Starting phenix.real_space_refine on Wed Mar 4 07:27:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ue7_20749/03_2026/6ue7_20749.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ue7_20749/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6ue7_20749/03_2026/6ue7_20749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ue7_20749/03_2026/6ue7_20749.map" model { file = "/net/cci-nas-00/data/ceres_data/6ue7_20749/03_2026/6ue7_20749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ue7_20749/03_2026/6ue7_20749.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.02, per 1000 atoms: 0.26 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: 0.97 Conformation dependent library (CDL) restraints added in 677.2 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: 0.50 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: 2.05 Time building geometry restraints manager: 1.29 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 - 22.78: 6958 22.78 - 45.56: 338 45.56 - 68.34: 42 68.34 - 91.12: 16 91.12 - 113.90: 4 Dihedral angle restraints: 7358 sinusoidal: 2848 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 7355 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: 5.530 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.910 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 13.758 113.898 4373 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 covalent geometry : bond 0.00699 (11966) covalent geometry : angle 1.05294 (16406) SS BOND : bond 0.00702 ( 25) SS BOND : angle 1.74149 ( 50) hydrogen bonds : bond 0.21842 ( 329) hydrogen bonds : angle 7.20593 ( 942) link_BETA1-4 : bond 0.01036 ( 5) link_BETA1-4 : angle 4.28985 ( 15) link_NAG-ASN : bond 0.00639 ( 11) link_NAG-ASN : angle 4.91727 ( 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 : 0.463 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: 0.6508 time to fit residues: 179.6294 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 : 0.464 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.108790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.079208 restraints weight = 24581.941| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.98 r_work: 0.3003 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12007 Z= 0.183 Angle : 0.778 11.391 16504 Z= 0.382 Chirality : 0.046 0.246 1995 Planarity : 0.006 0.052 2095 Dihedral : 8.531 60.695 1995 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.69 % Allowed : 16.44 % Favored : 79.87 % 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: -2.60 (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 0.010 0.001 ARG C 304 TYR 0.013 0.001 TYR G 327 PHE 0.018 0.002 PHE C 185 TRP 0.018 0.001 TRP C 37 HIS 0.003 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00421 (11966) covalent geometry : angle 0.75554 (16406) SS BOND : bond 0.00694 ( 25) SS BOND : angle 0.97018 ( 50) hydrogen bonds : bond 0.03393 ( 329) hydrogen bonds : angle 5.27887 ( 942) link_BETA1-4 : bond 0.00402 ( 5) link_BETA1-4 : angle 3.15229 ( 15) link_NAG-ASN : bond 0.00438 ( 11) link_NAG-ASN : angle 3.62996 ( 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 226 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 SER cc_start: 0.8973 (t) cc_final: 0.8387 (p) REVERT: A 382 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7848 (mtp85) REVERT: A 385 GLN cc_start: 0.9234 (tt0) cc_final: 0.8983 (tt0) REVERT: A 389 GLU cc_start: 0.8427 (tt0) cc_final: 0.7882 (tt0) REVERT: A 449 ASP cc_start: 0.9265 (p0) cc_final: 0.8856 (p0) REVERT: B 340 LYS cc_start: 0.9329 (tttm) cc_final: 0.8986 (ttmm) REVERT: C 8 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8247 (tm-30) REVERT: C 85 ASP cc_start: 0.9077 (t0) cc_final: 0.8853 (t0) REVERT: C 213 LYS cc_start: 0.5532 (tttt) cc_final: 0.4948 (mtpp) REVERT: C 221 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8549 (tmtt) REVERT: F 433 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8498 (ttp) REVERT: G 250 ARG cc_start: 0.7615 (ptm160) cc_final: 0.7399 (ptm160) REVERT: G 315 TRP cc_start: 0.5819 (m100) cc_final: 0.5323 (p-90) REVERT: G 345 PHE cc_start: 0.7518 (m-80) cc_final: 0.7110 (m-80) REVERT: D 82 GLN cc_start: 0.8895 (mp10) cc_final: 0.8588 (pm20) REVERT: D 126 GLU cc_start: 0.8755 (tt0) cc_final: 0.8366 (tp30) outliers start: 44 outliers final: 14 