Starting phenix.real_space_refine on Fri Sep 11 21:52:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ue7_20749/09_2026/6ue7_20749.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ue7_20749/09_2026/6ue7_20749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ue7_20749/09_2026/6ue7_20749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ue7_20749/09_2026/6ue7_20749.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ue7_20749/09_2026/6ue7_20749.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ue7_20749/09_2026/6ue7_20749.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ue7_20749/09_2026/6ue7_20749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ue7_20749/09_2026/6ue7_20749.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.014 sd= 0.361 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 64 5.16 5 C 7378 2.51 5 N 1991 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11701 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1559 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 7, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1621 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 17, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4109 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1632 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 80 Chain: "G" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1556 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 18, 'TRANS': 204} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 7, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1003 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.26, per 1000 atoms: 0.28 Number of scatterers: 11701 At special positions: 0 Unit cell: (127.35, 181.346, 122.256, 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 64 16.00 O 2268 8.00 N 1991 7.00 C 7378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=25, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS B 299 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS D 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS C 46 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.05 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS F 311 " distance=2.05 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.04 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS G 299 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 323 " distance=2.03 Simple disulfide: pdb=" SG CYS F 299 " - pdb=" SG CYS G 242 " distance=2.04 Simple disulfide: pdb=" SG CYS F 369 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 471 " - pdb=" SG CYS D 15 " distance=2.03 Simple disulfide: pdb=" SG CYS G 266 " - pdb=" SG CYS G 323 " distance=2.04 Simple disulfide: pdb=" SG CYS G 369 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 134 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 501 " - " ASN A 263 " " NAG B 501 " - " ASN B 263 " " NAG B 502 " - " ASN B 459 " " NAG C 601 " - " ASN C 65 " " NAG C 605 " - " ASN C 168 " " NAG C 608 " - " ASN C 481 " " NAG C 609 " - " ASN C 403 " " NAG E 1 " - " ASN C 72 " " NAG H 1 " - " ASN C 451 " " NAG I 1 " - " ASN F 263 " " NAG J 1 " - " ASN D 49 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 646.8 milliseconds 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 34 sheets defined 10.0% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.715A pdb=" N LEU A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 391 through 395 removed outlier: 4.201A pdb=" N TYR A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.815A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 355 through 362 removed outlier: 3.991A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 362' Processing helix chain 'B' and resid 391 through 395 removed outlier: 4.111A pdb=" N TYR B 395 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 removed outlier: 4.179A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.953A pdb=" N SER C 87 " --> pdb=" O GLN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 removed outlier: 4.132A pdb=" N THR C 170 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.649A pdb=" N ASP C 196 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 193 through 197' Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.715A pdb=" N VAL C 245 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.555A pdb=" N GLU C 359 " --> pdb=" O ASN C 356 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 360' Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.838A pdb=" N GLU C 392 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.518A pdb=" N ASP C 417 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 418' Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 517 through 521 Processing helix chain 'F' and resid 252 through 258 Processing helix chain 'F' and resid 311 through 317 removed outlier: 4.341A pdb=" N TRP F 315 " --> pdb=" O CYS F 311 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS F 317 " --> pdb=" O GLU F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 395 removed outlier: 4.181A pdb=" N TYR F 395 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 425 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.505A pdb=" N LEU G 256 " --> pdb=" O ALA G 252 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU G 257 " --> pdb=" O LEU G 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 252 through 257' Processing helix chain 'G' and resid 355 through 360 removed outlier: 3.821A pdb=" N LEU G 359 " --> pdb=" O PRO G 355 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 355 through 360' Processing helix chain 'G' and resid 421 through 427 removed outlier: 3.764A pdb=" N GLY G 427 " --> pdb=" O ASP G 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA2, first strand: chain 'A' and resid 296 through 297 removed outlier: 3.543A pdb=" N ASP A 297 " --> pdb=" O CYS A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 324 removed outlier: 3.551A pdb=" N LEU A 338 " --> pdb=" O PHE A 321 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 336 " --> pdb=" O CYS A 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.921A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.921A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N PHE A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA7, first strand: chain 'A' and resid 459 through 462 removed outlier: 6.410A pdb=" N ASN A 459 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL B 462 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N SER A 461 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N PHE D 61 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER B 461 " --> pdb=" O PHE D 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 249 removed outlier: 3.790A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 264 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 281 removed outlier: 3.654A pdb=" N THR B 324 " --> pdb=" O THR B 280 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 338 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.746A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.746A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.726A pdb=" N VAL C 10 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N SER C 110 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 12 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG C 89 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS C 35 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER C 51 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AB6, first strand: chain 'C' and resid 123 through 125 removed outlier: 7.177A pdb=" N VAL C 124 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLN C 199 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 150 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 130 through 135 Processing sheet with id=AB8, first strand: chain 'C' and resid 226 through 229 removed outlier: 3.618A pdb=" N GLY C 308 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 251 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS C 250 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASN C 266 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 252 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 234 through 239 Processing sheet with id=AC1, first strand: chain 'C' and resid 340 through 344 removed outlier: 3.776A pdb=" N THR C 433 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 424 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS C 364 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP C 382 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP C 366 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 348 through 354 Processing sheet with id=AC3, first strand: chain 'C' and resid 460 through 462 Processing sheet with id=AC4, first strand: chain 'C' and resid 486 through 487 removed outlier: 4.007A pdb=" N GLN C 486 " --> pdb=" O LYS C 479 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS C 479 " --> pdb=" O GLN C 486 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU C 536 " --> pdb=" O VAL C 528 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLN C 530 " --> pdb=" O TYR C 534 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 245 through 249 removed outlier: 3.761A pdb=" N THR F 265 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 268 " --> pdb=" O VAL F 304 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 279 through 280 removed outlier: 3.975A pdb=" N THR F 280 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU F 334 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.848A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N PHE F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 396 " --> pdb=" O ILE F 416 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.848A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N PHE F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 388 through 389 Processing sheet with id=AD1, first strand: chain 'G' and resid 458 through 463 removed outlier: 3.796A pdb=" N MET F 464 " --> pdb=" O VAL G 463 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS F 457 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE D 38 " --> pdb=" O HIS F 457 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN F 459 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE D 40 " --> pdb=" O ASN F 459 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER F 461 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL D 42 " --> pdb=" O SER F 461 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL F 463 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER D 20 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL D 7 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 245 through 247 removed outlier: 3.811A pdb=" N SER G 247 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL G 304 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU G 295 " --> pdb=" O SER G 303 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.074A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 396 " --> pdb=" O ILE G 416 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.074A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR G 410 " --> pdb=" O GLU G 403 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AD6, first strand: chain 'D' and resid 75 through 78 Processing sheet with id=AD7, first strand: chain 'D' and resid 111 through 116 removed outlier: 3.548A pdb=" N ALA D 112 " --> pdb=" O THR D 127 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 942 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: 1.87 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2144 1.32 - 1.45: 3329 1.45 - 1.58: 6419 1.58 - 1.71: 1 1.71 - 1.84: 73 Bond restraints: 11966 Sorted by residual: bond pdb=" C PRO F 309 " pdb=" O PRO F 309 " ideal model delta sigma weight residual 1.233 1.195 0.038 1.10e-02 8.26e+03 1.20e+01 bond pdb=" C GLU B 403 " pdb=" N PRO B 404 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.33e-02 5.65e+03 9.51e+00 bond pdb=" N SER F 260 " pdb=" CA SER F 260 " ideal model delta sigma weight residual 1.458 1.485 -0.027 9.00e-03 1.23e+04 8.75e+00 bond pdb=" C LEU F 351 " pdb=" N LEU F 352 " ideal model delta sigma weight residual 1.331 1.270 0.061 2.07e-02 2.33e+03 8.70e+00 bond pdb=" C PRO F 314 " pdb=" O PRO F 314 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.26e-02 6.30e+03 8.63e+00 ... (remaining 11961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 15869 2.56 - 5.11: 461 5.11 - 7.67: 58 7.67 - 10.23: 14 10.23 - 12.78: 4 Bond angle restraints: 16406 Sorted by residual: angle pdb=" C VAL C 165 " pdb=" N ASN C 166 " pdb=" CA ASN C 166 " ideal model delta sigma weight residual 120.60 130.47 -9.87 1.53e+00 4.27e-01 4.16e+01 angle pdb=" C ASN C 329 " pdb=" N GLU C 330 " pdb=" CA GLU C 330 " ideal model