Starting phenix.real_space_refine on Wed Jul 30 01:20:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ue7_20749/07_2025/6ue7_20749.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ue7_20749/07_2025/6ue7_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_20749/07_2025/6ue7_20749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ue7_20749/07_2025/6ue7_20749.map" model { file = "/net/cci-nas-00/data/ceres_data/6ue7_20749/07_2025/6ue7_20749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ue7_20749/07_2025/6ue7_20749.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} 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: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} 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: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} 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, 'ASN:plan1': 1, 'ASP:plan': 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: 8.45, per 1000 atoms: 0.72 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: 3.21 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.91 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: 4.31 Time building geometry restraints manager: 3.82 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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.710 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.670 ------------------------------------------------------------------------------- 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 : 2.95 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.002 TRP C 366 HIS 0.005 0.001 HIS G 436 PHE 0.040 0.003 PHE C 136 TYR 0.020 0.002 TYR B 327 ARG 0.005 0.001 ARG A 382 Details of bonding type rmsd link_NAG-ASN : bond 0.00639 ( 11) link_NAG-ASN : angle 4.91727 ( 33) link_BETA1-4 : bond 0.01036 ( 5) link_BETA1-4 : angle 4.28985 ( 15) hydrogen bonds : bond 0.21842 ( 329) hydrogen bonds : angle 7.20593 ( 942) SS BOND : bond 0.00702 ( 25) SS BOND : angle 1.74149 ( 50) covalent geometry : bond 0.00699 (11966) covalent geometry : angle 1.05294 (16406) *********************** 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 : 1.442 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: 0.7667 (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 345 PHE cc_start: 0.7317 (m-80) cc_final: 0.7023 (m-80) outliers start: 6 outliers final: 2 residues processed: 257 average time/residue: 1.2761 time to fit residues: 353.8505 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 : 1.258 ------------------------------------------------------------------------------- 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 131 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 0.0170 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 133 ASN C 218 GLN C 412 GLN C 426 ASN ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 457 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.112111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082200 restraints weight = 24309.031| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 4.00 r_work: 0.3051 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12007 Z= 0.135 Angle : 0.748 12.110 16504 Z= 0.366 Chirality : 0.044 0.237 1995 Planarity : 0.006 0.050 2095 Dihedral : 8.602 65.396 1995 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.27 % Allowed : 16.53 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.20), residues: 1551 helix: -2.68 (0.45), residues: 85 sheet: -0.42 (0.21), residues: 626 loop : -2.41 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 37 HIS 0.002 0.001 HIS A 243 PHE 0.017 0.001 PHE G 321 TYR 0.011 0.001 TYR G 327 ARG 0.009 0.001 ARG C 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 11) link_NAG-ASN : angle 3.53121 ( 33) link_BETA1-4 : bond 0.00630 ( 5) link_BETA1-4 : angle 3.10997 ( 15) hydrogen bonds : bond 0.03175 ( 329) hydrogen bonds : angle 5.25322 ( 942) SS BOND : bond 0.00335 ( 25) SS BOND : angle 0.87537 ( 50) covalent geometry : bond 0.00307 (11966) covalent geometry : angle 0.72560 (16406) *********************** 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 232 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 SER cc_start: 0.8995 (t) cc_final: 0.8393 (p) REVERT: A 382 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7753 (mtp85) REVERT: A 385 GLN cc_start: 0.9221 (tt0) cc_final: 0.8962 (tt0) REVERT: A 389 GLU cc_start: 0.8472 (tt0) cc_final: 0.7861 (tt0) REVERT: A 449 ASP cc_start: 0.9218 (p0) cc_final: 0.8779 (p0) REVERT: C 185 PHE cc_start: 0.6923 (p90) cc_final: 0.6503 (p90) REVERT: C 213 LYS cc_start: 0.5290 (tttt) cc_final: 0.4716 (mtpp) REVERT: F 449 ASP cc_start: 0.9189 (p0) cc_final: 0.8977 (p0) REVERT: G 315 TRP cc_start: 0.5859 (m100) cc_final: 0.5334 (p-90) REVERT: G 345 PHE cc_start: 0.7397 (m-80) cc_final: 0.6801 (m-80) REVERT: D 5 ARG cc_start: 0.6529 (mmp80) cc_final: 0.6314 (mpp80) REVERT: D 82 GLN cc_start: 0.8821 (mp10) cc_final: 0.8599 (pm20) REVERT: D 105 ASP cc_start: 0.9136 (t0) cc_final: 0.8873 (t0) REVERT: D 126 GLU cc_start: 0.8656 (tt0) cc_final: 0.8446 (tt0) outliers start: 39 outliers final: 11 residues processed: 214 average time/residue: 1.2152 time to fit residues: 281.4840 Evaluate side-chains 172 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 121 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 337 SER 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 454 LYS Chi-restraints excluded: chain G residue 410 THR 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 117 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 436 HIS ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN G 385 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.104821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.075841 restraints weight = 24834.958| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.99 r_work: 0.2951 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12007 Z= 0.247 Angle : 0.795 11.209 16504 Z= 0.393 Chirality : 0.046 0.212 1995 Planarity : 0.005 0.050 2095 Dihedral : 7.384 54.759 1993 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 4.95 % Allowed : 16.36 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.20), residues: 1551 helix: -1.44 (0.52), residues: 83 sheet: -0.38 (0.21), residues: 628 loop : -2.28 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 366 HIS 0.007 0.001 HIS D 64 PHE 0.022 0.002 PHE C 75 TYR 0.021 0.002 TYR C 154 ARG 0.006 0.001 ARG C 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 11) link_NAG-ASN : angle 3.50601 ( 33) link_BETA1-4 : bond 0.00535 ( 5) link_BETA1-4 : angle 3.12336 ( 15) hydrogen bonds : bond 0.04245 ( 329) hydrogen bonds : angle 5.12257 ( 942) SS BOND : bond 0.00424 ( 25) SS BOND : angle 1.24810 ( 50) covalent geometry : bond 0.00580 (11966) covalent geometry : angle 0.77299 (16406) *********************** 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 226 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 167 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 385 GLN cc_start: 0.9225 (tt0) cc_final: 0.8990 (tt0) REVERT: A 449 ASP cc_start: 0.9306 (p0) cc_final: 0.8929 (p0) REVERT: B 466 GLU cc_start: 0.8442 (pm20) cc_final: 0.8197 (mp0) REVERT: C 184 LEU cc_start: 0.4609 (mt) cc_final: 0.4157 (mp) REVERT: C 185 PHE cc_start: 0.6907 (p90) cc_final: 0.6059 (p90) REVERT: C 213 LYS cc_start: 0.5816 (tttt) cc_final: 0.5193 (mtpp) REVERT: C 414 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8099 (p) REVERT: F 378 ASP cc_start: 0.8279 (p0) cc_final: 0.7984 (p0) REVERT: F 423 ASP cc_start: 0.9265 (m-30) cc_final: 0.9057 (m-30) REVERT: G 265 THR cc_start: 0.8035 (m) cc_final: 0.7544 (p) REVERT: G 345 PHE cc_start: 0.7623 (m-80) cc_final: 0.7298 (m-80) REVERT: G 370 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8293 (tp) REVERT: G 372 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8191 (tmm-80) REVERT: D 48 GLU cc_start: 0.8614 (mt-10) cc_final: 0.7844 (mp0) REVERT: D 82 GLN cc_start: 0.9043 (mp10) cc_final: 0.8760 (pm20) REVERT: D 105 ASP cc_start: 0.9221 (t0) cc_final: 0.8948 (t0) REVERT: D 126 GLU cc_start: 0.8753 (tt0) cc_final: 0.8376 (tp30) REVERT: D 127 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.8950 (p) outliers start: 59 outliers final: 29 residues processed: 204 average time/residue: 1.3284 time to fit residues: 295.5813 Evaluate side-chains 184 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 73 ASP 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 135 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 HIS D 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.103542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.075386 restraints weight = 24741.327| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.93 r_work: 0.2945 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12007 