) cc_final: 0.8869 (m) REVERT: E 554 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7484 (mp) REVERT: F 27 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8569 (mm-30) REVERT: F 107 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8885 (tp) REVERT: F 257 TYR cc_start: 0.9076 (m-80) cc_final: 0.8785 (m-80) REVERT: F 344 LYS cc_start: 0.8134 (ptpp) cc_final: 0.7888 (pttp) REVERT: F 539 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8734 (mt-10) REVERT: S 208 VAL cc_start: 0.8399 (t) cc_final: 0.7961 (p) REVERT: S 209 ASN cc_start: 0.7216 (t0) cc_final: 0.6783 (t0) REVERT: S 265 GLU cc_start: 0.7567 (tt0) cc_final: 0.7212 (tm-30) REVERT: S 285 GLU cc_start: 0.7411 (pm20) cc_final: 0.6903 (pm20) REVERT: S 286 GLU cc_start: 0.7961 (mp0) cc_final: 0.6192 (mp0) REVERT: S 290 MET cc_start: 0.7486 (tpp) cc_final: 0.7189 (tpp) REVERT: S 391 THR cc_start: 0.8301 (t) cc_final: 0.8027 (p) REVERT: S 397 ARG cc_start: 0.9027 (mtm-85) cc_final: 0.8772 (mtm180) REVERT: S 415 SER cc_start: 0.8955 (t) cc_final: 0.8478 (p) outliers start: 68 outliers final: 54 residues processed: 459 average time/residue: 0.3791 time to fit residues: 282.8322 Evaluate side-chains 461 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 397 time to evaluate : 2.923 ------------------------------------------------------------------------------- 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 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 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 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 333 VAL Chi-restraints excluded: chain B residue 378 LYS 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 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 470 ILE Chi-restraints excluded: chain D residue 53 HIS 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 477 THR Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 546 THR 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 278 HIS Chi-restraints excluded: chain E residue 283 ILE Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 473 MET 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 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 546 THR 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 262 THR 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 89 optimal weight: 9.9990 chunk 277 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 312 optimal weight: 1.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN E 425 GLN F 5 ASN ** F 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.115578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.084289 restraints weight = 36420.590| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 1.70 r_work: 0.2637 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 27764 Z= 0.203 Angle : 0.534 10.486 37832 Z= 0.265 Chirality : 0.041 0.161 4091 Planarity : 0.004 0.040 4910 Dihedral : 4.842 46.903 3711 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.51 % Allowed : 15.74 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 3397 helix: -0.27 (0.32), residues: 264 sheet: -0.40 (0.18), residues: 734 loop : -0.45 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 299 HIS 0.005 0.001 HIS E 53 PHE 0.020 0.002 PHE A 98 TYR 0.011 0.001 TYR F 111 ARG 0.015 0.001 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 390) hydrogen bonds : angle 5.43781 ( 852) covalent geometry : bond 0.00492 (27764) covalent geometry : angle 0.53352 (37832) ********************** 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 469 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 395 time to evaluate : 3.102 Fit side-chains REVERT: A 51 GLU cc_start: 0.8373 (pm20) cc_final: 0.7313 (pt0) REVERT: A 407 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.9085 (ttp-170) REVERT: A 497 ARG cc_start: 0.8771 (mtm-85) cc_final: 0.8164 (mtm180) REVERT: A 554 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7601 (mp) REVERT: B 344 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7858 (mtmm) REVERT: B 378 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8582 (pttt) REVERT: B 417 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7827 (mtt90) REVERT: B 534 HIS cc_start: 0.7885 (m-70) cc_final: 0.6681 (p90) REVERT: C 201 SER cc_start: 0.8933 (m) cc_final: 0.8262 (p) REVERT: D 107 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8871 (tp) REVERT: D 133 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8576 (m-30) REVERT: D 279 GLU cc_start: 0.7539 (mp0) cc_final: 0.6983 (mp0) REVERT: E 107 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8897 (tp) REVERT: E 125 GLU cc_start: 0.8433 (tm-30) cc_final: 0.7904 (tm-30) REVERT: E 208 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8470 (mt-10) REVERT: E 404 GLN cc_start: 0.8427 (pm20) cc_final: 0.7648 (pm20) REVERT: E 489 THR cc_start: 0.9135 (m) cc_final: 0.8888 (m) REVERT: E 554 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7581 (mp) REVERT: F 27 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8613 (mm-30) REVERT: F 107 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8912 (tp) REVERT: F 257 TYR cc_start: 0.9175 (m-80) cc_final: 0.8848 (m-80) REVERT: F 344 LYS cc_start: 0.8128 (ptpp) cc_final: 0.7901 (pttp) REVERT: F 543 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8324 (tm-30) REVERT: S 208 VAL cc_start: 0.8433 (t) cc_final: 0.7983 (p) REVERT: S 209 ASN cc_start: 0.7209 (t0) cc_final: 0.6768 (t0) REVERT: S 285 GLU cc_start: 0.7427 (pm20) cc_final: 0.6913 (pm20) REVERT: S 286 GLU cc_start: 0.7921 (mp0) cc_final: 0.6008 (mp0) REVERT: S 290 MET cc_start: 0.7517 (tpp) cc_final: 0.7208 (tpp) REVERT: S 415 SER cc_start: 0.8971 (t) cc_final: 0.8479 (p) outliers start: 74 outliers final: 58 residues processed: 443 average time/residue: 0.3675 time to fit residues: 265.2778 Evaluate side-chains 457 residues out of total 2955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 389 time to evaluate : 3.128 ------------------------------------------------------------------------------- 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 407 ARG 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 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 333 VAL Chi-restraints excluded: chain B residue 378 LYS 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 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 294 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 470 ILE 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 107 LEU 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 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 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 230 MET Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 543 GLU Chi-restraints excluded: chain F residue 546 THR 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 262 THR Chi-restraints excluded: chain S residue 318 ILE 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 245 optimal weight: 3.9990 chunk 196 optimal weight: 0.0040 chunk 207 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 305 optimal weight: 1.9990 chunk 253 optimal weight: 10.0000 chunk 299 optimal weight: 7.9990 chunk 193 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.118208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.086986 restraints weight = 36291.747| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.72 r_work: 0.2680 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27764 Z= 0.108 Angle : 0.495 10.429 37832 Z= 0.246 Chirality : 0.040 0.152 4091 Planarity : 0.004 0.047 4910 Dihedral : 4.671 45.068 3711 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.27 % Allowed : 15.98 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 3397 helix: -0.23 (0.32), residues: 264 sheet: -0.38 (0.18), residues: 734 loop : -0.38 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 299 HIS 0.006 0.001 HIS D 52 PHE 0.016 0.001 PHE A 98 TYR 0.008 0.001 TYR E 337 ARG 0.014 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 390) hydrogen bonds : angle 5.31675 ( 852) covalent geometry : bond 0.00255 (27764) covalent geometry : angle 0.49486 (37832) =============================================================================== Job complete usr+sys time: 18387.38 seconds wall clock time: 322 minutes 26.20 seconds (19346.20 seconds total)