Starting phenix.real_space_refine on Sun Feb 25 06:57:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe0_33153/02_2024/7xe0_33153_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe0_33153/02_2024/7xe0_33153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe0_33153/02_2024/7xe0_33153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe0_33153/02_2024/7xe0_33153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe0_33153/02_2024/7xe0_33153_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe0_33153/02_2024/7xe0_33153_updated.pdb" } resolution = 3.33 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= 0.001 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 P 15 5.49 5 S 235 5.16 5 C 31840 2.51 5 N 8330 2.21 5 O 9295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 311": "NH1" <-> "NH2" Residue "C GLU 330": "OE1" <-> "OE2" Residue "C ASP 524": "OD1" <-> "OD2" Residue "E ASP 59": "OD1" <-> "OD2" Residue "E ARG 311": "NH1" <-> "NH2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 391": "OD1" <-> "OD2" Residue "E ASP 524": "OD1" <-> "OD2" Residue "E PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 678": "OD1" <-> "OD2" Residue "G ASP 59": "OD1" <-> "OD2" Residue "G GLU 71": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I GLU 470": "OE1" <-> "OE2" Residue "I TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 401": "OE1" <-> "OE2" Residue "J TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 419": "OD1" <-> "OD2" Residue "J TYR 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 49715 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 838, 6701 Classifications: {'peptide': 838} Link IDs: {'PTRANS': 32, 'TRANS': 805} Chain breaks: 1 Chain: "B" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3211 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 381} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 6701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 838, 6701 Classifications: {'peptide': 838} Link IDs: {'PTRANS': 32, 'TRANS': 805} Chain breaks: 1 Chain: "E" Number of atoms: 6701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 838, 6701 Classifications: {'peptide': 838} Link IDs: {'PTRANS': 32, 'TRANS': 805} Chain breaks: 1 Chain: "G" Number of atoms: 6701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 838, 6701 Classifications: {'peptide': 838} Link IDs: {'PTRANS': 32, 'TRANS': 805} Chain breaks: 1 Chain: "I" Number of atoms: 6701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 838, 6701 Classifications: {'peptide': 838} Link IDs: {'PTRANS': 32, 'TRANS': 805} Chain breaks: 1 Chain: "D" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3211 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 381} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3211 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 381} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3211 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 381} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "J" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3211 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 381} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.49, per 1000 atoms: 0.51 Number of scatterers: 49715 At special positions: 0 Unit cell: (245.3, 244.2, 104.5, 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 235 16.00 P 15 15.00 O 9295 8.00 N 8330 7.00 C 31840 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.64 Conformation dependent library (CDL) restraints added in 9.6 seconds 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11750 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 246 helices and 37 sheets defined 43.0% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.86 Creating SS restraints... Processing helix chain 'A' and resid 25 through 52 removed outlier: 3.516A pdb=" N VAL A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 86 Processing helix chain 'A' and resid 116 through 140 removed outlier: 3.934A pdb=" N GLU A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.551A pdb=" N LYS A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 246 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.800A pdb=" N GLU A 291 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 294 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 334 through 344 removed outlier: 3.684A pdb=" N ARG A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 367 removed outlier: 3.714A pdb=" N LYS A 366 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 411 through 423 removed outlier: 3.597A pdb=" N LYS A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 417 " --> pdb=" O MET A 413 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 4.136A pdb=" N LEU A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 469 through 481 Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.812A pdb=" N LEU A 508 " --> pdb=" O MET A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.396A pdb=" N GLY A 619 " --> pdb=" O MET A 616 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 620 " --> pdb=" O GLU A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 681 through 688 removed outlier: 3.817A pdb=" N LEU A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY A 688 " --> pdb=" O VAL A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 717 removed outlier: 3.637A pdb=" N SER A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 717 " --> pdb=" O GLU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 793 removed outlier: 3.954A pdb=" N THR A 793 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 809 Processing helix chain 'A' and resid 841 through 843 No H-bonds generated for 'chain 'A' and resid 841 through 843' Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'B' and resid 142 through 149 removed outlier: 3.535A pdb=" N GLU B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 removed outlier: 3.842A pdb=" N ASN B 189 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 200 removed outlier: 3.677A pdb=" N SER B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 197 through 200' Processing helix chain 'B' and resid 211 through 225 removed outlier: 3.782A pdb=" N LYS B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.571A pdb=" N ILE B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 241 " --> pdb=" O ILE B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 275 removed outlier: 3.559A pdb=" N SER B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 269 