Z= 0.215 Angle : 0.766 12.786 16504 Z= 0.375 Chirality : 0.045 0.210 1995 Planarity : 0.005 0.043 2095 Dihedral : 7.067 54.218 1993 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 4.36 % Allowed : 17.95 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.21), residues: 1551 helix: -1.09 (0.53), residues: 88 sheet: -0.29 (0.21), residues: 631 loop : -2.21 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 37 HIS 0.005 0.001 HIS D 64 PHE 0.029 0.001 PHE C 136 TYR 0.018 0.001 TYR C 154 ARG 0.004 0.000 ARG G 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 11) link_NAG-ASN : angle 3.28189 ( 33) link_BETA1-4 : bond 0.00277 ( 5) link_BETA1-4 : angle 2.75462 ( 15) hydrogen bonds : bond 0.03519 ( 329) hydrogen bonds : angle 4.91604 ( 942) SS BOND : bond 0.00452 ( 25) SS BOND : angle 1.45532 ( 50) covalent geometry : bond 0.00508 (11966) covalent geometry : angle 0.74544 (16406) *********************** 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 216 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 164 time to evaluate : 1.443 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8033 (mtm180) REVERT: B 385 GLN cc_start: 0.9257 (tt0) cc_final: 0.8935 (tt0) REVERT: C 185 PHE cc_start: 0.6472 (p90) cc_final: 0.5925 (p90) REVERT: C 213 LYS cc_start: 0.5882 (tttt) cc_final: 0.5285 (mtpp) REVERT: C 414 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8121 (p) REVERT: F 378 ASP cc_start: 0.8363 (p0) cc_final: 0.8117 (p0) REVERT: F 423 ASP cc_start: 0.9322 (m-30) cc_final: 0.9072 (m-30) REVERT: F 433 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8546 (ttp) REVERT: G 265 THR cc_start: 0.7887 (m) cc_final: 0.7395 (p) REVERT: G 370 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8285 (tp) REVERT: G 372 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8183 (ttp80) REVERT: G 403 GLU cc_start: 0.8873 (pm20) cc_final: 0.8034 (pm20) REVERT: G 437 GLU cc_start: 0.7545 (mp0) cc_final: 0.7310 (mp0) REVERT: D 48 GLU cc_start: 0.8792 (mt-10) cc_final: 0.7961 (mp0) REVERT: D 70 LYS cc_start: 0.9466 (pttt) cc_final: 0.9260 (ptpp) REVERT: D 82 GLN cc_start: 0.9128 (mp10) cc_final: 0.8858 (pm20) REVERT: D 105 ASP cc_start: 0.9274 (t0) cc_final: 0.8954 (t0) REVERT: D 126 GLU cc_start: 0.8838 (tt0) cc_final: 0.8391 (tp30) REVERT: D 127 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.8884 (p) outliers start: 52 outliers final: 25 residues processed: 198 average time/residue: 1.9941 time to fit residues: 425.3394 Evaluate side-chains 184 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 3.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 164 TYR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 247 ASN 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 337 SER Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 349 VAL Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 114 optimal weight: 0.3980 chunk 36 optimal weight: 0.0170 chunk 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 0.0270 chunk 85 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.106500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078188 restraints weight = 24887.522| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.95 r_work: 0.3011 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12007 Z= 0.118 Angle : 0.693 10.414 16504 Z= 0.338 Chirality : 0.043 0.200 1995 Planarity : 0.004 0.048 2095 Dihedral : 6.514 54.143 1993 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.78 % Allowed : 18.62 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.21), residues: 1551 helix: -0.92 (0.53), residues: 89 sheet: -0.05 (0.21), residues: 619 loop : -2.03 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 37 HIS 0.001 0.000 HIS D 64 PHE 0.017 0.001 PHE C 75 TYR 0.015 0.001 TYR C 164 ARG 0.004 0.000 ARG D 17 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 11) link_NAG-ASN : angle 2.87036 ( 33) link_BETA1-4 : bond 0.00413 ( 5) link_BETA1-4 : angle 2.40070 ( 15) hydrogen bonds : bond 0.02743 ( 329) hydrogen bonds : angle 4.66195 ( 942) SS BOND : bond 0.00395 ( 25) SS BOND : angle 1.12449 ( 50) covalent geometry : bond 0.00280 (11966) covalent geometry : angle 0.67663 (16406) *********************** 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: 45 poor density : 165 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8135 (mtm180) REVERT: A 389 GLU cc_start: 0.8734 (tt0) cc_final: 