Starting phenix.real_space_refine on Mon Feb 19 10:07:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg2_22310/02_2024/7jg2_22310_neut_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg2_22310/02_2024/7jg2_22310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg2_22310/02_2024/7jg2_22310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg2_22310/02_2024/7jg2_22310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg2_22310/02_2024/7jg2_22310_neut_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jg2_22310/02_2024/7jg2_22310_neut_trim.pdb" } resolution = 3.3 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= -0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians S 84 5.16 5 C 7755 2.51 5 N 2068 2.21 5 O 2487 1.98 5 H 11858 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "B ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 267": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 309": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 336": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 443": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24252 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3469 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 17, 'TRANS': 213} Chain: "B" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3381 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 17, 'TRANS': 206} Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3467 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 17, 'TRANS': 213} Chain: "D" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3470 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 17, 'TRANS': 213} Chain: "E" Number of atoms: 8191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8191 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 26, 'TRANS': 508} Chain breaks: 1 Chain: "J" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2062 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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: "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: "C" 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: "D" 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 Time building chain proxies: 10.78, per 1000 atoms: 0.44 Number of scatterers: 24252 At special positions: 0 Unit cell: (99.756, 118.012, 173.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 O 2487 8.00 N 2068 7.00 C 7755 6.00 H 11858 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 318 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 318 " distance=2.62 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS D 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS E 470 " distance=1.52 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 427 " distance=2.41 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS J 14 " distance=2.03 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS D 296 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 318 " distance=2.03 Simple disulfide: pdb=" SG CYS D 364 " - pdb=" SG CYS D 427 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 38 " - pdb=" SG CYS E 46 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 202 " distance=2.21 Simple disulfide: pdb=" SG CYS E 239 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS E 253 " - pdb=" SG CYS E 260 " distance=2.03 Simple disulfide: pdb=" SG CYS E 352 " - pdb=" SG CYS E 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 366 " - pdb=" SG CYS E 376 " distance=2.03 Simple disulfide: pdb=" SG CYS E 466 " - pdb=" SG CYS E 528 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 487 " distance=1.54 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 101 " distance=2.03 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 109 " - pdb=" SG CYS J 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=1, symmetry=0 Links applied ALPHA1-3 " MAN F 4 " - " MAN F 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 501 " - " ASN A 437 " " NAG C 501 " - " ASN C 437 " " NAG C 502 " - " ASN C 452 " " NAG D 501 " - " ASN D 452 " " NAG F 1 " - " ASN E 72 " " NAG G 1 " - " ASN E 129 " " NAG H 1 " - " ASN E 188 " " NAG I 1 " - " ASN J 48 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.44 Conformation dependent library (CDL) restraints added in 2.5 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 39 sheets defined 12.0% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.809A pdb=" N ALA A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.599A pdb=" N LEU B 251 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 323 through 325 No H-bonds generated for 'chain 'B' and resid 323 through 325' Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.906A pdb=" N LEU B 354 " --> pdb=" O PRO B 350 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 355 " --> pdb=" O SER B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 355' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.857A pdb=" N PHE B 438 " --> pdb=" O PRO B 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 305 through 312 removed outlier: 3.968A pdb=" N ARG C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.689A pdb=" N GLY