Starting phenix.real_space_refine on Fri Jan 19 14:46:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/01_2024/6ue7_20749.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/01_2024/6ue7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/01_2024/6ue7_20749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/01_2024/6ue7_20749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/01_2024/6ue7_20749.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ue7_20749/01_2024/6ue7_20749.pdb" } 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 Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "C GLU 330": "OE1" <-> "OE2" Residue "C TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 458": "OE1" <-> "OE2" Residue "C PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 5": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 6.62, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 4.23 Conformation dependent library (CDL) restraints added in 2.5 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: 1.44 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: 3.86 Time building geometry restraints manager: 4.63 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: 99.55 - 106.46: 478 106.46 - 113.38: 6722 113.38 - 120.29: 3995 120.29 - 127.21: 5025 127.21 - 134.12: 186 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 2.440 nonbonded pdb=" OG1 THR A 282 " pdb=" OG1 THR A 322 " model vdw 2.278 2.440 nonbonded pdb=" O GLY B 469 " pdb=" OG SER G 356 " model vdw 2.297 2.440 nonbonded pdb=" O SER F 284 " pdb=" OG SER F 284 " model vdw 2.308 2.440 nonbonded pdb=" OG SER C 256 " pdb=" O ASN C 260 " model vdw 2.316 2.440 ... (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 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 12.830 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.960 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.390 ------------------------------------------------------------------------------- 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 11966 Z= 0.463 Angle : 1.053 12.783 16406 Z= 0.576 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 253 time to evaluate : 1.335 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: 1.2085 time to fit residues: 335.2319 Evaluate side-chains 174 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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: 3.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11966 Z= 0.223 Angle : 0.720 11.914 16406 Z= 0.357 Chirality : 0.044 0.234 1995 Planarity : 0.006 0.051 2095 Dihedral : 8.765 65.373 1995 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 3.86 % Allowed : 16.61 % Favored : 79.53 % 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: -2.39 (0.20), residues: 1551 helix: -2.63 (0.46), residues: 85 sheet: -0.49 (0.21), residues: 628 loop : -2.43 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 37 HIS 0.002 0.001 HIS A 243 PHE 0.016 0.001 PHE G 321 TYR 0.012 0.001 TYR G 327 ARG 0.011 0.001 ARG C 304 *********************** 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 227 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 181 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 382 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7229 (mtp85) REVERT: A 389 GLU cc_start: 0.6967 (tt0) cc_final: 0.6370 (tt0) REVERT: A 449 ASP cc_start: 0.8501 (p0) cc_final: 0.8147 (p0) REVERT: B 361 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8660 (mt) REVERT: C 174 ARG cc_start: 0.7712 (ptm160) cc_final: 0.7393 (ptm160) REVERT: C 213 LYS cc_start: 0.5593 (tttt) cc_final: 0.5251 (mtpp) REVERT: G 315 TRP cc_start: 0.6267 (m100) cc_final: 0.5919 (p-90) REVERT: G 345 PHE cc_start: 0.7381 (m-80) cc_final: 0.7103 (m-80) outliers start: 46 outliers final: 15 residues processed: 203 average time/residue: 1.2584 time to fit residues: 276.0377 Evaluate side-chains 176 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 361 LEU 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 453 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 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 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN F 402 GLN ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11966 Z= 0.231 Angle : 0.685 10.332 16406 Z= 0.338 Chirality : 0.043 0.203 1995 Planarity : 0.005 0.044 2095 Dihedral : 7.494 59.799 1993 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 5.45 % Allowed : 16.28 % Favored : 78.27 % 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: -1.99 (0.21), residues: 1551 helix: -1.57 (0.52), residues: 84 sheet: -0.26 (0.21), residues: 634 loop : -2.22 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 37 HIS 0.004 0.001 HIS D 64 PHE 0.018 0.001 PHE C 75 TYR 0.016 0.001 TYR C 164 ARG 0.005 0.000 ARG C 304 *********************** 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 231 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 166 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: C 174 ARG cc_start: 0.7817 (ptm160) cc_final: 0.7450 (ptm160) REVERT: C 213 LYS cc_start: 0.5698 (tttt) cc_final: 0.5304 (mtpp) REVERT: C 366 TRP cc_start: 0.8993 (OUTLIER) cc_final: 0.8228 (t60) REVERT: F 250 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7603 (ppp80) REVERT: F 433 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.6940 (ttp) REVERT: G 265 THR cc_start: 0.8408 (m) cc_final: 0.8138 (p) REVERT: G 370 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8337 (tp) outliers start: 65 outliers final: 27 residues processed: 207 average time/residue: 1.1902 time to fit residues: 266.6405 Evaluate side-chains 182 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 151 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 304 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 230 ASP 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 366 TRP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 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 423 ASP 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 370 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 52 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 40 optimal weight: 0.0770 overall best weight: 1.