0.8393 (tt0) REVERT: B 340 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9104 (ttmt) REVERT: B 357 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8579 (pp20) REVERT: B 385 GLN cc_start: 0.9241 (tt0) cc_final: 0.8950 (tt0) REVERT: C 213 LYS cc_start: 0.5943 (tttt) cc_final: 0.5270 (mtpp) REVERT: C 366 TRP cc_start: 0.9152 (OUTLIER) cc_final: 0.8643 (t60) REVERT: C 414 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8030 (p) REVERT: F 378 ASP cc_start: 0.8270 (p0) cc_final: 0.8032 (p0) REVERT: F 410 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8728 (p) REVERT: F 423 ASP cc_start: 0.9319 (m-30) cc_final: 0.9059 (m-30) REVERT: G 265 THR cc_start: 0.7872 (m) cc_final: 0.7438 (p) REVERT: G 370 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8118 (tp) REVERT: G 372 ARG cc_start: 0.8415 (ttp80) cc_final: 0.7813 (tmm-80) REVERT: G 403 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: D 48 GLU cc_start: 0.8683 (mt-10) cc_final: 0.7717 (mp0) REVERT: D 55 SER cc_start: 0.8313 (m) cc_final: 0.7291 (t) REVERT: D 82 GLN cc_start: 0.9058 (mp10) cc_final: 0.8808 (pm20) REVERT: D 105 ASP cc_start: 0.9193 (t0) cc_final: 0.8804 (t0) REVERT: D 126 GLU cc_start: 0.8798 (tt0) cc_final: 0.8329 (tp30) REVERT: D 127 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8920 (p) outliers start: 45 outliers final: 18 residues processed: 194 average time/residue: 1.2430 time to fit residues: 260.4668 Evaluate side-chains 180 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS 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 410 THR Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 8 LEU 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 152 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 73 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 142 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 155 optimal weight: 0.0020 chunk 3 optimal weight: 4.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** 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 = 0.3565 r_free = 0.3565 target = 0.105143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.076977 restraints weight = 25006.955| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.98 r_work: 0.2978 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12007 Z= 0.128 Angle : 0.703 13.389 16504 Z= 0.341 Chirality : 0.043 0.192 1995 Planarity : 0.004 0.044 2095 Dihedral : 6.295 54.413 1993 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.70 % Allowed : 18.71 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.21), residues: 1551 helix: -0.51 (0.55), residues: 83 sheet: 0.01 (0.21), residues: 622 loop : -1.92 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 37 HIS 0.003 0.001 HIS G 436 PHE 0.017 0.001 PHE C 75 TYR 0.017 0.001 TYR B 327 ARG 0.003 0.000 ARG A 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 11) link_NAG-ASN : angle 2.73931 ( 33) link_BETA1-4 : bond 0.00379 ( 5) link_BETA1-4 : angle 2.15610 ( 15) hydrogen bonds : bond 0.02726 ( 329) hydrogen bonds : angle 4.56742 ( 942) SS BOND : bond 0.00259 ( 25) SS BOND : angle 0.92701 ( 50) covalent geometry : bond 0.00307 (11966) covalent geometry : angle 0.68889 (16406) *********************** 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 214 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8000 (mtm180) REVERT: A 389 GLU cc_start: 0.8707 (tt0) cc_final: 0.8150 (tp30) REVERT: B 340 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9092 (ttmt) REVERT: B 357 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8587 (pp20) REVERT: B 385 GLN cc_start: 0.9238 (tt0) cc_final: 0.8922 (tt0) REVERT: C 9 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8956 (mm-30) REVERT: C 85 ASP cc_start: 0.9067 (m-30) cc_final: 0.8820 (t0) REVERT: C 213 LYS cc_start: 0.5927 (tttt) cc_final: 0.5248 (mtpp) REVERT: C 366 TRP cc_start: 0.9151 (OUTLIER) cc_final: 0.8652 (t60) REVERT: C 414 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8001 (p) REVERT: F 410 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8499 (t) REVERT: F 423 ASP cc_start: 0.9335 (m-30) cc_final: 0.9099 (m-30) REVERT: G 265 THR cc_start: 0.7582 (m) cc_final: 0.7153 (p) REVERT: G 370 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8165 (tp) REVERT: G 372 ARG cc_start: 0.8476 (ttp80) cc_final: 0.7850 (tmm-80) REVERT: G 403 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: D 48 GLU