delta sigma weight residual 121.54 132.30 -10.76 1.91e+00 2.74e-01 3.18e+01 angle pdb=" C LEU A 271 " pdb=" N ARG A 272 " pdb=" CA ARG A 272 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.36e+01 angle pdb=" CA MET A 464 " pdb=" CB MET A 464 " pdb=" CG MET A 464 " ideal model delta sigma weight residual 114.10 122.70 -8.60 2.00e+00 2.50e-01 1.85e+01 angle pdb=" N VAL C 264 " pdb=" CA VAL C 264 " pdb=" C VAL C 264 " ideal model delta sigma weight residual 112.12 108.69 3.43 8.40e-01 1.42e+00 1.67e+01 ... (remaining 16401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 6397 17.37 - 34.73: 522 34.73 - 52.10: 81 52.10 - 69.47: 15 69.47 - 86.83: 9 Dihedral angle restraints: 7024 sinusoidal: 2514 harmonic: 4510 Sorted by residual: dihedral pdb=" CB CYS D 72 " pdb=" SG CYS D 72 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 175.14 -82.14 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS D 109 " pdb=" SG CYS D 109 " pdb=" SG CYS D 134 " pdb=" CB CYS D 134 " ideal model delta sinusoidal sigma weight residual -86.00 -162.76 76.76 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS C 468 " pdb=" SG CYS C 468 " pdb=" SG CYS F 311 " pdb=" CB CYS F 311 " ideal model delta sinusoidal sigma weight residual -86.00 -158.95 72.95 1 1.00e+01 1.00e-02 6.78e+01 ... (remaining 7021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1688 0.079 - 0.159: 276 0.159 - 0.238: 26 0.238 - 0.318: 4 0.318 - 0.397: 1 Chirality restraints: 1995 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 8.89e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 65 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 1992 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.091 2.00e-02 2.50e+03 7.49e-02 7.02e+01 pdb=" C7 NAG I 1 " -0.023 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.067 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.121 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 259 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.73e+00 pdb=" C GLY F 259 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY F 259 " 0.018 2.00e-02 2.50e+03 pdb=" N SER F 260 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 166 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PRO C 167 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 167 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 167 " 0.037 5.00e-02 4.00e+02 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 101 2.62 - 3.19: 8771 3.19 - 3.76: 15578 3.76 - 4.33: 20774 4.33 - 4.90: 36789 Nonbonded interactions: 82013 Sorted by model distance: nonbonded pdb=" O3 NAG I 1 " pdb=" O7 NAG I 1 " model vdw 2.051 3.040 nonbonded pdb=" OG1 THR A 282 " pdb=" OG1 THR A 322 " model vdw 2.278 3.040 nonbonded pdb=" O GLY B 469 " pdb=" OG SER G 356 " model vdw 2.297 3.040 nonbonded pdb=" O SER F 284 " pdb=" OG SER F 284 " model vdw 2.308 3.040 nonbonded pdb=" OG SER C 256 " pdb=" O ASN C 260 " model vdw 2.316 3.040 ... (remaining 82008 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 421 or (resid 422 and (name N \ or name CA or name C or name O or name CB )) or resid 423 through 425 or (resid \ 426 and (name N or name CA or name C or name O or name CB )) or resid 427 throug \ h 445 or (resid 446 and (name N or name CA or name C or name O or name CB )) or \ resid 447 through 449 or (resid 450 and (name N or name CA or name C or name O o \ r name CB )) or resid 451 through 464)) selection = (chain 'B' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 34 \ 5 or (resid 346 and (name N or name CA or name C or name O or name CB )) or resi \ d 347 through 356 or (resid 357 and (name N or name CA or name C or name O or na \ me CB )) or resid 358 through 404 or (resid 405 through 406 and (name N or name \ CA or name C or name O or name CB )) or resid 407 through 449 or (resid 450 and \ (name N or name CA or name C or name O or name CB )) or resid 451 through 453 or \ resid 456 through 464)) selection = (chain 'F' and (resid 242 through 310 or (resid 311 through 313 and (name N or n \ ame CA or name C or name O or name CB )) or resid 314 through 345 or (resid 346 \ and (name N or name CA or name C or name O or name CB )) or resid 347 through 35 \ 6 or (resid 357 and (name N or name CA or name C or name O or name CB )) or resi \ d 358 through 424 or (resid 425 through 426 and (name N or name CA or name C or \ name O or name CB )) or resid 427 through 449 or (resid 450 and (name N or name \ CA or name C or name O or name CB )) or resid 451 through 453 or resid 456 throu \ gh 464)) selection = (chain 'G' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 356 or (resid 357 and (name N \ or name CA or name C or name O or name CB )) or resid 358 through 445 or (resid \ 446 and (name N or name CA or name C or name O or name CB )) or resid 447 throug \ h 453 or resid 456 through 464)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 5.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.600 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:6.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.007 0.077 12007 Z= 0.329 Angle : 1.085 14.709 16504 Z= 0.582 Chirality : 0.060 0.397 1995 Planarity : 0.008 0.075 2095 Dihedral : 12.902 86.832 4039 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.50 % Allowed : 7.47 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.19), residues: 1551 helix: -4.14 (0.30), residues: 79 sheet: -1.03 (0.20), residues: 629 loop : -2.83 (0.18), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 382 TYR 0.020 0.002 TYR B 327 PHE 0.040 0.003 PHE C 136 TRP 0.017 0.002 TRP C 366 HIS 0.005 0.001 HIS G 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.33 (11966) covalent geometry : angle 1.05294 / 0.58 (16406) SS BOND : bond 0.00702 / 0.55 ( 25) SS BOND : angle 1.74149 / 1.29 ( 50) hydrogen bonds : bond 0.21842 / 15.44 ( 329) hydrogen bonds : angle 7.20593 / 4.83 ( 942) link_BETA1-4 : bond 0.01036 / 0.63 ( 5) link_BETA1-4 : angle 4.28985 / 2.61 ( 15) link_NAG-ASN : bond 0.00639 / 0.40 ( 11) link_NAG-ASN : angle 4.91727 / 3.22 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 253 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 SER cc_start: 0.8523 (t) cc_final: 0.8291 (p) REVERT: A 423 ASP cc_start: 0.8101 (m-30) cc_final: 0.7666 (m-30) REVERT: A 449 ASP cc_start: 0.8408 (p0) cc_final: 0.8132 (p0) REVERT: C 213 LYS cc_start: 0.5328 (tttt) cc_final: 0.5003 (mtpp) REVERT: F 378 