C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 448 Processing helix chain 'D' and resid 247 through 252 removed outlier: 3.640A pdb=" N LEU D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 3.557A pdb=" N TRP D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 357 removed outlier: 3.518A pdb=" N ASN D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.675A pdb=" N TYR D 390 " --> pdb=" O PRO D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 434 through 438 removed outlier: 4.010A pdb=" N PHE D 438 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 33 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 193 through 197 removed outlier: 3.511A pdb=" N ALA E 197 " --> pdb=" O HIS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 246 removed outlier: 3.614A pdb=" N VAL E 245 " --> pdb=" O GLY E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 355 through 359 removed outlier: 3.675A pdb=" N SER E 359 " --> pdb=" O PRO E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 417 Processing helix chain 'E' and resid 469 through 473 Processing helix chain 'E' and resid 519 through 523 Processing helix chain 'J' and resid 64 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 244 removed outlier: 3.665A pdb=" N THR A 260 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 264 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL A 299 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 244 removed outlier: 3.665A pdb=" N THR A 260 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 259 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 276 Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 347 removed outlier: 3.946A pdb=" N THR A 363 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 347 removed outlier: 3.946A pdb=" N THR A 363 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 Processing sheet with id=AA7, first strand: chain 'B' and resid 457 through 458 removed outlier: 5.992A pdb=" N ILE A 458 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.245A pdb=" N THR B 260 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 303 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N THR B 262 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER B 301 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASN B 264 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B 299 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 266 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER B 300 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS B 288 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL B 302 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN B 286 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 276 Processing sheet with id=AB1, first strand: chain 'B' and resid 345 through 347 removed outlier: 3.853A pdb=" N THR B 363 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 410 " --> pdb=" O CYS B 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 375 through 379 Processing sheet with id=AB3, first strand: chain 'B' and resid 396 through 397 Processing sheet with id=AB4, first strand: chain 'C' and resid 240 through 244 removed outlier: 5.753A pdb=" N THR C 260 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU C 303 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N THR C 262 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER C 301 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN C 264 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 299 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER C 300 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS C 288 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL C 302 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN C 286 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 273 through 275 Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 347 removed outlier: 3.714A pdb=" N THR C 363 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 410 " --> pdb=" O CYS C 364 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 347 removed outlier: 3.714A pdb=" N THR C 363 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 410 " --> pdb=" O CYS C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 375 through 379 Processing sheet with id=AB9, first strand: chain 'D' and resid 457 through 458 removed outlier: 6.829A pdb=" N SER C 454 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE J 39 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER C 456 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL J 41 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 458 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR J 15 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP J 9 " --> pdb=" O THR J 15 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL J 17 " --> pdb=" O LEU J 7 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 240 through 244 removed outlier: 3.599A pdb=" N THR D 260 " --> pdb=" O GLN D 244 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR D 297 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 285 " --> pdb=" O VAL D 302 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 