residues processed: 205 average time/residue: 0.6375 time to fit residues: 140.5153 Evaluate side-chains 175 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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: 0.0970 chunk 148 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 139 optimal weight: 0.0270 chunk 140 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3598 r_free = 0.3598 target = 0.107626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078460 restraints weight = 24774.619| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.98 r_work: 0.2998 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12007 Z= 0.141 Angle : 0.721 10.836 16504 Z= 0.349 Chirality : 0.044 0.212 1995 Planarity : 0.005 0.045 2095 Dihedral : 7.181 55.696 1993 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 3.86 % Allowed : 17.20 % Favored : 78.94 % 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: -1.99 (0.21), residues: 1551 helix: -1.55 (0.53), residues: 84 sheet: -0.26 (0.21), residues: 634 loop : -2.23 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 304 TYR 0.009 0.001 TYR G 327 PHE 0.018 0.001 PHE C 75 TRP 0.014 0.001 TRP C 37 HIS 0.003 0.001 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00336 (11966) covalent geometry : angle 0.69991 (16406) SS BOND : bond 0.00328 ( 25) SS BOND : angle 1.03355 ( 50) hydrogen bonds : bond 0.03330 ( 329) hydrogen bonds : angle 4.91574 ( 942) link_BETA1-4 : bond 0.00506 ( 5) link_BETA1-4 : angle 3.05734 ( 15) link_NAG-ASN : bond 0.00393 ( 11) link_NAG-ASN : angle 3.27619 ( 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 209 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 SER cc_start: 0.8946 (t) cc_final: 0.8370 (p) REVERT: A 385 GLN cc_start: 0.9234 (tt0) cc_final: 0.8990 (tt0) REVERT: A 449 ASP cc_start: 0.9276 (p0) cc_final: 0.8876 (p0) REVERT: B 340 LYS cc_start: 0.9344 (tttm) cc_final: 0.9017 (ttmm) REVERT: C 85 ASP cc_start: 0.9081 (t0) cc_final: 0.8870 (t0) REVERT: C 185 PHE cc_start: 0.6523 (p90) cc_final: 0.6311 (p90) REVERT: C 213 LYS cc_start: 0.5547 (tttt) cc_final: 0.4936 (mtpp) REVERT: C 221 LYS cc_start: 0.8803 (ttmt) cc_final: 0.8467 (tmtt) REVERT: C 414 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7855 (p) REVERT: F 250 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8294 (ppp80) REVERT: F 423 ASP cc_start: 0.9251 (m-30) cc_final: 0.9027 (m-30) REVERT: G 265 THR cc_start: 0.8054 (m) cc_final: 0.7521 (t) REVERT: G 345 PHE cc_start: 0.7590 (m-80) cc_final: 0.7210 (m-80) REVERT: G 372 ARG cc_start: 0.8245 (tmm-80) cc_final: 0.7347 (tmm-80) REVERT: G 437 GLU cc_start: 0.7822 (mp0) cc_final: 0.7461 (mp0) REVERT: D 82 GLN cc_start: 0.8979 (mp10) cc_final: 0.8774 (pm20) REVERT: D 105 ASP cc_start: 0.9136 (t0) cc_final: 0.8847 (t0) REVERT: D 126 GLU cc_start: 0.8748 (tt0) cc_final: 0.8374 (tp30) REVERT: D 127 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.8941 (p) outliers start: 46 outliers final: 18 residues processed: 197 average time/residue: 0.6290 time to fit residues: 133.5282 Evaluate side-chains 175 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 414 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 322 THR 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 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: 5.9990 chunk 14 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 148 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3572 r_free = 0.3572 target = 0.105626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.076867 restraints weight = 24939.805| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.97 r_work: 0.2969 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 12007 Z= 0.175 Angle : 0.722 10.306 16504 Z= 0.353 Chirality : 0.044 0.200 1995 Planarity : 0.004 0.040 2095 Dihedral : 6.866 54.113 1993 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.36 % Allowed : 17.20 % Favored : 78.44 % 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: -1.86 (0.21), residues: 1551 helix: -1.28 (0.53), residues: 90 sheet: -0.17 (0.21), residues: 639 loop : -2.17 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 382 TYR 0.014 0.001 TYR C 164 PHE 0.019 0.001 PHE C 75 TRP 0.013 0.001 TRP C 37 HIS 0.004 0.001 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00418 (11966) covalent