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 291 through 316 removed outlier: 4.263A pdb=" N VAL B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 308 " --> pdb=" O THR B 304 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASP B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 336 through 346 removed outlier: 3.908A pdb=" N LEU B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 365 removed outlier: 3.644A pdb=" N SER B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 391 removed outlier: 3.652A pdb=" N GLU B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 391 " --> pdb=" O TYR B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 418 Processing helix chain 'B' and resid 424 through 440 removed outlier: 3.852A pdb=" N GLU B 433 " --> pdb=" O TYR B 429 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 439 " --> pdb=" O ASN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 456 through 480 removed outlier: 3.720A pdb=" N GLU B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS B 467 " --> pdb=" O VAL B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 removed outlier: 3.622A pdb=" N GLU B 513 " --> pdb=" O GLY B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 removed outlier: 3.533A pdb=" N ASP B 520 " --> pdb=" O VAL B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 removed outlier: 3.691A pdb=" N GLN B 538 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 551 Processing helix chain 'C' and resid 25 through 52 removed outlier: 3.589A pdb=" N VAL C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 86 Processing helix chain 'C' and resid 116 through 139 Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.834A pdb=" N LYS C 294 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 334 through 344 removed outlier: 3.621A pdb=" N ARG C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 367 removed outlier: 3.856A pdb=" N LYS C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS C 366 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS C 367 " --> pdb=" O ILE C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 381 Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 411 through 423 removed outlier: 3.673A pdb=" N LYS C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ILE C 416 " --> pdb=" O GLN C 412 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 436 removed outlier: 4.153A pdb=" N LEU C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 456 Processing helix chain 'C' and resid 470 through 481 Processing helix chain 'C' and resid 503 through 514 Processing helix chain 'C' and resid 595 through 597 No H-bonds generated for 'chain 'C' and resid 595 through 597' Processing helix chain 'C' and resid 616 through 620 removed outlier: 4.444A pdb=" N GLY C 619 " --> pdb=" O MET C 616 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C 620 " --> pdb=" O GLU C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 681 through 688 removed outlier: 3.670A pdb=" N LEU C 687 " --> pdb=" O PHE C 683 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY C 688 " --> pdb=" O VAL C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 717 removed outlier: 4.157A pdb=" N SER C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN C 717 " --> pdb=" O GLU C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 793 removed outlier: 3.909A pdb=" N THR C 793 " --> pdb=" O GLN C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 809 Processing helix chain 'C' and resid 861 through 863 No H-bonds generated for 'chain 'C' and resid 861 through 863' Processing helix chain 'E' and resid 25 through 52 removed outlier: 3.565A pdb=" N VAL E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU E 34 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS E 52 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 86 Processing helix chain 'E' and resid 116 through 139 removed outlier: 3.744A pdb=" N GLU E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 235 through 246 Processing helix chain 'E' and resid 263 through 272 Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.904A pdb=" N GLU E 291 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS E 295 " --> pdb=" O LEU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 316 No H-bonds generated for 'chain 'E' and resid 313 through 316' Processing helix chain 'E' and resid 334 through 345 removed outlier: 3.555A pdb=" N ARG E 344 " --> pdb=" O LEU E 340 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 345 " --> pdb=" O PHE E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 367 removed outlier: 4.156A pdb=" N LYS E 366 " --> pdb=" O GLU E 362 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS E 367 " --> pdb=" O ILE E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 381 removed outlier: 3.881A pdb=" N ALA E 378 " --> pdb=" O ILE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 399 Processing helix chain 'E' and resid 411 through 423 removed outlier: 4.852A pdb=" N ILE E 416 " --> pdb=" O GLN E 412 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU E 417 " --> pdb=" O MET E 413 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER E 420 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 436 removed outlier: 4.125A pdb=" N LEU E 435 " --> pdb=" O CYS E 431 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER E 436 " --> pdb=" O LEU E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 456 Processing helix chain 'E' and resid 470 through 481 Processing helix chain 'E' and resid 503 through 515 Processing helix chain 'E' and resid 595 through 597 No H-bonds generated for 'chain 'E' and resid 595 through 597' Processing helix chain 'E' and resid 616 through 620 removed outlier: 4.325A pdb=" N GLY E 619 " --> pdb=" O MET E 616 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 620 " --> pdb=" O GLU E 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 616 through 620' Processing helix chain 'E' and resid 681 through 688 removed outlier: 3.748A pdb=" N LEU E 687 " --> pdb=" O PHE E 683 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY E 688 " --> pdb=" O VAL E 684 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 717 removed outlier: 4.119A pdb=" N SER E 716 " --> pdb=" O GLU E 712 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN E 717 " --> pdb=" O GLU E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 793 removed outlier: 3.883A pdb=" N THR E 793 " --> pdb=" O GLN E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 