cc_start: 0.8736 (mt-10) cc_final: 0.7694 (mp0) REVERT: D 55 SER cc_start: 0.8442 (m) cc_final: 0.7479 (t) REVERT: D 82 GLN cc_start: 0.9055 (mp10) cc_final: 0.8809 (pm20) REVERT: D 105 ASP cc_start: 0.9137 (t0) cc_final: 0.8769 (t0) REVERT: D 126 GLU cc_start: 0.8850 (tt0) cc_final: 0.8395 (tp30) REVERT: D 127 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8908 (p) outliers start: 56 outliers final: 30 residues processed: 199 average time/residue: 1.2789 time to fit residues: 276.2937 Evaluate side-chains 193 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 356 SER 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 324 THR Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 397 THR 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 333 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 311 CYS 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 415 SER 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 370 LEU Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 136 optimal weight: 0.0770 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.103430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.075515 restraints weight = 25153.989| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.97 r_work: 0.2955 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12007 Z= 0.177 Angle : 0.727 10.181 16504 Z= 0.358 Chirality : 0.044 0.220 1995 Planarity : 0.004 0.045 2095 Dihedral : 6.415 54.514 1993 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 4.45 % Allowed : 19.21 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.21), residues: 1551 helix: -0.30 (0.56), residues: 84 sheet: 0.00 (0.21), residues: 623 loop : -1.90 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 37 HIS 0.005 0.001 HIS G 436 PHE 0.018 0.001 PHE C 75 TYR 0.013 0.001 TYR C 154 ARG 0.004 0.000 ARG C 43 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 11) link_NAG-ASN : angle 2.77673 ( 33) link_BETA1-4 : bond 0.00363 ( 5) link_BETA1-4 : angle 1.97110 ( 15) hydrogen bonds : bond 0.03126 ( 329) hydrogen bonds : angle 4.66729 ( 942) SS BOND : bond 0.00274 ( 25) SS BOND : angle 1.00973 ( 50) covalent geometry : bond 0.00422 (11966) covalent geometry : angle 0.71391 (16406) *********************** 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 208 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 155 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 363 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8189 (mm-30) REVERT: A 382 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7931 (mtm180) REVERT: A 389 GLU cc_start: 0.8711 (tt0) cc_final: 0.8105 (tp30) REVERT: B 340 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9120 (ttmm) REVERT: B 357 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8578 (pp20) REVERT: B 385 GLN cc_start: 0.9250 (tt0) cc_final: 0.8922 (tt0) REVERT: C 8 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8104 (tp30) REVERT: C 40 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: C 53 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8837 (pp20) REVERT: C 85 ASP cc_start: 0.9075 (m-30) cc_final: 0.8850 (t0) REVERT: C 213 LYS cc_start: 0.6034 (tttt) cc_final: 0.5327 (mtpp) REVERT: C 414 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8078 (p) REVERT: F 410 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8772 (p) REVERT: F 423 ASP cc_start: 0.9336 (m-30) cc_final: 0.9119 (m-30) REVERT: F 426 LYS cc_start: 0.9141 (ttpp) cc_final: 0.8840 (ptpp) REVERT: G 250 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.4501 (ptm-80) REVERT: G 265 THR cc_start: 0.7576 (m) cc_final: 0.7142 (p) REVERT: G 403 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: D 48 GLU cc_start: 0.8804 (mt-10) cc_final: 0.7791 (mp0) REVERT: D 55 SER cc_start: 0.8512 (m) cc_final: 0.7563 (t) REVERT: D 82 GLN cc_start: 0.9116 (mp10) cc_final: 0.8832 (pm20) REVERT: D 105 ASP cc_start: 0.9196 (t0) cc_final: 0.8839 (t0) REVERT: D 123 LYS cc_start: 0.8297 (mmmm) cc_final: 0.7599 (mmtm) REVERT: D 126 GLU cc_start: 0.8834 (tt0) cc_final: 0.8390 (tp30) REVERT: D 127 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8904 (p) outliers start: 53 outliers final: 33 residues processed: 192 average time/residue: 1.6482 time to fit residues: 342.9970 Evaluate side-chains 191 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 356 SER 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 