geometry : angle 0.70207 (16406) SS BOND : bond 0.00560 ( 25) SS BOND : angle 1.23939 ( 50) hydrogen bonds : bond 0.03291 ( 329) hydrogen bonds : angle 4.87474 ( 942) link_BETA1-4 : bond 0.00357 ( 5) link_BETA1-4 : angle 2.74292 ( 15) link_NAG-ASN : bond 0.00398 ( 11) link_NAG-ASN : angle 3.12300 ( 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 207 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 155 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 385 GLN cc_start: 0.9232 (tt0) cc_final: 0.9030 (tt0) REVERT: B 340 LYS cc_start: 0.9346 (tttm) cc_final: 0.9086 (ttmt) REVERT: B 357 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8531 (pp20) REVERT: B 362 ASN cc_start: 0.9164 (t0) cc_final: 0.8849 (t0) REVERT: B 406 GLN cc_start: 0.8986 (tp40) cc_final: 0.8679 (tp40) REVERT: C 8 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8383 (tm-30) REVERT: C 85 ASP cc_start: 0.9138 (t0) cc_final: 0.8904 (t0) REVERT: C 174 ARG cc_start: 0.6886 (ptm160) cc_final: 0.6683 (ptm160) REVERT: C 185 PHE cc_start: 0.6520 (p90) cc_final: 0.6040 (p90) REVERT: C 213 LYS cc_start: 0.5676 (tttt) cc_final: 0.5057 (mtpp) REVERT: C 221 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8441 (tmtt) REVERT: C 414 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7960 (p) REVERT: C 529 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8409 (ptpp) REVERT: F 423 ASP cc_start: 0.9301 (m-30) cc_final: 0.9055 (m-30) REVERT: F 433 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8601 (ttp) REVERT: G 265 THR cc_start: 0.7897 (m) cc_final: 0.7391 (p) REVERT: G 345 PHE cc_start: 0.7625 (m-80) cc_final: 0.7326 (m-80) REVERT: G 437 GLU cc_start: 0.7734 (mp0) cc_final: 0.7434 (mp0) REVERT: D 48 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7744 (mp0) REVERT: D 55 SER cc_start: 0.8476 (m) cc_final: 0.6982 (t) REVERT: D 82 GLN cc_start: 0.9093 (mp10) cc_final: 0.8806 (pm20) REVERT: D 105 ASP cc_start: 0.9194 (t0) cc_final: 0.8872 (t0) REVERT: D 126 GLU cc_start: 0.8799 (tt0) cc_final: 0.8402 (tp30) REVERT: D 127 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.8928 (p) outliers start: 52 outliers final: 26 residues processed: 190 average time/residue: 0.6687 time to fit residues: 136.6081 Evaluate side-chains 181 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 357 GLU 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 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 529 LYS Chi-restraints excluded: chain F residue 243 HIS 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 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 362 ASN Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain D residue 8 LEU 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: 4.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 14 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 0.0270 chunk 134 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 119 optimal weight: 0.0030 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.3636 r_free = 0.3636 target = 0.108872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.080051 restraints weight = 24925.590| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 4.00 r_work: 0.3041 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12007 Z= 0.111 Angle : 0.682 12.756 16504 Z= 0.328 Chirality : 0.042 0.191 1995 Planarity : 0.004 0.049 2095 Dihedral : 6.264 53.525 1993 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.36 % Allowed : 18.71 % Favored : 77.94 % 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: -1.58 (0.21), residues: 1551 helix: -0.98 (0.54), residues: 90 sheet: 0.06 (0.21), residues: 627 loop : -2.02 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 418 TYR 0.015 0.001 TYR B 327 PHE 0.015 0.001 PHE C 75 TRP 0.013 0.001 TRP C 37 HIS 0.001 0.000 HIS B 436 Details of bonding type rmsd covalent geometry : bond 0.00261 (11966) covalent geometry : angle 0.66687 (16406) SS BOND : bond 0.00424 ( 25) SS BOND : angle 1.08364 ( 50) hydrogen bonds : bond 0.02568 ( 329) hydrogen bonds : angle 4.60264 ( 942) link_BETA1-4 : bond 0.00516 ( 5) link_BETA1-4 : angle 2.34916 ( 15) link_NAG-ASN : bond 0.00350 ( 11) link_NAG-ASN : angle 2.68316 ( 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 210 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 