805 through 809 Processing helix chain 'E' and resid 841 through 843 No H-bonds generated for 'chain 'E' and resid 841 through 843' Processing helix chain 'E' and resid 861 through 863 No H-bonds generated for 'chain 'E' and resid 861 through 863' Processing helix chain 'G' and resid 25 through 52 removed outlier: 3.563A pdb=" N SER G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 86 Processing helix chain 'G' and resid 116 through 139 removed outlier: 3.865A pdb=" N GLU G 136 " --> pdb=" O LYS G 132 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG G 138 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN G 139 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 161 No H-bonds generated for 'chain 'G' and resid 159 through 161' Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 175 through 180 Processing helix chain 'G' and resid 207 through 216 Processing helix chain 'G' and resid 235 through 246 Processing helix chain 'G' and resid 263 through 272 Processing helix chain 'G' and resid 287 through 296 removed outlier: 3.937A pdb=" N GLU G 291 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS G 295 " --> pdb=" O LEU G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 315 No H-bonds generated for 'chain 'G' and resid 313 through 315' Processing helix chain 'G' and resid 334 through 344 removed outlier: 3.692A pdb=" N ARG G 344 " --> pdb=" O LEU G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 367 removed outlier: 4.170A pdb=" N LYS G 365 " --> pdb=" O GLU G 361 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS G 366 " --> pdb=" O GLU G 362 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS G 367 " --> pdb=" O ILE G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 381 Processing helix chain 'G' and resid 392 through 399 Processing helix chain 'G' and resid 411 through 423 removed outlier: 3.654A pdb=" N LYS G 415 " --> pdb=" O GLU G 411 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE G 416 " --> pdb=" O GLN G 412 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 417 " --> pdb=" O MET G 413 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER G 420 " --> pdb=" O ILE G 416 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR G 421 " --> pdb=" O LEU G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 436 removed outlier: 4.137A pdb=" N LEU G 435 " --> pdb=" O CYS G 431 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER G 436 " --> pdb=" O LEU G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 456 Processing helix chain 'G' and resid 470 through 481 Processing helix chain 'G' and resid 503 through 514 Processing helix chain 'G' and resid 595 through 597 No H-bonds generated for 'chain 'G' and resid 595 through 597' Processing helix chain 'G' and resid 616 through 620 removed outlier: 4.366A pdb=" N GLY G 619 " --> pdb=" O MET G 616 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS G 620 " --> pdb=" O GLU G 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 616 through 620' Processing helix chain 'G' and resid 662 through 664 No H-bonds generated for 'chain 'G' and resid 662 through 664' Processing helix chain 'G' and resid 681 through 688 removed outlier: 3.760A pdb=" N LEU G 687 " --> pdb=" O PHE G 683 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY G 688 " --> pdb=" O VAL G 684 " (cutoff:3.500A) Processing helix chain 'G' and resid 706 through 717 removed outlier: 3.639A pdb=" N SER G 714 " --> pdb=" O ALA G 710 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER G 716 " --> pdb=" O GLU G 712 " (cutoff:3.500A) Processing helix chain 'G' and resid 785 through 793 removed outlier: 3.918A pdb=" N GLN G 789 " --> pdb=" O SER G 785 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR G 793 " --> pdb=" O GLN G 789 " (cutoff:3.500A) Processing helix chain 'G' and resid 805 through 809 Processing helix chain 'G' and resid 841 through 843 No H-bonds generated for 'chain 'G' and resid 841 through 843' Processing helix chain 'G' and resid 861 through 863 No H-bonds generated for 'chain 'G' and resid 861 through 863' Processing helix chain 'I' and resid 25 through 52 removed outlier: 3.524A pdb=" N VAL I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU I 34 " --> pdb=" O ARG I 30 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS I 52 " --> pdb=" O SER I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 86 Processing helix chain 'I' and resid 116 through 140 removed outlier: 3.842A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU I 137 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG I 138 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN I 139 " --> pdb=" O ALA I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 161 No H-bonds generated for 'chain 'I' and resid 159 through 161' Processing helix chain 'I' and resid 165 through 167 No H-bonds generated for 'chain 'I' and resid 165 through 167' Processing helix chain 'I' and resid 175 through 185 removed outlier: 3.579A pdb=" N GLU I 184 " --> pdb=" O ASN I 180 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY I 185 " --> pdb=" O MET I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 216 Processing helix chain 'I' and resid 235 through 246 Processing helix chain 'I' and resid 263 through 272 Processing helix chain 'I' and resid 287 through 296 removed outlier: 3.897A pdb=" N GLU I 291 " --> pdb=" O LYS I 288 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS I 294 " --> pdb=" O GLU I 291 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N CYS I 295 " --> pdb=" O LEU I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 315 No H-bonds generated for 'chain 'I' and resid 313 through 315' Processing helix chain 'I' and resid 323 through 325 No H-bonds generated for 'chain 'I' and resid 323 through 325' Processing helix chain 'I' and resid 334 through 344 removed outlier: 3.693A pdb=" N ARG I 344 " --> pdb=" O LEU I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 357 through 367 removed outlier: 3.991A pdb=" N LYS I 366 " --> pdb=" O GLU I 362 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS I 367 " --> pdb=" O ILE I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 381 Processing helix chain 'I' and resid 392 through 399 Processing helix chain 'I' and resid 411 through 423 removed outlier: 3.610A pdb=" N LYS I 415 " --> pdb=" O GLU I 411 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE I 416 " --> pdb=" O GLN I 412 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU I 417 " --> pdb=" O MET I 413 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N SER I 420 " --> pdb=" O ILE I 416 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR I 421 " --> pdb=" O LEU I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 436 removed outlier: 4.144A pdb=" N LEU I 435 " --> pdb=" O CYS I 431 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER I 436 " --> pdb=" O LEU I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 456 Processing helix chain 'I' and resid 470 through 481 Processing helix chain 'I' and resid 503 through 515 Processing helix chain 'I' and resid 595 through 597 No H-bonds generated for 'chain 'I' and resid 595 through 597' Processing helix chain 'I' and resid 616 through 620 removed outlier: 4.366A pdb=" N GLY I 619 " --> pdb=" O MET I 616 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS I 620 " --> pdb=" O GLU I 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 616 through 620' Processing helix chain 'I' and resid 662 through 664 No H-bonds generated for 'chain 'I' and resid 662 through 664' Processing helix chain 'I' and resid 681 through 688 removed outlier: 3.711A pdb=" N LEU I 687 " --> pdb=" O PHE I 683 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY I 688 " --> pdb=" O VAL I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 706 through 717 removed outlier: 3.644A pdb=" N SER I 714 " --> pdb=" O ALA I 710 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER I 716 " --> pdb=" O GLU I 712 " (cutoff:3.500A) Processing helix chain 'I' and resid 785 through 793 removed outlier: 4.010A pdb=" N GLN I 789 " --> pdb=" O SER I 785 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR I 793 " --> pdb=" O GLN I 789 " (cutoff:3.500A) Processing helix chain 'I' and resid 805 through 809 Processing helix chain 'I' and resid 841 through 843 No H-bonds generated for 'chain 'I' and resid 841 through 843' Processing helix chain 'I' and resid 861 through 863 No H-bonds generated for 'chain 'I' and resid 861 through 863' Processing helix chain 'D' and resid 142 through 149 removed outlier: 3.577A pdb=" N GLU D 147 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TYR D 148 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 194 removed outlier: 3.827A pdb=" N ASN D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LYS D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 200 removed outlier: 3.672A pdb=" N SER D 200 " --> pdb=" O ILE D 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 197 through 200' Processing helix chain 'D' and resid 211 through 225 removed outlier: 3.766A pdb=" N LYS D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 removed outlier: 3.707A pdb=" N ILE D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU D 235 " --> pdb=" O GLU D 231 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 275 removed outlier: 3.524A pdb=" N PHE D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER D 261 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS D 271 " --> pdb=" O LEU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 288 Processing helix chain 'D' and resid 291 through 316 removed outlier: 3.717A pdb=" N ALA D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL D 302 " --> pdb=" O ALA D 298 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 308 " --> pdb=" O THR D 304 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE D 310 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASP D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER D 312 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER D 314 " --> pdb=" O PHE D 310 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 335 through 346 removed outlier: 3.668A pdb=" N THR D 338 " --> pdb=" O HIS D 335 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ALA D 342 " --> pdb=" O PHE D 339 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 345 " --> pdb=" O ALA D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 364 removed outlier: 3.549A pdb=" N SER D 352 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS D 364 " --> pdb=" O GLY D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 391 removed outlier: 3.722A pdb=" N GLU D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS D 391 " --> pdb=" O TYR D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 418 Processing helix chain 'D' and resid 424 through 440 removed outlier: 3.909A pdb=" N THR D 436 " --> pdb=" O HIS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 454 No H-bonds generated for 'chain 'D' and resid 452 through 454' Processing helix chain 'D' and resid 456 through 482 removed outlier: 3.596A pdb=" N GLU D 461 " --> pdb=" O ARG D 457 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 470 " --> pdb=" O THR D 466 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN D 471 " --> pdb=" O CYS D 467 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 472 " --> pdb=" O GLN D 468 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU D 481 " --> pdb=" O HIS D 477 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 removed outlier: 3.511A pdb=" N LYS D 512 " --> pdb=" O HIS D 509 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU D 513 " --> pdb=" O GLY D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 526 removed outlier: 3.569A pdb=" N ASP D 520 " --> pdb=" O VAL D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 541 through 551 Processing helix chain 'F' and resid 142 through 149 removed outlier: 3.777A pdb=" N GLU F 147 " --> pdb=" O LYS F 143 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TYR F 148 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 removed outlier: 3.844A pdb=" N ASN F 189 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 200 removed outlier: 3.589A pdb=" N SER F 200 " --> pdb=" O ILE F 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 197 through 200' Processing helix chain 'F' and resid 211 through 225 removed outlier: 3.758A pdb=" N LYS F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN F 225 " --> pdb=" O ASP F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 241 removed outlier: 3.939A pdb=" N ILE F 234 " --> pdb=" O PRO F 230 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU F 235 " --> pdb=" O GLU F 231 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL F 240 " --> pdb=" O GLU F 236 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU F 241 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 275 removed outlier: 4.556A pdb=" N SER F 261 " --> pdb=" O