324 THR Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 357 GLU 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 333 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 311 CYS 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 415 SER Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 250 ARG Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 362 ASN Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 ASN ** 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 = 0.3538 r_free = 0.3538 target = 0.103181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.075443 restraints weight = 25051.399| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 3.96 r_work: 0.2950 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12007 Z= 0.169 Angle : 0.744 13.889 16504 Z= 0.363 Chirality : 0.044 0.208 1995 Planarity : 0.004 0.044 2095 Dihedral : 6.415 54.064 1993 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.70 % Allowed : 19.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.21), residues: 1551 helix: -0.08 (0.57), residues: 84 sheet: -0.01 (0.21), residues: 623 loop : -1.84 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 37 HIS 0.005 0.001 HIS G 436 PHE 0.018 0.001 PHE C 75 TYR 0.011 0.001 TYR C 154 ARG 0.010 0.000 ARG G 372 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 11) link_NAG-ASN : angle 2.67924 ( 33) link_BETA1-4 : bond 0.00360 ( 5) link_BETA1-4 : angle 1.84973 ( 15) hydrogen bonds : bond 0.03078 ( 329) hydrogen bonds : angle 4.60927 ( 942) SS BOND : bond 0.00268 ( 25) SS BOND : angle 0.97820 ( 50) covalent geometry : bond 0.00406 (11966) covalent geometry : angle 0.73257 (16406) *********************** 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 207 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 151 time to evaluate : 1.433 Fit side-chains revert: symmetry clash REVERT: A 363 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8199 (mm-30) REVERT: A 382 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7917 (mtm180) REVERT: A 389 GLU cc_start: 0.8726 (tt0) cc_final: 0.8099 (tp30) REVERT: A 457 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.8088 (m90) REVERT: B 340 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9102 (ttmm) REVERT: B 357 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8578 (pp20) REVERT: B 385 GLN cc_start: 0.9242 (tt0) cc_final: 0.8896 (tt0) REVERT: C 40 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: C 85 ASP cc_start: 0.9080 (m-30) cc_final: 0.8841 (t0) REVERT: C 174 ARG cc_start: 0.6702 (ptm-80) cc_final: 0.6437 (ptm-80) REVERT: C 414 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8085 (p) REVERT: F 410 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8768 (p) REVERT: F 423 ASP cc_start: 0.9331 (m-30) cc_final: 0.9101 (m-30) REVERT: G 250 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.4550 (ptm-80) REVERT: G 265 THR cc_start: 0.7493 (m) cc_final: 0.7005 (p) REVERT: G 403 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: D 48 GLU cc_start: 0.8838 (mt-10) cc_final: 0.7822 (mp0) REVERT: D 55 SER cc_start: 0.8538 (m) cc_final: 0.7598 (t) REVERT: D 82 GLN cc_start: 0.9126 (mp10) cc_final: 0.8845 (pm20) REVERT: D 105 ASP cc_start: 0.9201 (t0) cc_final: 0.8851 (t0) REVERT: D 123 LYS cc_start: 0.8331 (mmmm) cc_final: 0.7719 (mmtm) REVERT: D 126 GLU cc_start: 0.8850 (tt0) cc_final: 0.8394 (tp30) REVERT: D 127 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8879 (p) outliers start: 56 outliers final: 36 residues processed: 190 average time/residue: 1.2765 time to fit residues: 262.8258 Evaluate side-chains 195 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 149 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 356 SER 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 324 THR Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 164 TYR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 311 CYS 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 415 SER Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 250 ARG 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 397 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 148 optimal weight: 0.0370 chunk 11 optimal weight: 0.0050 chunk 29 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.7274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.113751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.086640 restraints