ASP cc_start: 0.7652 (p0) cc_final: 0.7291 (p0) REVERT: G 250 ARG cc_start: 0.7426 (ptm160) cc_final: 0.7166 (ptm160) REVERT: G 345 PHE cc_start: 0.7317 (m-80) cc_final: 0.7022 (m-80) outliers start: 6 outliers final: 2 residues processed: 257 average time/residue: 0.6408 time to fit residues: 177.3064 Evaluate side-chains 174 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain F residue 311 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN B 385 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 412 GLN C 426 ASN ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 457 HIS D 88 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.108733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.079197 restraints weight = 24582.437| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.98 r_work: 0.3005 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12007 Z= 0.188 Angle : 0.775 11.391 16504 Z= 0.382 Chirality : 0.045 0.231 1995 Planarity : 0.006 0.053 2095 Dihedral : 5.937 35.192 1661 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.69 % Allowed : 16.36 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.20), residues: 1551 helix: -2.59 (0.45), residues: 85 sheet: -0.51 (0.21), residues: 630 loop : -2.45 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 5 TYR 0.014 0.001 TYR G 327 PHE 0.021 0.002 PHE G 321 TRP 0.018 0.001 TRP C 37 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (11966) covalent geometry : angle 0.75521 / 0.38 (16406) SS BOND : bond 0.00337 / 0.27 ( 25) SS BOND : angle 1.01505 / 0.80 ( 50) hydrogen bonds : bond 0.03439 / 2.37 ( 329) hydrogen bonds : angle 5.27755 / 3.51 ( 942) link_BETA1-4 : bond 0.00383 / 0.20 ( 5) link_BETA1-4 : angle 2.45510 / 1.61 ( 15) link_NAG-ASN : bond 0.00435 / 0.28 ( 11) link_NAG-ASN : angle 3.56055 / 2.45 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 SER cc_start: 0.8967 (t) cc_final: 0.8379 (p) REVERT: A 382 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7835 (mtp85) REVERT: A 385 GLN cc_start: 0.9228 (tt0) cc_final: 0.8990 (tt0) REVERT: A 389 GLU cc_start: 0.8420 (tt0) cc_final: 0.7859 (tt0) REVERT: A 423 ASP cc_start: 0.8890 (m-30) cc_final: 0.8613 (m-30) REVERT: A 449 ASP cc_start: 0.9264 (p0) cc_final: 0.8856 (p0) REVERT: B 340 LYS cc_start: 0.9332 (tttm) cc_final: 0.8988 (ttmm) REVERT: C 8 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8255 (tm-30) REVERT: C 85 ASP cc_start: 0.9083 (t0) cc_final: 0.8876 (t0) REVERT: C 213 LYS cc_start: 0.5543 (tttt) cc_final: 0.4954 (mtpp) REVERT: C 221 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8557 (tmtt) REVERT: F 433 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8505 (ttp) REVERT: G 315 TRP cc_start: 0.5911 (m100) cc_final: 0.5380 (p-90) REVERT: G 345 PHE cc_start: 0.7514 (m-80) cc_final: 0.7107 (m-80) REVERT: G 437 GLU cc_start: 0.7597 (mp0) cc_final: 0.7351 (mp0) REVERT: D 82 GLN cc_start: 0.8931 (mp10) cc_final: 0.8642 (pm20) REVERT: D 126 GLU cc_start: 0.8779 (tt0) cc_final: 0.8391 (tp30) outliers start: 44 outliers final: 15 residues processed: 205 average time/residue: 0.6405 time to fit residues: 141.5509 Evaluate side-chains 176 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain D residue 73 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 144 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN B 316 ASN B 385 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.107143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.078030 restraints weight = 24771.164| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.97 r_work: 0.2989 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12007 Z= 0.156 Angle : 0.726 10.877 16504 Z= 0.353 Chirality : 0.043 0.201 1995 Planarity : 0.005 0.044 2095 Dihedral : 5.337 27.489 1659 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.03 % Allowed : 17.37 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.21), residues: 1551 helix: -1.78 (0.50), residues: 90 sheet: -0.30 (0.21), residues: 637 loop : -2.29 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 372 TYR 0.014 0.001 TYR C 164 PHE 0.018 0.001 PHE C 75 TRP 0.014 0.001 TRP C 37 HIS 0.004 0.001 HIS D 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (11966) covalent geometry : angle 0.70697 / 0.35 (16406) SS BOND : bond 0.00473 / 0.33 ( 25) SS BOND : angle 1.13942 / 0.77 ( 50) hydrogen bonds : bond 0.03490 / 2.48 ( 329) hydrogen bonds : angle 4.95069 / 3.31 ( 942) link_BETA1-4 : bond 0.00313 / 0.16 ( 5) link_BETA1-4 : angle 2.11641 / 1.30 ( 15) link_NAG-ASN : bond 0.00417 / 0.25 ( 11) link_NAG-ASN : angle 3.30975 / 2.26 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 375 SER cc_start: 0.8941 (t) cc_final: 0.8631 (p) REVERT: A 382 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7954 (mtm180) REVERT: A 385 GLN cc_start: 0.9236 (tt0) cc_final: 0.8990 (tt0) REVERT: A 389 GLU cc_start: 0.8447 (tt0) cc_final: 0.7812 (tt0) REVERT: A 449 ASP cc_start: 0.9261 (p0) cc_final: 0.8845 (p0) REVERT: B 340 LYS cc_start: 0.9345 (tttm) cc_final: 0.9017 (ttmm) REVERT: C 8 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8313 (tm-30) REVERT: C 85 ASP cc_start: 0.9061 (t0) cc_final: 0.8858 (t0) REVERT: C 213 LYS cc_start: 0.5566 (tttt) cc_final: 0.4949 (mtpp) REVERT: C 221 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8568 (tptp) REVERT: C 414 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7889 (p) REVERT: F 250 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8274 (ppp80) REVERT: F 378 ASP cc_start: 0.8299 (p0) cc_final: 0.8099 (p0) REVERT: F 423 ASP cc_start: 0.9252 (m-30) cc_final: 0.9024 (m-30) REVERT: G 265 THR cc_start: 0.8036 (m) cc_final: 0.7445 (p) REVERT: G 345 PHE cc_start: 0.7598 (m-80) cc_final: 0.7218 (m-80) REVERT: G 370 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8303 (tp) REVERT: G 372 ARG cc_start: 0.8239 (tmm-80) cc_final: 0.7353 (tmm-80) REVERT: D 48 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7861 (mp0) REVERT: D 82 GLN cc_start: 0.8997 (mp10) cc_final: 0.8770 (pm20) REVERT: D 105 ASP cc_start: 0.9150 (t0) cc_final: 0.8863 (t0) REVERT: D 126 GLU cc_start: 0.8737 (tt0) cc_final: 0.8353 (tp30) REVERT: D 127 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.8920 (p) outliers start: 48 outliers final: 21 residues processed: 197 average time/residue: 0.6213 time to fit residues: 132.3411 Evaluate side-chains 181 