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 11966 Z= 0.292 Angle : 0.700 9.428 16406 Z= 0.350 Chirality : 0.044 0.198 1995 Planarity : 0.005 0.050 2095 Dihedral : 7.232 59.758 1993 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 5.45 % Allowed : 17.62 % Favored : 76.93 % 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: -1.93 (0.21), residues: 1551 helix: -1.26 (0.54), residues: 89 sheet: -0.21 (0.21), residues: 628 loop : -2.21 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 366 HIS 0.004 0.001 HIS D 64 PHE 0.019 0.001 PHE C 75 TYR 0.015 0.001 TYR C 154 ARG 0.005 0.001 ARG C 144 *********************** 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 223 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 158 time to evaluate : 1.318 Fit side-chains revert: symmetry clash REVERT: A 389 GLU cc_start: 0.7115 (tt0) cc_final: 0.6683 (tp30) REVERT: C 9 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: F 250 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7585 (ppp80) REVERT: F 425 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9040 (mttt) REVERT: F 433 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.6963 (ttp) REVERT: G 265 THR cc_start: 0.8270 (m) cc_final: 0.7947 (p) REVERT: G 370 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8300 (tp) REVERT: D 55 SER cc_start: 0.7906 (m) cc_final: 0.7588 (t) outliers start: 65 outliers final: 37 residues processed: 199 average time/residue: 1.2710 time to fit residues: 273.5617 Evaluate side-chains 192 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 282 THR 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 304 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 164 TYR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 230 ASP 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 333 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain F residue 425 LYS 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 8 LEU Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 80 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.0970 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11966 Z= 0.193 Angle : 0.671 10.821 16406 Z= 0.329 Chirality : 0.043 0.192 1995 Planarity : 0.004 0.039 2095 Dihedral : 6.886 59.894 1993 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.70 % Allowed : 18.79 % Favored : 76.51 % 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: -1.73 (0.21), residues: 1551 helix: -1.03 (0.54), residues: 90 sheet: -0.06 (0.21), residues: 617 loop : -2.09 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 37 HIS 0.002 0.000 HIS D 64 PHE 0.017 0.001 PHE C 75 TYR 0.012 0.001 TYR C 164 ARG 0.003 0.000 ARG G 372 *********************** 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 212 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 156 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8726 (ttmt) REVERT: C 8 GLU cc_start: 0.7404 (tm-30) cc_final: 0.7033 (tm-30) REVERT: C 9 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: C 366 TRP cc_start: 0.9007 (OUTLIER) cc_final: 0.8377 (t60) REVERT: F 250 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7576 (ppp80) REVERT: G 265 THR cc_start: 0.8266 (m) cc_final: 0.7941 (p) REVERT: G 370 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8265 (tp) REVERT: D 48 GLU cc_start: 0.6851 (mp0) cc_final: 0.6432 (mp0) REVERT: D 55 SER cc_start: 0.7940 (m) cc_final: 0.7674 (t) outliers start: 56 outliers final: 31 residues processed: 192 average time/residue: 1.2329 time to fit residues: 256.0541 Evaluate side-chains 184 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 437 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 340 LYS Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 402 GLN Chi-restraints excluded: chain C residue 9 GLU 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 366 TRP Chi-restraints excluded: chain C residue 453 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 250 ARG Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain F residue 466 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 349 VAL Chi-restraints excluded: chain G residue 362 ASN Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 80 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.0270 chunk 135 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11966 Z= 0.202 Angle : 0.661 10.017 16406 Z= 0.324 Chirality : 0.043 0.202 1995 Planarity : 0.004 0.043 2095 Dihedral : 6.623 59.658 1993 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.36 % Allowed : 20.47 % 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: -1.58 (0.21), residues: 1551 helix: -0.71 (0.55), residues: 84 sheet: 0.05 (0.21), residues: 616 loop : -2.00 