240 through 244 removed outlier: 3.599A pdb=" N THR D 260 " --> pdb=" O GLN D 244 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR D 297 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 290 " --> pdb=" O SER D 298 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 273 through 276 removed outlier: 5.183A pdb=" N HIS D 322 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY D 326 " --> pdb=" O HIS D 322 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 345 through 346 Processing sheet with id=AC5, first strand: chain 'D' and resid 345 through 346 Processing sheet with id=AC6, first strand: chain 'D' and resid 383 through 384 removed outlier: 4.045A pdb=" N GLU D 383 " --> pdb=" O HIS D 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AC8, first strand: chain 'E' and resid 46 through 51 removed outlier: 6.715A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER E 51 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS E 35 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR E 36 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY E 93 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 46 through 51 removed outlier: 6.715A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER E 51 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS E 35 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER E 89 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 120 through 124 removed outlier: 4.682A pdb=" N HIS E 120 " --> pdb=" O ASN E 214 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP E 216 " --> pdb=" O HIS E 120 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU E 199 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS E 145 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP E 160 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU E 147 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 131 through 135 removed outlier: 3.764A pdb=" N TYR E 186 " --> pdb=" O PHE E 176 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 225 through 230 removed outlier: 6.386A pdb=" N GLU E 225 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE E 326 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU E 227 " --> pdb=" O PHE E 326 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN E 328 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LYS E 229 " --> pdb=" O ASN E 328 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS E 303 " --> pdb=" O MET E 255 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS E 250 " --> pdb=" O ASN E 265 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASN E 265 " --> pdb=" O LYS E 250 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU E 252 " --> pdb=" O ILE E 263 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 225 through 230 removed outlier: 6.386A pdb=" N GLU E 225 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE E 326 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU E 227 " --> pdb=" O PHE E 326 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN E 328 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LYS E 229 " --> pdb=" O ASN E 328 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS E 303 " --> pdb=" O MET E 255 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 235 through 239 removed outlier: 3.660A pdb=" N LEU E 292 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 339 through 343 removed outlier: 3.564A pdb=" N TRP E 421 " --> pdb=" O CYS E 366 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS E 366 " --> pdb=" O TRP E 421 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 347 through 353 removed outlier: 3.532A pdb=" N ALA E 395 " --> pdb=" O ILE E 408 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 454 through 457 removed outlier: 6.276A pdb=" N ALA E 454 " --> pdb=" O ALA E 545 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU E 547 " --> pdb=" O ALA E 454 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA E 456 " --> pdb=" O GLU E 547 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP E 525 " --> pdb=" O TRP E 482 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TRP E 479 " --> pdb=" O LEU E 490 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 454 through 457 removed outlier: 6.276A pdb=" N ALA E 454 " --> pdb=" O ALA E 545 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU E 547 " --> pdb=" O ALA E 454 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA E 456 " --> pdb=" O GLU E 547 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR E 535 " --> pdb=" O GLN E 532 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 462 through 467 removed outlier: 3.627A pdb=" N LEU E 510 " --> pdb=" O GLU E 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 74 through 75 Processing sheet with id=AE3, first strand: chain 'J' and resid 111 through 118 420 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.91 Time building geometry restraints manager: 19.