385 GLN cc_start: 0.9250 (tt0) cc_final: 0.9041 (tt0) REVERT: B 264 LEU cc_start: 0.8281 (tt) cc_final: 0.7871 (mp) REVERT: B 340 LYS cc_start: 0.9285 (tttm) cc_final: 0.9045 (ttmt) REVERT: B 357 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8554 (pp20) REVERT: C 8 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8383 (tm-30) REVERT: C 85 ASP cc_start: 0.9102 (t0) cc_final: 0.8880 (t0) REVERT: C 213 LYS cc_start: 0.5719 (tttt) cc_final: 0.5088 (mtpp) REVERT: C 414 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7862 (p) REVERT: C 529 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8409 (ptpp) REVERT: F 410 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8709 (p) REVERT: F 423 ASP cc_start: 0.9300 (m-30) cc_final: 0.9042 (m-30) REVERT: G 265 THR cc_start: 0.7821 (m) cc_final: 0.7334 (p) REVERT: G 345 PHE cc_start: 0.7612 (m-80) cc_final: 0.7377 (m-80) REVERT: G 437 GLU cc_start: 0.7755 (mp0) cc_final: 0.7440 (mp0) REVERT: D 21 ARG cc_start: 0.8504 (ttp-170) cc_final: 0.8138 (ttp-110) REVERT: D 48 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7655 (mp0) REVERT: D 55 SER cc_start: 0.8453 (m) cc_final: 0.7545 (t) REVERT: D 105 ASP cc_start: 0.9095 (t0) cc_final: 0.8727 (t0) REVERT: D 108 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8607 (mtpp) REVERT: D 126 GLU cc_start: 0.8806 (tt0) cc_final: 0.8405 (tp30) REVERT: D 127 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.8934 (p) outliers start: 40 outliers final: 17 residues processed: 197 average time/residue: 0.6338 time to fit residues: 134.5955 Evaluate side-chains 175 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 467 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 485 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain F residue 243 HIS 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 253 LEU Chi-restraints excluded: chain G residue 362 ASN 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: 0.6980 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 362 ASN B 436 HIS ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.076308 restraints weight = 24794.898| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.92 r_work: 0.2963 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4059 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= 0.175 Angle : 0.722 10.449 16504 Z= 0.354 Chirality : 0.043 0.187 1995 Planarity : 0.004 0.043 2095 Dihedral : 6.428 55.157 1993 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 3.94 % Allowed : 18.71 % Favored : 77.35 % 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: -1.53 (0.21), residues: 1551 helix: -0.39 (0.58), residues: 83 sheet: 0.03 (0.21), residues: 631 loop : -1.99 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 418 TYR 0.015 0.001 TYR C 154 PHE 0.019 0.001 PHE C 75 TRP 0.013 0.001 TRP C 366 HIS 0.005 0.001 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00420 (11966) covalent geometry : angle 0.70779 (16406) SS BOND : bond 0.00314 ( 25) SS BOND : angle 1.10274 ( 50) hydrogen bonds : bond 0.03289 ( 329) hydrogen bonds : angle 4.77045 ( 942) link_BETA1-4 : bond 0.00369 ( 5) link_BETA1-4 : angle 2.10748 ( 15) link_NAG-ASN : bond 0.00395 ( 11) link_NAG-ASN : angle 2.79601 ( 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 202 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8175 (mtm180) REVERT: A 457 HIS cc_start: 0.8445 (OUTLIER) cc_final: 0.8156 (m90) REVERT: B 340 LYS cc_start: 0.9282 (tttm) cc_final: 0.9051 (ttmt) REVERT: C 8 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8373 (tm-30) REVERT: C 40 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: C 85 ASP cc_start: 0.9158 (t0) cc_final: 0.8910 (t0) REVERT: C 164 TYR cc_start: 0.6090 (t80) cc_final: 0.5555 (m-80) REVERT: C 213 LYS cc_start: 0.6017 (tttt) cc_final: 0.5340 (mtpp) REVERT: C 414 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8016 (p) REVERT: C 529 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8422 (ptpp) REVERT: F 410 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8748 (p) REVERT: F 423 ASP cc_start: 0.9325 (m-30) cc_final: 0.9057 (m-30) REVERT: G 265 THR cc_start: 0.7905 (m) cc_final: 0.7444 (p) REVERT: G 372 ARG cc_start: 0.8220 (tmm-80) cc_final: 0.7354 (tmm-80) REVERT: G 378 ASP cc_start: 0.8461 (m-30) cc_final: 0.8039 (m-30) REVERT: G 403 GLU cc_start: 0.9051 (pm20) cc_final: 0.8306 (pm20) REVERT: G 433 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8358 (mmm) REVERT: G 437 GLU cc_start: 0.7865 (mp0) cc_final: 0.7479 (mp0) REVERT: G 445 GLN cc_start: 0.8825 (mt0) cc_final: 0.8555 (tp40) REVERT: D 21 ARG cc_start: 0.8523 (ttp-170) cc_final: 0.8132 (ttp-110) REVERT: D 48 GLU cc_start: 0.8715 (mt-10) cc_final: 0.7722 (mp0) REVERT: D 55 SER cc_start: 0.8468 (m) cc_final: 0.7618 (t) REVERT: D 105 ASP cc_start: 0.9197 (t0) cc_final: 0.8828 (t0) REVERT: D 126 GLU cc_start: 0.8813 (tt0) cc_final: 0.8377 (tp30) REVERT: D 127 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8947 (p) outliers start: 47 outliers final: 22 residues processed: 188 average time/residue: 0.6400 time to fit residues: 129.4975 Evaluate side-chains 179 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 416 ILE 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 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 307 CYS 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 466 GLU Chi-restraints excluded: chain G residue 362 ASN Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 433 MET 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: 4.9990 chunk 110 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 114 optimal weight: 0.0570 chunk 50 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 121 optimal weight: 6.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 436 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.106103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.077705 restraints weight = 24885.727| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.98 r_work: 0.2987 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12007 Z= 0.125 Angle : 0.692 12.115 16504 Z= 0.337 Chirality : 0.043 0.186 1995 Planarity : 0.004 0.042 2095 Dihedral : 6.135 53.800 1993 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.94 % Allowed : 20.39 % Favored : 76.68 % 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: -1.36 (0.21), residues: 1551 helix: -0.18 (0.58), residues: 83 sheet: 0.13 (0.21), residues: 623 loop : -1.86 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 17 TYR 0.008 0.001 TYR G 327 PHE 0.016 0.001 PHE C 75 TRP 0.012 0.001 TRP C 37 HIS 0.002 0.000 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00300 (11966) covalent geometry : angle 0.68020 (16406) SS BOND : bond 0.00228 ( 25) SS BOND : angle 0.91758 ( 50) hydrogen bonds : bond 0.02706 ( 329) hydrogen bonds : angle 4.54986 ( 942) link_BETA1-4 : bond 0.00580 ( 5) link_BETA1-4 : angle 1.94916 ( 15) link_NAG-ASN : bond 0.00298 ( 11) link_NAG-ASN : angle 2.51573 ( 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 196 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 457 HIS cc_start: 0.8438 (m170) cc_final: 0.8124 (m90) REVERT: B 340 LYS cc_start: 0.9263 (tttm) cc_final: 0.9043 (ttmt) REVERT: B 357 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8587 (pp20) REVERT: C 8 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8358 (tm-30) REVERT: C 40 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: C 85 ASP cc_start: 0.9166 (t0) cc_final: 0.8855 (t0) REVERT: C 164 TYR cc_start: 0.6164 (t80) cc_final: 0.5614 (m-80) REVERT: C 213 LYS cc_start: 0.6094 (tttt) cc_final: 0.5397 (mtpp) REVERT: C 414 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7951 (p) REVERT: C 529 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8412 (ptpp) REVERT: F 410 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8480 (t) REVERT: F 423 ASP cc_start: 0.9338 (m-30) cc_final: 0.9081 (m-30) REVERT: F 433 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8642 (ttp) REVERT: G 265 THR cc_start: 0.7600 (m) cc_final: 0.7182 (p) REVERT: G 372 ARG cc_start: 0.8107 (tmm-80) cc_final: 0.7281 (tmm-80) REVERT: G 378 ASP cc_start: 0.8580 (m-30) cc_final: 0.8243 (m-30) REVERT: G 403 GLU cc_start: 0.9000 (pm20) cc_final: 0.8138 (pm20) REVERT: G 437 GLU cc_start: 0.7804 (mp0) cc_final: 0.7530 (mp0) REVERT: D 21 ARG cc_start: 0.8513 (ttp-170) cc_final: 0.8245 (ttp-110) REVERT: D 48 GLU cc_start: 0.8639 (mt-10) cc_final: 0.7708 (mp0) REVERT: D 55 SER cc_start: 0.8484 (m) cc_final: 0.7387 (t) REVERT: D 105 ASP cc_start: 0.9122 (t0) cc_final: 0.8774 (t0) REVERT: D 126 GLU cc_start: 