GLN F 257 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE F 269 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS F 271 " --> pdb=" O LEU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 288 Processing helix chain 'F' and resid 291 through 316 removed outlier: 3.599A pdb=" N LYS F 295 " --> pdb=" O ASP F 291 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS F 308 " --> pdb=" O THR F 304 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE F 310 " --> pdb=" O LYS F 306 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASP F 311 " --> pdb=" O MET F 307 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER F 312 " --> pdb=" O LYS F 308 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS F 315 " --> pdb=" O ASP F 311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET F 316 " --> pdb=" O SER F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 321 No H-bonds generated for 'chain 'F' and resid 319 through 321' Processing helix chain 'F' and resid 335 through 346 removed outlier: 3.591A pdb=" N THR F 338 " --> pdb=" O HIS F 335 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ALA F 342 " --> pdb=" O PHE F 339 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS F 345 " --> pdb=" O ALA F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 365 removed outlier: 3.627A pdb=" N SER F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 364 " --> pdb=" O GLY F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 3.773A pdb=" N GLU F 385 " --> pdb=" O ARG F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 418 removed outlier: 3.509A pdb=" N LYS F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER F 413 " --> pdb=" O LYS F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 440 removed outlier: 4.003A pdb=" N THR F 436 " --> pdb=" O HIS F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 454 Processing helix chain 'F' and resid 456 through 480 removed outlier: 3.826A pdb=" N GLU F 461 " --> pdb=" O ARG F 457 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR F 466 " --> pdb=" O SER F 462 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N CYS F 467 " --> pdb=" O VAL F 463 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN F 468 " --> pdb=" O SER F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 514 removed outlier: 4.243A pdb=" N GLU F 513 " --> pdb=" O HIS F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 516 through 526 Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 541 through 551 Processing helix chain 'H' and resid 142 through 149 removed outlier: 3.612A pdb=" N GLU H 147 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N TYR H 148 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 191 removed outlier: 3.853A pdb=" N ASN H 189 " --> pdb=" O PHE H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 200 removed outlier: 3.643A pdb=" N SER H 200 " --> pdb=" O ILE H 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 197 through 200' Processing helix chain 'H' and resid 211 through 225 removed outlier: 3.526A pdb=" N LYS H 219 " --> pdb=" O ASP H 215 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN H 225 " --> pdb=" O ASP H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 241 removed outlier: 3.652A pdb=" N ILE H 234 " --> pdb=" O PRO H 230 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLU H 235 " --> pdb=" O GLU H 231 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL H 240 " --> pdb=" O GLU H 236 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 241 " --> pdb=" O ILE H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 275 removed outlier: 3.528A pdb=" N PHE H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER H 261 " --> pdb=" O GLN H 257 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE H 269 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE H 270 " --> pdb=" O ALA H 266 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS H 271 " --> pdb=" O LEU H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 288 Processing helix chain 'H' and resid 291 through 316 removed outlier: 3.866A pdb=" N LYS H 295 " --> pdb=" O ASP H 291 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL H 302 " --> pdb=" O ALA H 298 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS H 308 " --> pdb=" O THR H 304 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE H 310 " --> pdb=" O LYS H 306 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ASP H 311 " --> pdb=" O MET H 307 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER H 312 " --> pdb=" O LYS H 308 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS H 315 " --> pdb=" O ASP H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 321 No H-bonds generated for 'chain 'H' and resid 319 through 321' Processing helix chain 'H' and resid 335 through 346 removed outlier: 3.889A pdb=" N ASP H 341 " --> pdb=" O THR H 338 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA H 342 " --> pdb=" O PHE H 339 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS H 345 " --> pdb=" O ALA H 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 348 through 364 removed outlier: 3.971A pdb=" N LYS H 364 " --> pdb=" O GLY H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 391 removed outlier: 3.786A pdb=" N GLU H 385 " --> pdb=" O ARG H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 418 Processing helix chain 'H' and resid 424 through 440 removed outlier: 3.733A pdb=" N THR H 436 " --> pdb=" O HIS H 432 " (cutoff:3.500A) Processing helix chain 'H' and resid 450 through 454 Processing helix chain 'H' and resid 456 through 480 removed outlier: 4.065A pdb=" N CYS H 467 " --> pdb=" O VAL H 463 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN H 468 " --> pdb=" O SER H 464 " (cutoff:3.500A) Processing helix chain 'H' and resid 509 through 514 removed outlier: 3.651A pdb=" N GLU H 513 " --> pdb=" O GLY H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 516 through 526 removed outlier: 3.607A pdb=" N ASP H 520 " --> pdb=" O VAL H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 534 through 539 removed outlier: 3.691A pdb=" N GLN H 538 " --> pdb=" O ASN H 534 " (cutoff:3.500A) Processing helix chain 'H' and resid 541 through 551 Processing helix chain 'J' and resid 142 through 149 removed outlier: 3.583A pdb=" N GLU J 147 " --> pdb=" O LYS J 143 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR J 148 " --> pdb=" O ASP J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 194 removed outlier: 3.811A