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11850 1.02 - 1.22: 10 1.22 - 1.42: 4969 1.42 - 1.61: 7586 1.61 - 1.81: 104 Bond restraints: 24519 Sorted by residual: bond pdb=" ND2 ASN J 107 " pdb="HD21 ASN J 107 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN J 89 " pdb="HD21 ASN J 89 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN J 59 " pdb="HD21 ASN J 59 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN J 59 " pdb="HD22 ASN J 59 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN J 92 " pdb="HD21 ASN J 92 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 24514 not shown) Histogram of bond angle deviations from ideal: 71.29 - 85.95: 2 85.95 - 100.61: 6 100.61 - 115.27: 31795 115.27 - 129.93: 12425 129.93 - 144.59: 86 Bond angle restraints: 44314 Sorted by residual: angle pdb="HD21 ASN E 129 " pdb=" ND2 ASN E 129 " pdb="HD22 ASN E 129 " ideal model delta sigma weight residual 120.00 71.29 48.71 3.00e+00 1.11e-01 2.64e+02 angle pdb=" CG ASN E 129 " pdb=" ND2 ASN E 129 " pdb="HD22 ASN E 129 " ideal model delta sigma weight residual 120.00 73.31 46.69 3.00e+00 1.11e-01 2.42e+02 angle pdb=" CG ASN E 129 " pdb=" ND2 ASN E 129 " pdb="HD21 ASN E 129 " ideal model delta sigma weight residual 120.00 144.59 -24.59 3.00e+00 1.11e-01 6.72e+01 angle pdb=" N ILE C 443 " pdb=" CA ILE C 443 " pdb=" C ILE C 443 " ideal model delta sigma weight residual 107.24 118.87 -11.63 1.68e+00 3.54e-01 4.80e+01 angle pdb=" C SER A 255 " pdb=" CA SER A 255 " pdb=" CB SER A 255 " ideal model delta sigma weight residual 112.07 102.25 9.82 1.54e+00 4.22e-01 4.07e+01 ... (remaining 44309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.88: 11424 23.88 - 47.76: 419 47.76 - 71.63: 95 71.63 - 95.51: 21 95.51 - 119.39: 9 Dihedral angle restraints: 11968 sinusoidal: 6755 harmonic: 5213 Sorted by residual: dihedral pdb=" CB CYS B 261 " pdb=" SG CYS B 261 " pdb=" SG CYS B 318 " pdb=" CB CYS B 318 " ideal model delta sinusoidal sigma weight residual 93.00 158.70 -65.70 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " pdb=" SG CYS A 296 " pdb=" CB CYS A 296 " ideal model delta sinusoidal sigma weight residual -86.00 -132.75 46.75 1 1.00e+01 1.00e-02 3.02e+01 dihedral pdb=" C SER A 255 " pdb=" N SER A 255 " pdb=" CA SER A 255 " pdb=" CB SER A 255 " ideal model delta harmonic sigma weight residual -122.60 -110.48 -12.12 0 2.50e+00 1.60e-01 2.35e+01 ... (remaining 11965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1842 0.099 - 0.198: 159 0.198 - 0.297: 16 0.297 - 0.396: 2 0.396 - 0.495: 1 Chirality restraints: 2020 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 -2.24 -0.16 2.00e-02 2.50e+03 6.17e+01 chirality pdb=" CA THR E 119 " pdb=" N THR E 119 " pdb=" C THR E 119 " pdb=" CB THR E 119 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CA SER A 255 " pdb=" N SER A 255 " pdb=" C SER A 255 " pdb=" CB SER A 255 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 2017 not shown) Planarity restraints: 3693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 111 " 0.239 2.00e-02 2.50e+03 3.18e-01 1.52e+03 pdb=" CD GLN E 111 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN E 111 " -0.231 2.00e-02 2.50e+03 pdb=" NE2 GLN E 111 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN E 111 " -0.494 2.00e-02 2.50e+03 pdb="HE22 GLN E 111 " 0.504 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN J 81 " 0.230 2.00e-02 2.50e+03 2.89e-01 1.25e+03 pdb=" CD GLN J 81 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN J 81 " -0.221 2.00e-02 2.50e+03 pdb=" NE2 GLN J 81 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN J 81 " -0.442 2.00e-02 2.50e+03 pdb="HE22 GLN J 81 " 0.451 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 268 " -0.234 2.00e-02 2.50e+03 2.41e-01 8.70e+02 pdb=" CG ASN D 268 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN D 268 " 0.224 2.00e-02 2.50e+03 pdb=" ND2 ASN D 268 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 268 " -0.353 2.00e-02 2.50e+03 pdb="HD22 ASN D 268 " 0.344 2.00e-02 2.50e+03 ... (remaining 3690 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 278 2.06 - 2.69: 37526 2.69 - 3.33: 66756 3.33 - 3.96: 86210 3.96 - 4.60: 133434 Nonbonded interactions: 324204 Sorted by model distance: nonbonded pdb=" HB2 PRO A 435 " pdb=" O CYS J 134 " model vdw 1.419 2.620 nonbonded pdb="HH22 ARG C 245 " pdb=" OE2 GLU C 432 " model vdw 1.615 1.850 nonbonded pdb=" OD1 ASN A 268 " pdb=" HE2 HIS A 322 " model vdw 1.627 1.850 nonbonded pdb=" OD1 ASN E 166 " pdb=" H SER E 168 " model vdw 1.664 1.850 nonbonded pdb=" HH TYR E 468 " pdb=" O PHE E 472 " model vdw 1.679 1.850 ... (remaining 324199 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 237 through 305 or (resid 306 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 307 through 451 or (resid 452 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name ND2 or name H or name HA or name \ HB2 or name HB3 or name HD21)) or resid 453 through 460)) selection = (chain 'B' and (resid 237 through 260 or (resid 261 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 262 through 305 or (resid 306 and (name N or name CA or name C or n \ ame O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or re \ sid 307 through 317 or (resid 318 and (name N or name CA or name C or name O or \ name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 