0.8838 (tt0) cc_final: 0.8408 (tp30) REVERT: D 127 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.8920 (p) outliers start: 35 outliers final: 17 residues processed: 187 average time/residue: 0.6260 time to fit residues: 126.1704 Evaluate side-chains 175 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 40 GLN 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 307 CYS 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 370 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 362 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 136 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.105288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.077114 restraints weight = 24919.130| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.97 r_work: 0.2978 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12007 Z= 0.146 Angle : 0.716 10.347 16504 Z= 0.349 Chirality : 0.043 0.182 1995 Planarity : 0.004 0.041 2095 Dihedral : 6.171 54.190 1993 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.19 % Allowed : 21.14 % Favored : 75.67 % 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: -1.35 (0.21), residues: 1551 helix: 0.07 (0.58), residues: 84 sheet: 0.09 (0.21), residues: 621 loop : -1.84 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 17 TYR 0.011 0.001 TYR C 55 PHE 0.017 0.001 PHE C 75 TRP 0.010 0.001 TRP C 37 HIS 0.003 0.001 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00352 (11966) covalent geometry : angle 0.70545 (16406) SS BOND : bond 0.00243 ( 25) SS BOND : angle 0.91537 ( 50) hydrogen bonds : bond 0.02870 ( 329) hydrogen bonds : angle 4.54073 ( 942) link_BETA1-4 : bond 0.00353 ( 5) link_BETA1-4 : angle 1.77823 ( 15) link_NAG-ASN : bond 0.00304 ( 11) link_NAG-ASN : angle 2.50187 ( 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 191 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.460 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8149 (mtm180) REVERT: B 340 LYS cc_start: 0.9257 (tttm) cc_final: 0.9046 (ttmt) REVERT: C 8 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8406 (tm-30) REVERT: C 40 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8093 (tm-30) REVERT: C 85 ASP cc_start: 0.9174 (t0) cc_final: 0.8868 (t0) REVERT: C 164 TYR cc_start: 0.6216 (t80) cc_final: 0.5633 (m-10) REVERT: C 213 LYS cc_start: 0.6095 (tttt) cc_final: 0.5407 (mtpp) REVERT: C 414 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.7993 (p) REVERT: C 529 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8417 (ptpp) REVERT: F 410 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8506 (t) REVERT: F 423 ASP cc_start: 0.9325 (m-30) cc_final: 0.9103 (m-30) REVERT: F 433 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8647 (ttp) REVERT: G 265 THR cc_start: 0.7483 (m) cc_final: 0.6995 (p) REVERT: G 403 GLU cc_start: 0.8946 (pm20) cc_final: 0.8102 (pm20) REVERT: G 437 GLU cc_start: 0.7851 (mp0) cc_final: 0.7578 (mp0) REVERT: G 445 GLN cc_start: 0.8817 (mt0) cc_final: 0.8481 (tt0) REVERT: D 21 ARG cc_start: 0.8508 (ttp-170) cc_final: 0.8307 (ttp-110) REVERT: D 48 GLU cc_start: 0.8659 (mt-10) cc_final: 0.7690 (mp0) REVERT: D 55 SER cc_start: 0.8454 (m) cc_final: 0.7524 (t) REVERT: D 105 ASP cc_start: 0.9134 (t0) cc_final: 0.8798 (t0) REVERT: D 126 GLU cc_start: 0.8827 (tt0) cc_final: 0.8382 (tp30) REVERT: D 127 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.8909 (p) outliers start: 38 outliers final: 21 residues processed: 182 average time/residue: 0.6370 time to fit residues: 125.0672 Evaluate side-chains 179 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 304 VAL 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 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 307 CYS 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 370 LEU Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 362 ASN Chi-restraints excluded: chain G residue 410 THR 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: 0.8980 chunk 49 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 0.0060 chunk 64 optimal weight: 0.0570 chunk 151 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 457 HIS C 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.116393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088902 restraints weight = 23985.926| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.93 