pdb=" N ASN J 189 " --> pdb=" O PHE J 185 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 200 removed outlier: 3.666A pdb=" N SER J 200 " --> pdb=" O ILE J 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 197 through 200' Processing helix chain 'J' and resid 211 through 225 removed outlier: 3.813A pdb=" N LYS J 219 " --> pdb=" O ASP J 215 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN J 225 " --> pdb=" O ASP J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 230 through 241 removed outlier: 3.601A pdb=" N ILE J 234 " --> pdb=" O PRO J 230 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLU J 235 " --> pdb=" O GLU J 231 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL J 240 " --> pdb=" O GLU J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 275 removed outlier: 4.788A pdb=" N SER J 261 " --> pdb=" O GLN J 257 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE J 269 " --> pdb=" O PHE J 265 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE J 270 " --> pdb=" O ALA J 266 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS J 271 " --> pdb=" O LEU J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 281 through 288 Processing helix chain 'J' and resid 291 through 316 removed outlier: 3.631A pdb=" N LYS J 295 " --> pdb=" O ASP J 291 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL J 302 " --> pdb=" O ALA J 298 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS J 308 " --> pdb=" O THR J 304 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE J 310 " --> pdb=" O LYS J 306 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ASP J 311 " --> pdb=" O MET J 307 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER J 312 " --> pdb=" O LYS J 308 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS J 315 " --> pdb=" O ASP J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 319 through 321 No H-bonds generated for 'chain 'J' and resid 319 through 321' Processing helix chain 'J' and resid 325 through 327 No H-bonds generated for 'chain 'J' and resid 325 through 327' Processing helix chain 'J' and resid 334 through 346 removed outlier: 3.975A pdb=" N LYS J 337 " --> pdb=" O SER J 334 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR J 338 " --> pdb=" O HIS J 335 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ALA J 342 " --> pdb=" O PHE J 339 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS J 345 " --> pdb=" O ALA J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 348 through 365 removed outlier: 3.558A pdb=" N SER J 352 " --> pdb=" O ALA J 348 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 389 removed outlier: 3.609A pdb=" N GLU J 385 " --> pdb=" O ARG J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 403 through 418 removed outlier: 3.523A pdb=" N LYS J 412 " --> pdb=" O ALA J 408 " (cutoff:3.500A) Processing helix chain 'J' and resid 424 through 440 removed outlier: 4.105A pdb=" N THR J 436 " --> pdb=" O HIS J 432 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 454 removed outlier: 3.585A pdb=" N SER J 454 " --> pdb=" O ASP J 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 450 through 454' Processing helix chain 'J' and resid 456 through 482 removed outlier: 3.737A pdb=" N GLU J 461 " --> pdb=" O ARG J 457 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU J 470 " --> pdb=" O THR J 466 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN J 471 " --> pdb=" O CYS J 467 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU J 472 " --> pdb=" O GLN J 468 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU J 481 " --> pdb=" O HIS J 477 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER J 482 " --> pdb=" O ARG J 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 509 through 514 removed outlier: 3.617A pdb=" N GLU J 513 " --> pdb=" O GLY J 510 " (cutoff:3.500A) Processing helix chain 'J' and resid 516 through 526 removed outlier: 3.521A pdb=" N ASP J 520 " --> pdb=" O VAL J 516 " (cutoff:3.500A) Processing helix chain 'J' and resid 534 through 539 removed outlier: 3.694A pdb=" N GLN J 538 " --> pdb=" O ASN J 534 " (cutoff:3.500A) Processing helix chain 'J' and resid 541 through 552 Processing sheet with id= A, first strand: chain 'A' and resid 194 through 199 Processing sheet with id= B, first strand: chain 'A' and resid 225 through 228 Processing sheet with id= C, first strand: chain 'A' and resid 486 through 488 Processing sheet with id= D, first strand: chain 'A' and resid 538 through 540 removed outlier: 6.563A pdb=" N SER A 558 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL A 581 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N TYR A 603 " --> pdb=" O LEU A 582 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 649 through 651 removed outlier: 7.260A pdb=" N VAL A 670 " --> pdb=" O LEU A 650 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 723 through 727 removed outlier: 3.606A pdb=" N LEU A 696 " --> pdb=" O SER A 723 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 725 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU A 674 " --> pdb=" O ASP A 699 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS A 701 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N LEU A 676 " --> pdb=" O HIS A 701 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 778 through 780 removed outlier: 6.353A pdb=" N GLU A 831 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ILE A 802 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARG A 833 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ASN A 804 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE A 835 " --> pdb=" O ASN A 804 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARG A 854 " --> pdb=" O CYS A 832 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N PHE A 834 " --> pdb=" O ARG A 854 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N TRP A 856 " --> pdb=" O PHE A 834 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 858 through 860 removed outlier: 6.474A pdb=" N ASP A 885 " --> pdb=" O PHE A 859 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 195 through 199 removed outlier: 7.160A pdb=" N LEU C 306 " --> pdb=" O ILE C 196 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE C 198 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR C 308 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 279 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR C 309 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE C 281 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA C 225 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASP C 282 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL C 227 " --> pdb=" O ASP C 282 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 486 through 488 Processing sheet with id= K, first strand: chain 'C' and resid 538 through 541 removed outlier: 6.550A pdb=" N SER C 558 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE C 541 " --> pdb=" O SER C 558 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR C 560 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 581 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N VAL C 561 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASP C 583 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR C 603 " --> pdb=" O LEU C 582 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 649 through 651 removed outlier: 7.226A pdb=" N VAL C 670 " --> pdb=" O LEU C 650 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 723 through 727 removed outlier: 3.656A pdb=" N LEU C 696 " --> pdb=" O SER C 723 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP C 725 " --> pdb=" O LEU C 696 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU C 674 " --> pdb=" O ASP C 699 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N HIS C 701 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N LEU C 676 " --> pdb=" O HIS C 701 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 778 through 780 removed outlier: 6.394A pdb=" N GLU C 831 " --> pdb=" O LEU C 800 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ILE C 802 " --> pdb=" O GLU C 831 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG C 833 " --> pdb=" O ILE C 802 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ASN C 804 " --> pdb=" O ARG C 833 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE C 835 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG C 854 " --> pdb=" O CYS C 832 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE C 834 " --> pdb=" O ARG C 854 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N TRP C 856 " --> pdb=" O PHE C 834 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 858 through 860 removed outlier: 6.381A pdb=" N ASP C 885 " --> pdb=" O PHE C 859 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'E' and resid 195 through 199 removed outlier: 6.931A pdb=" N LEU E 306 " --> pdb=" O ILE E 196 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ILE E 198 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR E 308 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 279 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N THR E 309 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE E 281 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ALA E 225 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASP E 282 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL E 227 " --> pdb=" O ASP E 282 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 486 through 488 Processing sheet with id= R, first strand: chain 'E' and resid 538 through 540 removed outlier: 6.696A pdb=" N SER E 558 " --> pdb=" O LEU E 539 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL E 581 " --> pdb=" O VAL E 559 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR E 603 " --> pdb=" O LEU E 582 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 626 through 628 removed outlier: 6.880A pdb=" N CYS E 649 " --> pdb=" O LEU E 627 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL E 670 " --> pdb=" O LEU E 650 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 723 through 727 removed outlier: 3.697A pdb=" N LEU E 696 " --> pdb=" O SER E 723 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP E 725 " --> pdb=" O LEU E 696 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU E 674 " --> pdb=" O ASP E 699 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS E 701 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N LEU E 676 " --> pdb=" O HIS E 701 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 778 through 780 removed outlier: 6.370A pdb=" N GLU E 831 " --> pdb=" O LEU E 800 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE E 802 " --> pdb=" O GLU E 831 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG E 833 " --> pdb=" O ILE E 802 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ASN E 804 " --> pdb=" O ARG E 833 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE E 835 " --> pdb=" O ASN E 804 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG E 854 " --> pdb=" O CYS E 832 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE E 834 " --> pdb=" O ARG E 854 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N TRP E 856 " --> pdb=" O PHE E 834 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 858 through 860 removed outlier: 6.369A pdb=" N ASP E 885 " --> pdb=" O PHE E 859 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'G' and resid 194 through 199 Processing sheet with id= X, first strand: chain 'G' and resid 225 through 228 Processing sheet with id= Y, first strand: chain 'G' and resid 486 through 488 Processing sheet with id= Z, first strand: chain 'G' and resid 538 through 541 removed outlier: 6.767A pdb=" N SER G 558 " --> pdb=" O LEU G 539 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE G 541 " --> pdb=" O SER G 558 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR G 560 " --> pdb=" O ILE G 541 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL G 581 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N VAL G 561 " --> pdb=" O VAL G 581 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASP G 583 " --> pdb=" O VAL G 561 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N TYR G 603 " --> pdb=" O LEU G 582 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'G' and resid 649 through 651 removed outlier: 7.340A pdb=" N VAL G 670 " --> pdb=" O LEU G 650 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G' and resid 723 through 727 removed outlier: 3.626A pdb=" N LEU G 696 " --> pdb=" O SER G 723 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP G 725 " --> pdb=" O LEU G 696 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU G 674 " --> pdb=" O ASP G 699 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N HIS G 701 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N LEU G 676 " --> pdb=" O HIS G 701 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 778 through 780 removed outlier: 6.401A pdb=" N GLU G 831 " --> pdb=" O LEU G 800 