319 t \ hrough 436 or (resid 437 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 o \ r name HD21)) or resid 438 through 451 or (resid 452 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name ND2 or name H or name \ HA or name HB2 or name HB3 or name HD21)) or resid 453 through 460)) selection = (chain 'C' and resid 237 through 460) selection = (chain 'D' and (resid 237 through 305 or (resid 306 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 307 through 436 or (resid 437 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name ND2 or name H or name HA or name \ HB2 or name HB3 or name HD21)) or resid 438 through 460)) } ncs_group { reference = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.340 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: 0.340 Extract box with map and model: 15.140 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 75.350 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12661 Z= 0.212 Angle : 0.712 11.635 17251 Z= 0.409 Chirality : 0.053 0.495 2020 Planarity : 0.003 0.038 2216 Dihedral : 12.465 119.390 4906 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.80 % Favored : 88.14 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Cbeta Deviations : 0.14 % 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: -3.98 (0.19), residues: 1568 helix: -3.64 (0.30), residues: 106 sheet: -2.78 (0.17), residues: 625 loop : -2.33 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP E 479 HIS 0.001 0.000 HIS C 380 PHE 0.004 0.000 PHE A 369 TYR 0.010 0.000 TYR J 104 ARG 0.001 0.000 ARG E 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 THR cc_start: 0.8121 (m) cc_final: 0.7870 (m) REVERT: A 338 ASN cc_start: 0.5476 (p0) cc_final: 0.5266 (p0) REVERT: A 465 ILE cc_start: 0.8461 (mm) cc_final: 0.8193 (mt) REVERT: E 438 VAL cc_start: 0.6225 (t) cc_final: 0.5995 (t) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.5418 time to fit residues: 296.2201 Evaluate side-chains 210 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 40 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 0.0770 chunk 123 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 142 optimal weight: 4.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 GLN C 268 ASN C 291 GLN ** D 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS ** J 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 44 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12661 Z= 0.184 Angle : 0.567 5.772 17251 Z= 0.286 Chirality : 0.044 0.200 2020 Planarity : 0.004 0.053 2216 Dihedral : 9.356 116.465 2013 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.31 % Favored : 93.56 % Rotamer: Outliers : 1.51 % Allowed : 10.48 % Favored : 88.01 % 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: -3.33 (0.20), residues: 1568 helix: -2.87 (0.37), residues: 114 sheet: -2.32 (0.18), residues: 638 loop : -1.91 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 419 HIS 0.008 0.001 HIS C 322 PHE 0.026 0.001 PHE E 75 TYR 0.012 0.001 TYR C 297 ARG 0.005 0.000 ARG J 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ILE cc_start: 0.8430 (mm) cc_final: 0.8212 (mt) REVERT: J 9 ASP cc_start: 0.6205 (OUTLIER) cc_final: 0.5599 (m-30) outliers start: 21 outliers final: 11 residues processed: 234 average time/residue: 0.5539 time to fit residues: 189.9737 Evaluate side-chains 207 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 195 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 22 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN D 264 ASN E 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12661 Z= 0.225 Angle : 0.564 10.717 17251 Z= 0.280 Chirality : 0.045 0.194 2020 Planarity : 0.004 0.061 2216 Dihedral : 7.458 113.570 2013 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.91 % Favored : 92.03 % Rotamer: Outliers : 2.15 % Allowed : 11.56 % Favored : 86.29 % 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: -2.84 (0.21), residues: 1568 helix: -2.20 (0.41), residues: 113 sheet: -1.97 (0.19), residues: 651 loop : -1.65 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 479 HIS 0.007 0.001 HIS E 303 PHE 0.020 0.002 PHE E 75 TYR 0.014 0.001 TYR E 390 ARG 0.003 0.001 ARG B 245 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 202 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASP cc_start: 0.5479 (p0) cc_final: 0.5269 (p0) REVERT: A 465 ILE cc_start: 0.8540 (mm) cc_final: 0.8283 (mt) REVERT: B 274 PHE cc_start: 0.4530 (m-80) cc_final: 0.4189 (m-80) REVERT: C 456 SER cc_start: 0.7942 (m) cc_final: 0.7595 (p) REVERT: E 106 SER cc_start: 0.7028 (t) cc_final: 0.6542 (t) REVERT: J 9 ASP cc_start: 0.6138 (OUTLIER) cc_final: 0.5772 (m-30) outliers start: 30 outliers final: 22 residues processed: 220 average time/residue: 0.5160 time to fit residues: 165.3299 Evaluate side-chains 200 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 237 CYS Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 36 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 135 optimal weight: 0.1980 chunk 40 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN D 264 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN J 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12661 Z= 0.232 Angle : 0.544 7.380 17251 Z= 0.272 Chirality : 0.044 0.207 2020 Planarity : 0.004 0.055 2216 Dihedral : 6.921 106.549 2013 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 2.30 % Allowed : 11.92 % Favored : 85.79 % 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: -2.61 (0.21), residues: 1568 helix: -1.88 (0.43), residues: 114 sheet: -1.85 (0.19), residues: 670 loop : -1.46 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 479 HIS 0.004 0.001 HIS J 63 PHE 0.019 0.001 PHE E 75 TYR 0.008 0.001 TYR C 297 ARG 0.006 0.000 ARG E 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 182 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 ASP cc_start: 0.5551 (p0) cc_final: 0.5296 (p0) REVERT: A 465 ILE cc_start: 0.8579 (mm) cc_final: 0.8314 (mt) REVERT: B 274 PHE cc_start: 0.4550 (m-80) cc_final: 0.4238 (m-80) REVERT: C 456 SER cc_start: 0.8055 (m) cc_final: 0.7701 (p) REVERT: J 9 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.5850 (m-30) REVERT: J 124 MET cc_start: 0.7105 (mmt) cc_final: 0.6760 (mmt) outliers start: 32 outliers final: 24 residues processed: 203 average time/residue: 0.5275 time to fit residues: 155.1841 Evaluate side-chains 193 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 GLN Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 36 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 HIS ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12661 Z= 0.246 Angle : 0.553 7.257 17251 Z= 0.275 Chirality : 0.044 0.214 2020 Planarity : 0.004 0.051 2216 Dihedral : 6.680 99.842 2013 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.46 % Favored : 92.47 % Rotamer: Outliers : 2.30 % Allowed : 12.78 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.43 (0.21), residues: 1568 helix: -1.53 (0.45), residues: 114 sheet: -1.70 (0.19), residues: 660 loop : -1.41 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 479 HIS 0.006 0.001 HIS E 309 PHE 0.019 0.002 PHE D 369 TYR 0.009 0.001 TYR C 297 ARG 0.004 0.000 ARG J 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ILE cc_start: 0.8623 (mm) cc_final: 0.8336 (mt) REVERT: C 456 SER cc_start: 0.8208 (m) cc_final: 0.7847 (p) REVERT: D 346 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7296 (tp) REVERT: J 113 MET cc_start: 0.7445 (tmm) cc_final: 0.6537 (tmm) REVERT: J 124 MET cc_start: 0.7170 (mmt) cc_final: 0.6878 (mmt) outliers start: 32 outliers final: 25 residues processed: 198 average time/residue: 0.5514 time to fit residues: 157.1060 Evaluate side-chains 181 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 36 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 12 optimal weight: 0.0970 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12661 Z= 0.257 Angle : 0.570 7.031 17251 Z= 0.283 Chirality : 0.045 0.223 2020 Planarity : 0.005 0.062 2216 Dihedral : 6.398 92.237 2013 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.20 % Rotamer: Outliers : 2.94 % Allowed : 13.07 % Favored : 83.99 % 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: -2.26 (0.21), residues: 1568 helix: -1.51 (0.45), residues: 113 sheet: -1.56 (0.19), residues: 661 loop : -1.31 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 310 HIS 0.005 0.001 HIS B 431 PHE 0.022 0.002 PHE D 369 TYR 0.018 0.001 TYR E 526 ARG 0.004 0.000 ARG J 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 159 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 456 SER cc_start: 0.8373 (m) cc_final: 0.8041 (p) REVERT: D 346 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7454 (tp) REVERT: D 409 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8132 (m) REVERT: E 394 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7110 (tp) REVERT: J 9 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.6471 (t0) outliers start: 41 outliers final: 29 residues processed: 192 average time/residue: 0.5024 time to fit residues: 143.6121 Evaluate side-chains 178 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 145 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 36 ASN Chi-restraints excluded: chain J residue 125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 151 optimal weight: 0.2980 chunk 94 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.6288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12661 Z= 0.188 Angle : 0.531 7.054 17251 Z= 0.261 Chirality : 0.043 0.223 2020 Planarity : 0.004 0.067 2216 Dihedral : 6.114 86.259 2013 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.72 % Allowed : 15.00 % Favored : 83.27 % 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: -2.02 (0.22), residues: 1568 helix: -1.28 (0.46), residues: 113 sheet: -1.44 (0.19), residues: 667 loop : -1.11 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 479 HIS 0.003 0.001 HIS B 431 PHE 0.017 0.001 PHE B 274 TYR 0.009 0.001 TYR E 468 ARG 0.004 0.000 ARG J 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 PHE cc_start: 0.4632 (m-80) cc_final: 0.4093 (m-80) REVERT: B 394 GLU cc_start: 0.7576 (pm20) cc_final: 0.7355 (pm20) REVERT: C 456 SER cc_start: 0.8383 (m) cc_final: 0.8039 (p) REVERT: E 394 