r_work: 0.3225 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12007 Z= 0.122 Angle : 0.720 17.667 16504 Z= 0.347 Chirality : 0.043 0.177 1995 Planarity : 0.004 0.044 2095 Dihedral : 5.967 53.392 1993 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.60 % Allowed : 21.98 % Favored : 75.42 % 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: -1.24 (0.21), residues: 1551 helix: 0.26 (0.60), residues: 84 sheet: 0.10 (0.21), residues: 642 loop : -1.75 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 382 TYR 0.009 0.001 TYR C 55 PHE 0.015 0.001 PHE C 75 TRP 0.014 0.001 TRP G 315 HIS 0.001 0.000 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00297 (11966) covalent geometry : angle 0.71194 (16406) SS BOND : bond 0.00211 ( 25) SS BOND : angle 0.81145 ( 50) hydrogen bonds : bond 0.02546 ( 329) hydrogen bonds : angle 4.36785 ( 942) link_BETA1-4 : bond 0.00407 ( 5) link_BETA1-4 : angle 1.66222 ( 15) link_NAG-ASN : bond 0.00312 ( 11) link_NAG-ASN : angle 2.30110 ( 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 187 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8033 (mtm180) REVERT: B 340 LYS cc_start: 0.9224 (tttm) cc_final: 0.8994 (ttmt) REVERT: B 385 GLN cc_start: 0.9173 (tt0) cc_final: 0.8916 (tt0) REVERT: C 8 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8229 (tm-30) REVERT: C 40 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: C 85 ASP cc_start: 0.9168 (t0) cc_final: 0.8906 (t0) REVERT: C 164 TYR cc_start: 0.6191 (t80) cc_final: 0.5582 (m-80) REVERT: C 174 ARG cc_start: 0.6191 (ptm-80) cc_final: 0.5984 (ptm-80) REVERT: C 213 LYS cc_start: 0.5707 (tttt) cc_final: 0.5087 (mtpp) REVERT: C 414 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7796 (p) REVERT: C 529 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8228 (ptpp) REVERT: F 410 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8727 (p) REVERT: F 423 ASP cc_start: 0.9305 (m-30) cc_final: 0.9088 (m-30) REVERT: F 426 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8738 (ptpp) REVERT: F 445 GLN cc_start: 0.9496 (pt0) cc_final: 0.9093 (tt0) REVERT: G 265 THR cc_start: 0.7341 (m) cc_final: 0.6839 (p) REVERT: G 403 GLU cc_start: 0.8786 (pm20) cc_final: 0.7979 (pm20) REVERT: G 437 GLU cc_start: 0.7684 (mp0) cc_final: 0.7438 (mp0) REVERT: G 445 GLN cc_start: 0.8871 (mt0) cc_final: 0.8584 (tp40) REVERT: D 21 ARG cc_start: 0.8319 (ttp-170) cc_final: 0.8097 (ttp80) REVERT: D 48 GLU cc_start: 0.8669 (mt-10) cc_final: 0.7625 (mp0) REVERT: D 55 SER cc_start: 0.8324 (m) cc_final: 0.7169 (t) REVERT: D 105 ASP cc_start: 0.9042 (t0) cc_final: 0.8634 (t0) REVERT: D 124 MET cc_start: 0.9067 (mmm) cc_final: 0.8851 (tpp) REVERT: D 126 GLU cc_start: 0.8729 (tt0) cc_final: 0.8282 (tp30) REVERT: D 127 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8859 (p) outliers start: 31 outliers final: 20 residues processed: 179 average time/residue: 0.5951 time to fit residues: 115.0293 Evaluate side-chains 174 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 437 GLU Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 40 GLN 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 307 CYS 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 410 THR Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 362 ASN 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: 7.9990 chunk 65 optimal weight: 0.0670 chunk 136 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 457 HIS B 362 ASN C 266 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.115485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088005 restraints weight = 24295.371| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.97 r_work: 0.3211 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12007 Z= 0.138 Angle : 0.717 13.132 16504 Z= 0.350 Chirality : 0.043 0.194 1995 Planarity : 0.004 0.043 2095 Dihedral : 5.992 53.816 1993 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.60 % Allowed : 21.98 % Favored : 75.42 % 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: -1.22 (0.21), residues: 1551 helix: 0.37 (0.61), residues: 84 sheet: 0.12 (0.21), residues: 644 loop : -1.76 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 418 TYR 0.011 0.001 TYR C 55 PHE 0.016 0.001 PHE C 75 TRP 0.010 0.001 TRP C 37 HIS 0.009 0.001 HIS A 