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 37 HIS 0.002 0.000 HIS D 64 PHE 0.017 0.001 PHE C 75 TYR 0.016 0.001 TYR B 327 ARG 0.004 0.000 ARG C 416 *********************** 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 205 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 153 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: B 385 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8435 (tt0) REVERT: C 8 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7258 (tm-30) REVERT: C 9 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6757 (mp0) REVERT: C 366 TRP cc_start: 0.9057 (OUTLIER) cc_final: 0.8457 (t60) REVERT: G 265 THR cc_start: 0.8303 (m) cc_final: 0.8007 (p) REVERT: G 370 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8240 (tp) REVERT: D 48 GLU cc_start: 0.6989 (mp0) cc_final: 0.6595 (mp0) REVERT: D 55 SER cc_start: 0.7983 (m) cc_final: 0.7701 (t) outliers start: 52 outliers final: 34 residues processed: 186 average time/residue: 1.2581 time to fit residues: 252.9722 Evaluate side-chains 189 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 151 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 16 ASN 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 230 ASP 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 366 TRP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain F residue 243 HIS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 454 LYS 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 370 LEU 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 32 ASP Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 80 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 ASN ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11966 Z= 0.201 Angle : 0.674 12.482 16406 Z= 0.328 Chirality : 0.043 0.208 1995 Planarity : 0.004 0.041 2095 Dihedral : 6.450 59.993 1993 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.61 % Allowed : 20.81 % Favored : 74.58 % 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: -1.45 (0.21), residues: 1551 helix: -0.65 (0.55), residues: 84 sheet: 0.06 (0.21), residues: 626 loop : -1.87 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 37 HIS 0.002 0.000 HIS D 64 PHE 0.016 0.001 PHE C 75 TYR 0.009 0.001 TYR G 327 ARG 0.005 0.000 ARG F 346 *********************** 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 213 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 158 time to evaluate : 1.384 Fit side-chains revert: symmetry clash REVERT: B 385 GLN cc_start: 0.8616 (tt0) cc_final: 0.8408 (tt0) REVERT: C 8 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7216 (tm-30) REVERT: C 9 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: C 366 TRP cc_start: 0.9067 (OUTLIER) cc_final: 0.8476 (t60) REVERT: F 250 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7761 (ppp80) REVERT: G 265 THR cc_start: 0.8167 (m) cc_final: 0.7873 (p) REVERT: G 370 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8208 (tp) REVERT: D 48 GLU cc_start: 0.7111 (mp0) cc_final: 0.6894 (mp0) outliers start: 55 outliers final: 31 residues processed: 193 average time/residue: 1.2206 time to fit residues: 254.7643 Evaluate side-chains 186 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 437 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 9 GLU 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 366 TRP Chi-restraints excluded: chain C residue 453 THR 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 250 ARG 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 253 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 80 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 102 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11966 Z= 0.195 Angle : 0.666 9.974 16406 Z= 0.326 Chirality : 0.043 0.210 1995 Planarity : 0.004 0.044 2095 Dihedral : 6.288 59.729 1993 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.45 % Allowed : 21.31 % Favored : 74.24 % 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: -1.37 (0.21), residues: 1551 helix: -0.36 (0.58), residues: 84 sheet: 0.11 (0.21), residues: 624 loop : -1.84 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 37 HIS 0.002 0.000 HIS D 64 PHE 0.016 0.001 PHE C 75 TYR 0.018 0.001 TYR C 55 ARG 0.006 0.000 ARG D 21 *********************** 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 205 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 152 time to evaluate : 1.973 Fit side-chains revert: symmetry clash REVERT: B 385 GLN cc_start: 0.8628 (tt0) cc_final: 0.8399 (tt0) REVERT: C 9 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: C 366 TRP cc_start: 0.9069 (OUTLIER) cc_final: 0.8488 (t60) REVERT: F 250 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7776 (ppp80) REVERT: F 433 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.7028 (ttp) REVERT: G 265 THR cc_start: 0.8140 (m) cc_final: 0.7805 (p) REVERT: G 370 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8161 (tp) REVERT: G 372 ARG cc_start: 0.8156 (tmm-80) cc_final: 0.7834 (tmm-80) REVERT: D 48 GLU cc_start: 0.7143 (mp0) cc_final: 0.6699 (mp0) REVERT: D 55 SER cc_start: 0.7976 (m) cc_final: 0.7641 (t) outliers start: 53 outliers final: 33 residues processed: 185 average time/residue: 1.2350 time to fit residues: 247.5959 Evaluate side-chains 188 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 437 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 9 GLU Chi-restraints excluded: chain C residue 16 ASN 