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.106044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077375 restraints weight = 24877.073| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.97 r_work: 0.2979 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 12007 Z= 0.153 Angle : 0.699 10.459 16504 Z= 0.342 Chirality : 0.043 0.190 1995 Planarity : 0.004 0.038 2095 Dihedral : 5.242 29.474 1659 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.11 % Allowed : 17.70 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.21), residues: 1551 helix: -0.90 (0.57), residues: 83 sheet: -0.12 (0.21), residues: 639 loop : -2.11 (0.21), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 250 TYR 0.011 0.001 TYR C 154 PHE 0.018 0.001 PHE C 75 TRP 0.012 0.001 TRP C 37 HIS 0.004 0.001 HIS G 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (11966) covalent geometry : angle 0.68435 / 0.34 (16406) SS BOND : bond 0.00302 / 0.25 ( 25) SS BOND : angle 0.94308 / 0.62 ( 50) hydrogen bonds : bond 0.03032 / 2.15 ( 329) hydrogen bonds : angle 4.76026 / 3.20 ( 942) link_BETA1-4 : bond 0.00261 / 0.16 ( 5) link_BETA1-4 : angle 1.75111 / 1.07 ( 15) link_NAG-ASN : bond 0.00377 / 0.23 ( 11) link_NAG-ASN : angle 3.01855 / 2.07 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8061 (mtm180) REVERT: A 385 GLN cc_start: 0.9237 (tt0) cc_final: 0.9033 (tt0) REVERT: A 389 GLU cc_start: 0.8429 (tt0) cc_final: 0.7787 (tt0) REVERT: B 340 LYS cc_start: 0.9342 (tttm) cc_final: 0.9087 (ttmt) REVERT: B 357 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8536 (pp20) REVERT: B 362 ASN cc_start: 0.9124 (t0) cc_final: 0.8903 (t0) REVERT: B 385 GLN cc_start: 0.9253 (tt0) cc_final: 0.9002 (tt0) REVERT: B 406 GLN cc_start: 0.8994 (tp40) cc_final: 0.8678 (tp40) REVERT: C 85 ASP cc_start: 0.9131 (t0) cc_final: 0.8896 (t0) REVERT: C 174 ARG cc_start: 0.6866 (ptm160) cc_final: 0.6652 (ptm160) REVERT: C 213 LYS cc_start: 0.5680 (tttt) cc_final: 0.5053 (mtpp) REVERT: C 221 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8444 (tmtt) REVERT: C 414 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.7929 (p) REVERT: C 529 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8403 (ptpp) REVERT: F 378 ASP cc_start: 0.8311 (p0) cc_final: 0.8080 (p0) REVERT: F 423 ASP cc_start: 0.9295 (m-30) cc_final: 0.9044 (m-30) REVERT: F 433 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8602 (ttp) REVERT: G 265 THR cc_start: 0.7923 (m) cc_final: 0.7411 (p) REVERT: G 345 PHE cc_start: 0.7618 (m-80) cc_final: 0.7360 (m-80) REVERT: G 370 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8232 (tp) REVERT: D 48 GLU cc_start: 0.8605 (mt-10) cc_final: 0.7931 (mp0) REVERT: D 82 GLN cc_start: 0.9074 (mp10) cc_final: 0.8816 (pm20) REVERT: D 105 ASP cc_start: 0.9169 (t0) cc_final: 0.8836 (t0) REVERT: D 126 GLU cc_start: 0.8809 (tt0) cc_final: 0.8377 (tp30) REVERT: D 127 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.8929 (p) outliers start: 49 outliers final: 23 residues processed: 192 average time/residue: 0.6385 time to fit residues: 132.1106 Evaluate side-chains 184 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 59 LYS Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 164 TYR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 349 VAL Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 100 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 119 optimal weight: 0.0570 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 ASN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.104326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.075938 restraints weight = 25005.879| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.95 r_work: 0.2955 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12007 Z= 0.188 Angle : 0.727 14.009 16504 Z= 0.355 Chirality : 0.044 0.187 1995 Planarity : 0.004 0.045 2095 Dihedral : 5.194 27.141 1659 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.70 % Allowed : 17.70 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.21), residues: 1551 helix: -0.75 (0.55), residues: 89 sheet: -0.15 (0.21), residues: 626 loop : -2.17 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 250 TYR 0.017 0.001 TYR C 164 PHE 0.019 0.001 PHE C 75 TRP 0.012 0.001 TRP C 37 HIS 0.004 0.001 HIS D 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (11966) covalent geometry : angle 0.71214 / 0.35 (16406) SS BOND : bond 0.00316 / 0.23 ( 25) SS BOND : angle 1.24468 / 0.81 ( 50) hydrogen bonds : bond 0.03279 / 2.32 ( 329) hydrogen bonds : angle 4.79963 / 3.22 ( 942) link_BETA1-4 : bond 0.00242 / 0.14 ( 5) link_BETA1-4 : angle 1.60182 / 0.96 ( 15) link_NAG-ASN : bond 0.00415 / 0.27 ( 11) link_NAG-ASN : angle 2.99883 / 2.06 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 358 GLU cc_start: 0.9265 (mt-10) cc_final: 0.9055 (mt-10) REVERT: A 382 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8001 (mtm180) REVERT: A 389 GLU cc_start: 0.8452 (tt0) cc_final: 0.7883 (tt0) REVERT: A 457 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.8150 (m90) REVERT: B 340 LYS cc_start: 0.9331 (tttm) cc_final: 0.9070 (ttmt) REVERT: B 385 GLN cc_start: 0.9254 (tt0) cc_final: 0.8985 (tt0) REVERT: C 8 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8414 (tm-30) REVERT: C 85 ASP cc_start: 0.9157 (t0) cc_final: 0.8905 (t0) REVERT: C 174 ARG cc_start: 0.6891 (ptm160) cc_final: 0.6644 (ptm160) REVERT: C 213 LYS cc_start: 0.5954 (tttt) cc_final: 0.5280 (mtpp) REVERT: C 414 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8023 (p) REVERT: C 529 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8428 (ptpp) REVERT: F 410 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8776 (p) REVERT: F 423 ASP cc_start: 0.9320 (m-30) cc_final: 0.9063 (m-30) REVERT: F 433 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8611 (ttp) REVERT: G 265 THR cc_start: 0.7815 (m) cc_final: 0.7318 (p) REVERT: G 370 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8238 (tp) REVERT: G 403 GLU cc_start: 0.8871 (pm20) cc_final: 0.8335 (pm20) REVERT: D 21 ARG cc_start: 0.8529 (ttp-170) cc_final: 0.8157 (ttp-110) REVERT: D 48 GLU cc_start: 0.8696 (mt-10) cc_final: 0.7689 (mp0) REVERT: D 55 SER cc_start: 0.8497 (m) cc_final: 0.7564 (t) REVERT: D 82 GLN cc_start: 0.9074 (mp10) cc_final: 0.8801 (pm20) REVERT: D 105 ASP cc_start: 0.9214 (t0) cc_final: 0.8839 (t0) REVERT: D 126 GLU cc_start: 0.8806 (tt0) cc_final: 0.8390 (tp30) REVERT: D 127 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.8922 (p) outliers start: 56 outliers final: 29 residues processed: 202 average time/residue: 0.6314 time to fit residues: 137.7960 Evaluate side-chains 190 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 349 VAL Chi-restraints excluded: chain G residue 362 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 ASN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.076726 restraints weight = 24985.973| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.95 r_work: 0.2981 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12007 Z= 0.177 Angle : 0.727 10.033 16504 Z= 0.356 Chirality : 0.044 0.186 1995 Planarity : 0.004 0.041 2095 Dihedral : 5.155 31.186 1659 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.53 % Allowed : 18.54 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.21), residues: 1551 helix: -0.32 (0.57), residues: 89 sheet: -0.09 (0.21), residues: 624 loop : -2.05 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 17 TYR 0.013 0.001 TYR C 154 PHE 0.018 0.001 PHE C 75 TRP 0.012 0.001 TRP C 37 HIS 0.004 0.001 HIS D 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (11966) covalent geometry : angle 0.71411 / 0.35 (16406) SS BOND : bond 0.00282 / 0.21 ( 25) SS BOND : angle 1.08655 / 0.73 ( 50) hydrogen bonds : bond 0.03175 / 2.25 ( 329) hydrogen bonds : angle 4.75411 / 3.19 ( 942) link_BETA1-4 : bond 0.00405 / 0.21 ( 5) link_BETA1-4 : angle 1.37214 / 0.82 ( 15) link_NAG-ASN : bond 0.00390 / 0.25 ( 11) link_NAG-ASN : angle 2.82331 / 1.93 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 159 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 358 GLU cc_start: 0.9248 (mt-10) cc_final: 0.9030 (mt-10) REVERT: A 382 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7948 (mtm180) REVERT: A 389 GLU cc_start: 0.8428 (tt0) cc_final: 0.7850 (tt0) REVERT: A 457 HIS cc_start: 0.8445 (m170) cc_final: 0.8185 (m90) REVERT: B 340 LYS cc_start: 0.9317 (tttm) cc_final: 0.9063 (ttmt) REVERT: B 357 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8583 (pp20) REVERT: B 385 GLN cc_start: 0.9272 (tt0) cc_final: 0.8954 (tt0) REVERT: C 8 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8458 (tm-30) REVERT: C 40 GLN cc_start: 0.8621 (pt0) cc_final: 0.8400 (pp30) REVERT: C 85 ASP cc_start: 0.9155 (t0) cc_final: 0.8844 (t0) REVERT: C 174 ARG cc_start: 0.6862 (ptm160) cc_final: 0.6606 (ptm160) REVERT: C 213 LYS cc_start: 0.6073 (tttt) cc_final: 0.5391 (mtpp) REVERT: C 414 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8037 (p) REVERT: C 508 LEU cc_start: 0.8806 (mt) cc_final: 0.8047 (tm) REVERT: C 529 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8443 (ptpp) REVERT: F 410 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8772 (p) REVERT: F 423 ASP cc_start: 0.9333 (m-30) cc_final: 0.9048 (m-30) REVERT: F 433 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8627 (ttp) REVERT: G 265 THR cc_start: 0.7834 (m) cc_final: 0.7406 (p) REVERT: G 370 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8168 (tp) REVERT: G 403 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8104 (pm20) REVERT: G 445 GLN cc_start: 0.8851 (mt0) cc_final: 0.8503 (tp40) REVERT: D 21 ARG cc_start: 0.8513 (ttp-170) cc_final: 0.8148 (ttp-110) REVERT: D 48 GLU cc_start: 0.8760 (mt-10) cc_final: 0.7791 (mp0) REVERT: D 55 SER cc_start: 0.8571 (m) cc_final: 0.7510 (t) REVERT: D 82 GLN cc_start: 0.9107 (mp10) cc_final: 0.8844 (pm20) REVERT: D 105 ASP cc_start: 0.9187 (t0) cc_final: 0.8856 (t0) REVERT: D 123 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7939 (mmtm) REVERT: D 126 GLU cc_start: 0.8827 (tt0) cc_final: 0.8365 (tp30) REVERT: D 127 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8914 (p) outliers start: 54 outliers final: 28 residues processed: 198 average time/residue: 0.6217 time to fit residues: 133.2124 Evaluate side-chains 194 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 362 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 9 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 114 optimal weight: 0.0670 chunk 50 optimal weight: 0.4980 chunk 117 optimal weight: 0.5980 chunk 108 optimal weight: 0.3980 chunk 121 optimal weight: 6.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.106348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.078247 restraints weight = 24925.456| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.96 r_work: 0.3010 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12007 Z= 0.122 Angle : 0.702 13.298 16504 Z= 0.340 Chirality : 0.043 0.181 1995 Planarity : 0.004 0.041 2095 Dihedral : 4.809 27.260 1659 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 3.27 % Allowed : 20.30 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.21), residues: 1551 helix: -0.16 (0.58), residues: 83 sheet: -0.02 (0.21), residues: 632 loop : -1.89 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 418 TYR 0.007 0.001 TYR C 164 PHE 0.016 0.001 PHE C 75 TRP 0.013 0.001 TRP C 37 HIS 0.004 0.000 HIS G 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (11966) covalent geometry : angle 0.69282 / 0.34 (16406) SS BOND : bond 0.00226 / 0.18 ( 25) SS BOND : angle 0.91356 / 0.61 ( 50) hydrogen bonds : bond 0.02642 / 1.88 ( 329) hydrogen bonds : angle 4.54598 / 3.08 ( 942) link_BETA1-4 : bond 0.00353 / 0.20 ( 5) link_BETA1-4 : angle 1.16525 / 0.69 ( 15) link_NAG-ASN : bond 0.00339 / 0.21 ( 11) link_NAG-ASN : angle 2.49289 / 1.72 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7885 (mtm180) REVERT: A 389 GLU cc_start: 0.8420 (tt0) cc_final: 0.7876 (tt0) REVERT: B 340 LYS cc_start: 0.9272 (tttm) cc_final: 0.9036 (ttmt) REVERT: B 357 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8582 (pp20) REVERT: B 385 GLN cc_start: 0.9246 (tt0) cc_final: 0.8945 (tt0) REVERT: C 8 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8395 (tm-30) REVERT: C 85 ASP cc_start: 0.9146 (t0) cc_final: 0.8888 (t0) REVERT: C 213 LYS cc_start: 0.6053 (tttt) cc_final: 0.5362 (mtpp) REVERT: C 414 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7969 (p) REVERT: C 529 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8422 (ptpp) REVERT: F 410 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8496 (t) REVERT: F 423 ASP cc_start: 0.9326 (m-30) cc_final: 0.9045 (m-30) REVERT: G 265 THR cc_start: 0.7589 (m) cc_final: 0.7140 (p) REVERT: G 370 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8136 (tp) REVERT: G 403 