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7154 (tp) REVERT: E 514 THR cc_start: 0.7715 (m) cc_final: 0.7474 (p) REVERT: J 9 ASP cc_start: 0.6677 (OUTLIER) cc_final: 0.6447 (t0) REVERT: J 113 MET cc_start: 0.7464 (tmm) cc_final: 0.6873 (tmm) outliers start: 24 outliers final: 20 residues processed: 174 average time/residue: 0.5348 time to fit residues: 139.3576 Evaluate side-chains 171 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 ASN D 264 ASN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12661 Z= 0.233 Angle : 0.553 7.263 17251 Z= 0.273 Chirality : 0.044 0.224 2020 Planarity : 0.004 0.063 2216 Dihedral : 5.955 78.226 2013 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.08 % Allowed : 15.36 % Favored : 82.56 % 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: -2.00 (0.21), residues: 1568 helix: -1.23 (0.46), residues: 113 sheet: -1.36 (0.20), residues: 655 loop : -1.19 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 482 HIS 0.004 0.001 HIS E 309 PHE 0.016 0.002 PHE E 75 TYR 0.012 0.001 TYR E 468 ARG 0.004 0.000 ARG J 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 157 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 PHE cc_start: 0.4643 (m-80) cc_final: 0.4066 (m-80) REVERT: B 276 TRP cc_start: 0.5782 (m100) cc_final: 0.5011 (m100) REVERT: C 456 SER cc_start: 0.8389 (m) cc_final: 0.8067 (p) REVERT: E 394 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7222 (tp) REVERT: E 482 TRP cc_start: 0.6491 (t60) cc_final: 0.6226 (t60) REVERT: E 514 THR cc_start: 0.7789 (m) cc_final: 0.7576 (p) REVERT: J 9 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.6562 (t0) outliers start: 29 outliers final: 24 residues processed: 182 average time/residue: 0.5505 time to fit residues: 148.7364 Evaluate side-chains 176 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 12661 Z= 0.229 Angle : 0.567 9.863 17251 Z= 0.277 Chirality : 0.044 0.222 2020 Planarity : 0.004 0.057 2216 Dihedral : 5.517 56.106 2013 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.08 % Allowed : 15.72 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.21), residues: 1568 helix: -1.40 (0.44), residues: 113 sheet: -1.24 (0.20), residues: 635 loop : -1.14 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 482 HIS 0.003 0.001 HIS J 63 PHE 0.016 0.001 PHE E 75 TYR 0.010 0.001 TYR J 104 ARG 0.005 0.000 ARG C 309 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 148 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 PHE cc_start: 0.4652 (m-80) cc_final: 0.4087 (m-80) REVERT: C 456 SER cc_start: 0.8450 (m) cc_final: 0.8145 (p) REVERT: E 514 THR cc_start: 0.7809 (m) cc_final: 0.7592 (p) REVERT: J 9 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6586 (t0) outliers start: 29 outliers final: 23 residues processed: 173 average time/residue: 0.5662 time to fit residues: 142.8245 Evaluate side-chains 166 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12661 Z= 0.226 Angle : 0.558 7.839 17251 Z= 0.272 Chirality : 0.044 0.224 2020 Planarity : 0.004 0.054 2216 Dihedral : 5.212 53.858 2013 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.15 % Allowed : 15.94 % Favored : 81.91 % 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: -1.81 (0.22), residues: 1568 helix: -1.16 (0.45), residues: 114 sheet: -1.20 (0.20), residues: 635 loop : -1.10 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 479 HIS 0.003 0.001 HIS B 431 PHE 0.016 0.001 PHE E 75 TYR 0.012 0.001 TYR E 468 ARG 0.003 0.000 ARG J 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 1.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 456 SER cc_start: 0.8459 (m) cc_final: 0.8164 (p) REVERT: D 267 ARG cc_start: 0.3570 (tpt170) cc_final: 0.3288 (tpt170) REVERT: E 394 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7227 (tp) REVERT: E 514 THR cc_start: 0.7854 (m) cc_final: 0.7640 (p) outliers start: 30 outliers final: 22 residues processed: 169 average time/residue: 0.5682 time to fit residues: 139.0687 Evaluate side-chains 165 residues out of total 1393 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 18 optimal weight: 0.0050 chunk 34 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.191626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.153593 restraints weight = 43262.858| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.80 r_work: 0.3835 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.7166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12661 Z= 0.168 Angle : 0.536 8.384 17251 Z= 0.261 Chirality : 0.044 0.254 2020 Planarity : 0.004 0.051 2216 Dihedral : 4.928 53.914 2013 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.58 % Allowed : 16.44 % Favored : 81.98 % 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: -1.59 (0.22), residues: 1568 helix: -0.91 (0.47), residues: 113 sheet: -1.11 (0.20), residues: 644 loop : -0.90 (0.24), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 479 HIS 0.002 0.001 HIS B 431 PHE 0.015 0.001 PHE E 75 TYR 0.010 0.001 TYR J 104 ARG 0.005 0.000 ARG J 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6263.70 seconds wall clock time: 111 minutes 52.84 seconds (6712.84 seconds total)