weight = 24432.236| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.94 r_work: 0.3194 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4680 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= 0.140 Angle : 0.731 11.088 16504 Z= 0.359 Chirality : 0.043 0.234 1995 Planarity : 0.004 0.049 2095 Dihedral : 6.300 53.814 1993 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.94 % Allowed : 20.89 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.21), residues: 1551 helix: 0.09 (0.58), residues: 84 sheet: 0.04 (0.21), residues: 622 loop : -1.79 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 37 HIS 0.004 0.001 HIS G 436 PHE 0.017 0.001 PHE C 75 TYR 0.025 0.001 TYR C 164 ARG 0.009 0.001 ARG G 372 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 11) link_NAG-ASN : angle 2.54374 ( 33) link_BETA1-4 : bond 0.00366 ( 5) link_BETA1-4 : angle 1.75847 ( 15) hydrogen bonds : bond 0.02847 ( 329) hydrogen bonds : angle 4.52790 ( 942) SS BOND : bond 0.00243 ( 25) SS BOND : angle 0.87309 ( 50) covalent geometry : bond 0.00339 (11966) covalent geometry : angle 0.72091 (16406) *********************** 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 200 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7853 (mtm180) REVERT: A 389 GLU cc_start: 0.8775 (tt0) cc_final: 0.8133 (tp30) REVERT: A 457 HIS cc_start: 0.8381 (m170) cc_final: 0.8029 (m90) REVERT: B 340 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9048 (ttmm) REVERT: B 357 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8578 (pp20) REVERT: B 385 GLN cc_start: 0.9179 (tt0) cc_final: 0.8806 (tt0) REVERT: C 40 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: C 85 ASP cc_start: 0.9155 (m-30) cc_final: 0.8846 (t0) REVERT: C 174 ARG cc_start: 0.6601 (ptm-80) cc_final: 0.6333 (ptm-80) REVERT: C 213 LYS cc_start: 0.4664 (tttm) cc_final: 0.4122 (mttm) REVERT: C 414 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7925 (p) REVERT: F 410 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8774 (p) REVERT: F 423 ASP cc_start: 0.9312 (m-30) cc_final: 0.9097 (m-30) REVERT: F 426 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8706 (ptpp) REVERT: G 265 THR cc_start: 0.7361 (m) cc_final: 0.6875 (p) REVERT: G 403 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: G 445 GLN cc_start: 0.8726 (tp40) cc_final: 0.8435 (tp40) REVERT: D 48 GLU cc_start: 0.8841 (mt-10) cc_final: 0.7737 (mp0) REVERT: D 55 SER cc_start: 0.8417 (m) cc_final: 0.7440 (t) REVERT: D 82 GLN cc_start: 0.9119 (mp10) cc_final: 0.8815 (pm20) REVERT: D 105 ASP cc_start: 0.9133 (t0) cc_final: 0.8717 (t0) REVERT: D 123 LYS cc_start: 0.8191 (mmmm) cc_final: 0.7577 (mmtm) REVERT: D 126 GLU cc_start: 0.8764 (tt0) cc_final: 0.8316 (tp30) REVERT: D 127 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8813 (p) outliers start: 47 outliers final: 31 residues processed: 184 average time/residue: 1.2203 time to fit residues: 243.0542 Evaluate side-chains 186 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 356 SER 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 324 THR Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 164 TYR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 VAL 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 415 SER Chi-restraints excluded: chain F residue 437 GLU 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 343 ASN Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 139 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.110800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.084014 restraints weight = 23513.153| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.91 r_work: 0.3138 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12007 Z= 0.188 Angle : 0.768 12.470 16504 Z= 0.376 Chirality : 0.044 0.246 1995 Planarity : 0.005 0.053 2095 Dihedral : 6.420 54.062 1993 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.52 % Allowed : 21.81 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.21), residues: 1551 helix: 0.19 (0.59), residues: 84 sheet: -0.02 (0.21), residues: 623 loop : -1.82 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 366 HIS 0.004 0.001 HIS G 436 PHE 0.019 0.001 PHE C 75 TYR 0.026 0.002 TYR C 164 ARG 0.009 0.001 ARG G 372 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 11) link_NAG-ASN : angle 2.63877 ( 33) link_BETA1-4 : bond 0.00341 ( 5) link_BETA1-4 : angle 1.72443 ( 15) hydrogen