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8134 (pm20) REVERT: G 445 GLN cc_start: 0.8840 (mt0) cc_final: 0.8491 (tp40) REVERT: D 21 ARG cc_start: 0.8492 (ttp-170) cc_final: 0.8111 (ttp-110) REVERT: D 48 GLU cc_start: 0.8721 (mt-10) cc_final: 0.7724 (mp0) REVERT: D 55 SER cc_start: 0.8525 (m) cc_final: 0.7561 (t) REVERT: D 82 GLN cc_start: 0.9087 (mp10) cc_final: 0.8810 (pm20) REVERT: D 105 ASP cc_start: 0.9140 (t0) cc_final: 0.8786 (t0) REVERT: D 123 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7945 (mmtm) REVERT: D 126 GLU cc_start: 0.8819 (tt0) cc_final: 0.8376 (tp30) REVERT: D 127 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8910 (p) outliers start: 39 outliers final: 17 residues processed: 187 average time/residue: 0.6172 time to fit residues: 124.5317 Evaluate side-chains 180 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 362 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 136 optimal weight: 0.0980 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 457 HIS ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.104660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076771 restraints weight = 24920.651| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.92 r_work: 0.2969 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12007 Z= 0.144 Angle : 0.706 9.744 16504 Z= 0.345 Chirality : 0.043 0.192 1995 Planarity : 0.004 0.041 2095 Dihedral : 4.814 27.521 1659 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.52 % Allowed : 20.55 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.21), residues: 1551 helix: -0.06 (0.59), residues: 83 sheet: 0.04 (0.21), residues: 629 loop : -1.87 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 43 TYR 0.010 0.001 TYR C 55 PHE 0.017 0.001 PHE C 75 TRP 0.011 0.001 TRP C 37 HIS 0.004 0.001 HIS G 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (11966) covalent geometry : angle 0.69668 / 0.34 (16406) SS BOND : bond 0.00253 / 0.19 ( 25) SS BOND : angle 0.91359 / 0.62 ( 50) hydrogen bonds : bond 0.02827 / 2.02 ( 329) hydrogen bonds : angle 4.56050 / 3.08 ( 942) link_BETA1-4 : bond 0.00315 / 0.18 ( 5) link_BETA1-4 : angle 1.17983 / 0.70 ( 15) link_NAG-ASN : bond 0.00325 / 0.21 ( 11) link_NAG-ASN : angle 2.50091 / 1.72 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7893 (mtm180) REVERT: A 389 GLU cc_start: 0.8429 (tt0) cc_final: 0.7853 (tt0) REVERT: B 340 LYS cc_start: 0.9265 (tttm) cc_final: 0.9040 (ttmt) REVERT: B 357 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8575 (pp20) REVERT: B 385 GLN cc_start: 0.9250 (tt0) cc_final: 0.8915 (tt0) REVERT: C 8 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8479 (tm-30) REVERT: C 40 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: C 85 ASP cc_start: 0.9141 (t0) cc_final: 0.8882 (t0) REVERT: C 213 LYS cc_start: 0.6028 (tttt) cc_final: 0.5334 (mtpp) REVERT: C 414 THR cc_start: 0.8362 (OUTLIER) cc_final: 0.8009 (p) REVERT: C 529 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8413 (ptpp) REVERT: F 410 THR cc_start: 0.9027 (OUTLIER) cc_final: 0.8497 (t) REVERT: F 423 ASP cc_start: 0.9317 (m-30) cc_final: 0.9076 (m-30) REVERT: G 265 THR cc_start: 0.7471 (m) cc_final: 0.6988 (p) REVERT: G 370 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8152 (tp) REVERT: G 403 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8035 (pm20) REVERT: G 445 GLN cc_start: 0.8832 (mt0) cc_final: 0.8516 (tp40) REVERT: D 21 ARG cc_start: 0.8508 (ttp-170) cc_final: 0.8113 (ttp-110) REVERT: D 48 GLU cc_start: 0.8742 (mt-10) cc_final: 0.7746 (mp0) REVERT: D 55 SER cc_start: 0.8521 (m) cc_final: 0.7562 (t) REVERT: D 82 GLN cc_start: 0.9090 (mp10) cc_final: 0.8820 (pm20) REVERT: D 105 ASP cc_start: 0.9159 (t0) cc_final: 0.8817 (t0) REVERT: D 126 GLU cc_start: 0.8824 (tt0) cc_final: 0.8405 (tp30) REVERT: D 127 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.8908 (p) outliers start: 42 outliers final: 23 residues processed: 186 average time/residue: 0.5981 time to fit residues: 120.4479 Evaluate side-chains 185 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 164 TYR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 362 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN A 457 HIS ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.111332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.083712 restraints weight = 24539.018| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.84 r_work: 0.3145 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12007 Z= 0.138 Angle : 0.729 16.468 16504 Z= 0.352 Chirality : 0.043 0.173 1995 Planarity : 0.004 0.042 2095 Dihedral : 4.765 26.817 1659 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 3.36 % Allowed : 21.48 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.21), residues: 1551 helix: 0.01 (0.58), residues: 84 sheet: -0.03 (0.21), residues: 641 loop : -1.81 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 418 TYR 0.009 0.001 TYR C 55 PHE 0.017 0.001 PHE C 75 TRP 0.011 0.001 TRP C 37 HIS 0.012 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (11966) covalent geometry : angle 0.72068 / 0.35 (16406) SS BOND : bond 0.00236 / 0.18 ( 25) SS BOND : angle 0.88581 / 0.61 ( 50) hydrogen bonds : bond 0.02753 / 1.97 ( 329) hydrogen bonds : angle 4.52804 / 3.06 ( 942) link_BETA1-4 : bond 0.00283 / 0.16 ( 5) link_BETA1-4 : angle 1.13771 / 0.68 ( 15) link_NAG-ASN : bond 0.00316 / 0.20 ( 11) link_NAG-ASN : angle 2.40758 / 1.65 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7879 (mtm180) REVERT: A 389 GLU cc_start: 0.8468 (tt0) cc_final: 0.7921 (tt0) REVERT: B 340 LYS cc_start: 0.9242 (tttm) cc_final: 0.9017 (ttmt) REVERT: B 357 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8594 (pp20) REVERT: B 385 GLN cc_start: 0.9229 (tt0) cc_final: 0.8886 (tt0) REVERT: C 8 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8399 (tm-30) REVERT: C 40 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: C 85 ASP cc_start: 0.9136 (t0) cc_final: 0.8872 (t0) REVERT: C 213 LYS cc_start: 0.5867 (tttt) cc_final: 0.5199 (mtpp) REVERT: C 414 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7949 (p) REVERT: C 529 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8322 (ptpp) REVERT: F 410 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8489 (t) REVERT: F 423 ASP cc_start: 0.9291 (m-30) cc_final: 0.9033 (m-30) REVERT: G 265 THR cc_start: 0.7381 (m) cc_final: 0.6873 (p) REVERT: G 370 