457 Details of bonding type rmsd covalent geometry : bond 0.00335 (11966) covalent geometry : angle 0.70874 (16406) SS BOND : bond 0.00231 ( 25) SS BOND : angle 0.82766 ( 50) hydrogen bonds : bond 0.02693 ( 329) hydrogen bonds : angle 4.40236 ( 942) link_BETA1-4 : bond 0.00368 ( 5) link_BETA1-4 : angle 1.60083 ( 15) link_NAG-ASN : bond 0.00281 ( 11) link_NAG-ASN : angle 2.33966 ( 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 186 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8026 (mtm180) REVERT: B 340 LYS cc_start: 0.9220 (tttm) cc_final: 0.9000 (ttmt) REVERT: B 385 GLN cc_start: 0.9175 (tt0) cc_final: 0.8907 (tt0) REVERT: C 8 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8256 (tm-30) REVERT: C 40 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: C 85 ASP cc_start: 0.9174 (t0) cc_final: 0.8851 (t0) REVERT: C 164 TYR cc_start: 0.6231 (t80) cc_final: 0.5550 (m-10) REVERT: C 174 ARG cc_start: 0.6201 (ptm-80) cc_final: 0.5967 (ptm-80) REVERT: C 213 LYS cc_start: 0.5679 (tttt) cc_final: 0.5057 (mtpp) REVERT: C 414 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7841 (p) REVERT: C 529 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8261 (ptpp) REVERT: F 410 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8758 (p) REVERT: F 423 ASP cc_start: 0.9298 (m-30) cc_final: 0.9079 (m-30) REVERT: F 426 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8699 (ptpp) REVERT: F 433 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8628 (ttp) REVERT: G 265 THR cc_start: 0.7359 (m) cc_final: 0.6852 (p) REVERT: G 403 GLU cc_start: 0.8811 (pm20) cc_final: 0.7852 (pm20) REVERT: G 437 GLU cc_start: 0.7743 (mp0) cc_final: 0.7449 (mp0) REVERT: G 445 GLN cc_start: 0.8863 (mt0) cc_final: 0.8627 (tp40) REVERT: D 21 ARG cc_start: 0.8342 (ttp-170) cc_final: 0.8122 (ttp80) REVERT: D 48 GLU cc_start: 0.8686 (mt-10) cc_final: 0.7602 (mp0) REVERT: D 55 SER cc_start: 0.8313 (m) cc_final: 0.7366 (t) REVERT: D 105 ASP cc_start: 0.9065 (t0) cc_final: 0.8666 (t0) REVERT: D 124 MET cc_start: 0.9086 (mmm) cc_final: 0.8813 (tpp) REVERT: D 126 GLU cc_start: 0.8710 (tt0) cc_final: 0.8273 (tp30) REVERT: D 127 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8863 (p) outliers start: 31 outliers final: 20 residues processed: 178 average time/residue: 0.5507 time to fit residues: 105.7018 Evaluate side-chains 181 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 437 GLU Chi-restraints excluded: chain A residue 457 HIS 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 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 307 CYS 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 410 THR Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 410 THR 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: 2.9990 chunk 17 optimal weight: 0.8980 chunk 135 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 109 optimal weight: 0.0270 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN A 457 HIS C 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.115451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088072 restraints weight = 24246.067| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.96 r_work: 0.3214 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12007 Z= 0.135 Angle : 0.724 14.682 16504 Z= 0.351 Chirality : 0.043 0.189 1995 Planarity : 0.004 0.042 2095 Dihedral : 5.969 53.651 1993 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.94 % Allowed : 21.39 % Favored : 75.67 % 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: -1.19 (0.21), residues: 1551 helix: 0.40 (0.61), residues: 84 sheet: 0.14 (0.21), residues: 644 loop : -1.75 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 418 TYR 0.011 0.001 TYR C 55 PHE 0.016 0.001 PHE C 75 TRP 0.011 0.001 TRP C 37 HIS 0.002 0.000 HIS D 64 Details of bonding type rmsd covalent geometry : bond 0.00332 (11966) covalent geometry : angle 0.71535 (16406) SS BOND : bond 0.00229 ( 25) SS BOND : angle 0.81726 ( 50) hydrogen bonds : bond 0.02674 ( 329) hydrogen bonds : angle 4.38724 ( 942) link_BETA1-4 : bond 0.00388 ( 5) link_BETA1-4 : angle 1.56095 ( 15) link_NAG-ASN : bond 0.00279 ( 11) link_NAG-ASN : angle 2.30561 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4550.22 seconds wall clock time: 78 minutes 1.87 seconds (4681.87 seconds total)