bonds : bond 0.03167 ( 329) hydrogen bonds : angle 4.61562 ( 942) SS BOND : bond 0.00278 ( 25) SS BOND : angle 0.97511 ( 50) covalent geometry : bond 0.00452 (11966) covalent geometry : angle 0.75738 (16406) ********************** 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 191 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: A 382 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7823 (mtm180) REVERT: A 389 GLU cc_start: 0.8752 (tt0) cc_final: 0.8085 (tp30) REVERT: A 457 HIS cc_start: 0.8343 (m170) cc_final: 0.8018 (m90) REVERT: B 340 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9066 (ttmm) REVERT: B 357 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8552 (pp20) REVERT: B 385 GLN cc_start: 0.9219 (tt0) cc_final: 0.8889 (tt0) REVERT: C 40 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8195 (tm-30) REVERT: C 85 ASP cc_start: 0.9176 (m-30) cc_final: 0.8862 (t0) REVERT: C 174 ARG cc_start: 0.6609 (ptm-80) cc_final: 0.6303 (ptm-80) REVERT: C 213 LYS cc_start: 0.4818 (tttm) cc_final: 0.4289 (mttm) REVERT: C 414 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7991 (p) REVERT: F 410 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8796 (p) REVERT: F 423 ASP cc_start: 0.9305 (m-30) cc_final: 0.9093 (m-30) REVERT: F 426 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8741 (ptpp) REVERT: G 250 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.4458 (ptm-80) REVERT: G 263 ASN cc_start: 0.5905 (m-40) cc_final: 0.5695 (m-40) REVERT: G 265 THR cc_start: 0.7411 (m) cc_final: 0.7010 (p) REVERT: G 403 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7912 (pm20) REVERT: G 445 GLN cc_start: 0.8703 (tp40) cc_final: 0.8391 (tp40) REVERT: D 48 GLU cc_start: 0.8872 (mt-10) cc_final: 0.7753 (mp0) REVERT: D 55 SER cc_start: 0.8476 (m) cc_final: 0.7537 (t) REVERT: D 82 GLN cc_start: 0.9115 (mp10) cc_final: 0.8793 (pm20) REVERT: D 105 ASP cc_start: 0.9159 (t0) cc_final: 0.8749 (t0) REVERT: D 123 LYS cc_start: 0.8290 (mmmm) cc_final: 0.7646 (mmtm) REVERT: D 126 GLU cc_start: 0.8790 (tt0) cc_final: 0.8310 (tp30) REVERT: D 127 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8842 (p) outliers start: 42 outliers final: 32 residues processed: 178 average time/residue: 1.1987 time to fit residues: 231.6418 Evaluate side-chains 187 residues out of total 1351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 356 SER 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 324 THR Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 164 TYR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 247 ASN Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 VAL 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 415 SER Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 250 ARG Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 362 ASN Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 403 GLU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 127 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 85 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 152 optimal weight: 0.0870 chunk 127 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.113061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.085735 restraints weight = 23606.946| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.96 r_work: 0.3153 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12007 Z= 0.141 Angle : 0.741 13.034 16504 Z= 0.362 Chirality : 0.043 0.212 1995 Planarity : 0.004 0.050 2095 Dihedral : 6.226 53.530 1993 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.19 % Allowed : 22.06 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.21), residues: 1551 helix: 0.24 (0.60), residues: 84 sheet: 0.06 (0.21), residues: 623 loop : -1.76 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 37 HIS 0.004 0.001 HIS G 436 PHE 0.017 0.001 PHE C 75 TYR 0.012 0.001 TYR C 55 ARG 0.009 0.000 ARG G 372 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 11) link_NAG-ASN : angle 2.45177 ( 33) link_BETA1-4 : bond 0.00384 ( 5) link_BETA1-4 : angle 1.63618 ( 15) hydrogen bonds : bond 0.02788 ( 329) hydrogen bonds : angle 4.49910 ( 942) SS BOND : bond 0.00248 ( 25) SS BOND : angle 0.85885 ( 50) covalent geometry : bond 0.00342 (11966) covalent geometry : angle 0.73149 (16406) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9411.13 seconds wall clock time: 164 minutes 49.03 seconds (9889.03 seconds total)