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8010 (tp) REVERT: G 403 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: G 445 GLN cc_start: 0.8845 (mt0) cc_final: 0.8542 (tp40) REVERT: D 21 ARG cc_start: 0.8401 (ttp-170) cc_final: 0.7994 (ttp-110) REVERT: D 48 GLU cc_start: 0.8749 (mt-10) cc_final: 0.7721 (mp0) REVERT: D 55 SER cc_start: 0.8450 (m) cc_final: 0.7530 (t) REVERT: D 82 GLN cc_start: 0.9064 (mp10) cc_final: 0.8779 (pm20) REVERT: D 105 ASP cc_start: 0.9114 (t0) cc_final: 0.8744 (t0) REVERT: D 124 MET cc_start: 0.9030 (mmm) cc_final: 0.8755 (tpp) REVERT: D 126 GLU cc_start: 0.8746 (tt0) cc_final: 0.8281 (tp30) REVERT: D 127 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8891 (p) outliers start: 40 outliers final: 24 residues processed: 181 average time/residue: 0.5942 time to fit residues: 116.4199 Evaluate side-chains 184 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 164 TYR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 362 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 28 optimal weight: 8.9990 chunk 65 optimal weight: 0.0570 chunk 136 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN A 457 HIS B 362 ASN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.111661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.084281 restraints weight = 24896.928| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.80 r_work: 0.3141 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.228 12007 Z= 0.248 Angle : 1.027 59.180 16504 Z= 0.587 Chirality : 0.048 0.819 1995 Planarity : 0.006 0.161 2095 Dihedral : 4.772 26.843 1659 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.45 % Favored : 91.49 % Rotamer: Outliers : 3.27 % Allowed : 21.39 % Favored : 75.34 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.21), residues: 1551 helix: 0.02 (0.58), residues: 84 sheet: -0.03 (0.21), residues: 641 loop : -1.83 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 174 TYR 0.352 0.004 TYR C 164 PHE 0.017 0.001 PHE C 75 TRP 0.011 0.001 TRP C 37 HIS 0.008 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 (11966) covalent geometry : angle 1.02278 / 0.59 (16406) SS BOND : bond 0.00258 / 0.20 ( 25) SS BOND : angle 0.88949 / 0.61 ( 50) hydrogen bonds : bond 0.02828 / 2.02 ( 329) hydrogen bonds : angle 4.53033 / 3.06 ( 942) link_BETA1-4 : bond 0.00532 / 0.27 ( 5) link_BETA1-4 : angle 1.21486 / 0.72 ( 15) link_NAG-ASN : bond 0.00329 / 0.20 ( 11) link_NAG-ASN : angle 2.41038 / 1.66 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3102 Ramachandran restraints generated. 1551 Oldfield, 0 Emsley, 1551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7891 (mtm180) REVERT: A 389 GLU cc_start: 0.8461 (tt0) cc_final: 0.7919 (tt0) REVERT: B 340 LYS cc_start: 0.9245 (tttm) cc_final: 0.9021 (ttmt) REVERT: B 357 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8585 (pp20) REVERT: B 385 GLN cc_start: 0.9232 (tt0) cc_final: 0.8884 (tt0) REVERT: C 8 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8400 (tm-30) REVERT: C 40 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8014 (tm-30) REVERT: C 85 ASP cc_start: 0.9135 (t0) cc_final: 0.8812 (t0) REVERT: C 213 LYS cc_start: 0.5860 (tttt) cc_final: 0.5196 (mtpp) REVERT: C 414 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7964 (p) REVERT: C 529 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8326 (ptpp) REVERT: F 410 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8494 (t) REVERT: F 423 ASP cc_start: 0.9285 (m-30) cc_final: 0.9029 (m-30) REVERT: G 265 THR cc_start: 0.7377 (m) cc_final: 0.6871 (p) REVERT: G 343 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7116 (p0) REVERT: G 370 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8018 (tp) REVERT: G 403 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8010 (pm20) REVERT: G 445 GLN cc_start: 0.8811 (mt0) cc_final: 0.8581 (tp40) REVERT: D 21 ARG cc_start: 0.8405 (ttp-170) cc_final: 0.7999 (ttp-110) REVERT: D 48 GLU cc_start: 0.8751 (mt-10) cc_final: 0.7724 (mp0) REVERT: D 55 SER cc_start: 0.8459 (m) cc_final: 0.7536 (t) REVERT: D 82 GLN cc_start: 0.9063 (mp10) cc_final: 0.8777 (pm20) REVERT: D 105 ASP cc_start: 0.9116 (t0) cc_final: 0.8747 (t0) REVERT: D 124 MET cc_start: 0.9026 (mmm) cc_final: 0.8753 (tpp) REVERT: D 126 GLU cc_start: 0.8751 (tt0) cc_final: 0.8283 (tp30) REVERT: D 127 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8893 (p) outliers start: 39 outliers final: 28 residues processed: 176 average time/residue: 0.6377 time to fit residues: 121.3055 Evaluate side-chains 191 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 464 MET Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 362 ASN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 164 TYR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 362 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 128 optimal weight: 0.0270 chunk 95 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 105 optimal weight: 0.0770 chunk 79 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.111407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.083997 restraints weight = 24815.769| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.82 r_work: 0.3142 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.506 12007 Z= 0.460 Angle : 0.947 37.764 16504 Z= 0.574 Chirality : 0.047 0.818 1995 Planarity : 0.007 0.206 2095 Dihedral : 4.773 26.843 1659 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.45 % Favored : 91.49 % Rotamer: Outliers : 3.27 % Allowed : 21.39 % Favored : 75.34 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.21), residues: 1551 helix: 0.02 (0.58), residues: 84 sheet: -0.03 (0.21), residues: 641 loop : -1.83 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 174 TYR 0.352 0.004 TYR C 164 PHE 0.017 0.001 PHE C 75 TRP 0.011 0.001 TRP C 37 HIS 0.004 0.001 HIS G 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00927 / 0.46 (11966) covalent geometry : angle 0.94157 / 0.57 (16406) SS BOND : bond 0.00258 / 0.20 ( 25) SS BOND : angle 0.88935 / 0.61 ( 50) hydrogen bonds : bond 0.02828 / 2.01 ( 329) hydrogen bonds : angle 4.53031 / 3.06 ( 942) link_BETA1-4 : bond 0.00511 / 0.26 ( 5) link_BETA1-4 : angle 1.21514 / 0.72 ( 15) link_NAG-ASN : bond 0.00329 / 0.20 ( 11) link_NAG-ASN : angle 2.41038 / 1.66 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4335.69 seconds wall clock time: 74 minutes 38.36 seconds (4478.36 seconds total)