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 366 TRP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 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 253 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 80 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11966 Z= 0.238 Angle : 0.704 12.971 16406 Z= 0.342 Chirality : 0.043 0.175 1995 Planarity : 0.004 0.045 2095 Dihedral : 6.267 56.901 1993 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.03 % Allowed : 21.98 % Favored : 73.99 % 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: -1.39 (0.21), residues: 1551 helix: -0.12 (0.59), residues: 84 sheet: 0.02 (0.21), residues: 629 loop : -1.82 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 366 HIS 0.003 0.001 HIS D 64 PHE 0.017 0.001 PHE C 75 TYR 0.016 0.001 TYR C 55 ARG 0.005 0.000 ARG F 346 *********************** 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 194 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 146 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: B 385 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: F 250 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7782 (ppp80) REVERT: F 433 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7034 (ttp) REVERT: G 265 THR cc_start: 0.8259 (m) cc_final: 0.7867 (p) REVERT: G 370 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8185 (tp) REVERT: G 372 ARG cc_start: 0.8121 (tmm-80) cc_final: 0.7821 (tmm-80) REVERT: D 48 GLU cc_start: 0.7213 (mp0) cc_final: 0.6330 (mp0) REVERT: D 55 SER cc_start: 0.8165 (m) cc_final: 0.6808 (t) REVERT: D 124 MET cc_start: 0.7862 (mmm) cc_final: 0.7660 (tpp) outliers start: 48 outliers final: 34 residues processed: 179 average time/residue: 1.2299 time to fit residues: 239.4933 Evaluate side-chains 181 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 143 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 408 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 16 ASN 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 266 ASN Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 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 253 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 32 ASP Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 80 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 0.0000 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11966 Z= 0.237 Angle : 0.700 12.185 16406 Z= 0.343 Chirality : 0.043 0.229 1995 Planarity : 0.004 0.051 2095 Dihedral : 6.257 56.924 1993 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 3.61 % Allowed : 22.06 % Favored : 74.33 % 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: -1.38 (0.21), residues: 1551 helix: 0.06 (0.60), residues: 84 sheet: 0.01 (0.21), residues: 629 loop : -1.81 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 37 HIS 0.003 0.001 HIS D 64 PHE 0.017 0.001 PHE C 75 TYR 0.012 0.001 TYR C 55 ARG 0.005 0.000 ARG F 346 ********************** 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 188 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: F 250 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7787 (ppp80) REVERT: F 433 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7043 (ttp) REVERT: G 265 THR cc_start: 0.8262 (m) cc_final: 0.7864 (p) REVERT: G 370 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8187 (tp) REVERT: G 372 ARG cc_start: 0.8110 (tmm-80) cc_final: 0.7806 (tmm-80) REVERT: D 48 GLU cc_start: 0.7260 (mp0) cc_final: 0.6388 (mp0) REVERT: D 55 SER cc_start: 0.8252 (m) cc_final: 0.6907 (t) outliers start: 43 outliers final: 33 residues processed: 173 average time/residue: 1.2147 time to fit residues: 227.8433 Evaluate side-chains 176 residues out of total 1351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 140 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 408 THR Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 16 ASN 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 230 ASP 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 453 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain F residue 250 ARG Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 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 253 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain G residue 370 LEU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain D residue 15 CYS Chi-restraints excluded: chain D residue 46 ASN Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 80 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 chunk 108 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.115194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.087918 restraints weight = 24037.682| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.93 r_work: 0.3217 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11966 Z= 0.193 Angle : 0.698 13.505 16406 Z= 0.337 Chirality : 0.043 0.211 1995 Planarity : 0.004 0.051 2095 Dihedral : 6.143 59.880 1993 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.27 % Allowed : 22.48 % Favored : 74.24 % 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: -1.28 (0.22), residues: 1551 helix: 0.10 (0.61), residues: 84 sheet: 0.08 (0.21), residues: 628 loop : -1.75 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 37 HIS 0.002 0.000 HIS D 64 PHE 0.015 0.001 PHE C 75 TYR 0.010 0.001 TYR C 55 ARG 0.005 0.000 ARG F 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4804.58 seconds wall clock time: 85 minutes 47.12 seconds (5147.12 seconds total)