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ILE G 802 " --> pdb=" O GLU G 831 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG G 833 " --> pdb=" O ILE G 802 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ASN G 804 " --> pdb=" O ARG G 833 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE G 835 " --> pdb=" O ASN G 804 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG G 854 " --> pdb=" O CYS G 832 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE G 834 " --> pdb=" O ARG G 854 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TRP G 856 " --> pdb=" O PHE G 834 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 858 through 860 removed outlier: 6.447A pdb=" N ASP G 885 " --> pdb=" O PHE G 859 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'I' and resid 194 through 199 removed outlier: 6.867A pdb=" N ILE I 279 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N THR I 309 " --> pdb=" O ILE I 279 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE I 281 " --> pdb=" O THR I 309 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALA I 225 " --> pdb=" O VAL I 280 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASP I 282 " --> pdb=" O ALA I 225 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL I 227 " --> pdb=" O ASP I 282 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 486 through 488 Processing sheet with id= AG, first strand: chain 'I' and resid 538 through 541 removed outlier: 6.718A pdb=" N SER I 558 " --> pdb=" O LEU I 539 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ILE I 541 " --> pdb=" O SER I 558 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR I 560 " --> pdb=" O ILE I 541 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL I 581 " --> pdb=" O VAL I 559 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N VAL I 561 " --> pdb=" O VAL I 581 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP I 583 " --> pdb=" O VAL I 561 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N TYR I 603 " --> pdb=" O LEU I 582 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'I' and resid 649 through 651 removed outlier: 7.222A pdb=" N VAL I 670 " --> pdb=" O LEU I 650 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'I' and resid 723 through 727 removed outlier: 4.028A pdb=" N LEU I 696 " --> pdb=" O SER I 723 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP I 725 " --> pdb=" O LEU I 696 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU I 674 " --> pdb=" O ASP I 699 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N HIS I 701 " --> pdb=" O LEU I 674 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N LEU I 676 " --> pdb=" O HIS I 701 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 778 through 780 removed outlier: 6.379A pdb=" N GLU I 831 " --> pdb=" O LEU I 800 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE I 802 " --> pdb=" O GLU I 831 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG I 833 " --> pdb=" O ILE I 802 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ASN I 804 " --> pdb=" O ARG I 833 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE I 835 " --> pdb=" O ASN I 804 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 858 through 860 removed outlier: 6.348A pdb=" N ASP I 885 " --> pdb=" O PHE I 859 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK 1480 hydrogen bonds defined for protein. 4242 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: 17.26 Time building geometry restraints manager: 22.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11638 1.33 - 1.45: 9831 1.45 - 1.57: 28811 1.57 - 1.69: 20 1.69 - 1.82: 380 Bond restraints: 50680 Sorted by residual: bond pdb=" N LEU A 770 " pdb=" CA LEU A 770 " ideal model delta sigma weight residual 1.458 1.494 -0.037 7.40e-03 1.83e+04 2.46e+01 bond pdb=" N TYR F 255 " pdb=" CA TYR F 255 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.16e-02 7.43e+03 6.31e+00 bond pdb=" N ARG C 311 " pdb=" CA ARG C 311 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.32e-02 5.74e+03 6.11e+00 bond pdb=" N ARG E 311 " pdb=" CA ARG E 311 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.32e-02 5.74e+03 6.06e+00 bond pdb=" N TYR B 255 " pdb=" CA TYR B 255 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.16e-02 7.43e+03 5.96e+00 ... (remaining 50675 not shown) Histogram of bond angle deviations from ideal: 94.21 - 103.27: 432 103.27 - 112.34: 26306 112.34 - 121.40: 29737 121.40 - 130.47: 11739 130.47 - 139.54: 221 Bond angle restraints: 68435 Sorted by residual: angle pdb=" N VAL C 570 " pdb=" CA VAL C 570 " pdb=" C VAL C 570 " ideal model delta sigma weight residual 113.71 108.99 4.72 9.50e-01 1.11e+00 2.47e+01 angle pdb=" N GLU C 167 " pdb=" CA GLU C 167 " pdb=" C GLU C 167 " ideal model delta sigma weight residual 114.62 109.06 5.56 1.14e+00 7.69e-01 2.38e+01 angle pdb=" N VAL G 570 " pdb=" CA VAL G 570 " pdb=" C VAL G 570 " ideal model delta sigma weight residual 113.71 109.11 4.60 9.50e-01 1.11e+00 2.34e+01 angle pdb=" N ILE E 217 " pdb=" CA ILE E 217 " pdb=" C ILE E 217 " ideal model delta sigma weight residual 106.21 111.22 -5.01 1.07e+00 8.73e-01 2.19e+01 angle pdb=" CA LEU A 770 " pdb=" C LEU A 770 " pdb=" O LEU A 770 " ideal model delta sigma weight residual 120.48 117.42 3.06 7.70e-01 1.69e+00 1.58e+01 ... (remaining 68430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 28388 17.80 - 35.60: 2142 35.60 - 53.40: 372 53.40 - 71.20: 93 71.20 - 89.00: 35 Dihedral angle restraints: 31030 sinusoidal: 12930 harmonic: 18100 Sorted by residual: dihedral pdb=" CD ARG G 305 " pdb=" NE ARG G 305 " pdb=" CZ ARG G 305 " pdb=" NH1 ARG G 305 " ideal model delta sinusoidal sigma weight residual 0.00 87.68 -87.68 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CD ARG A 305 " pdb=" NE ARG A 305 " pdb=" CZ ARG A 305 " pdb=" NH1 ARG A 305 " ideal model delta sinusoidal sigma weight residual 0.00 -86.93 86.93 1 1.00e+01 1.00e-02 9.09e+01 dihedral pdb=" CA ALA A 389 " pdb=" C ALA A 389 " pdb=" N LYS A 390 " pdb=" CA LYS A 390 " ideal model delta harmonic sigma weight residual 180.00 153.76 26.24 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 31027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 5567 0.045 - 0.090: 1729 0.090 - 0.134: 401 0.134 - 0.179: 47 0.179 - 0.224: 6 Chirality restraints: 7750 Sorted by residual: chirality pdb=" CG LEU F 193 " pdb=" CB LEU F 193 " pdb=" CD1 LEU F 193 " pdb=" CD2 LEU F 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU H 193 " pdb=" CB LEU H 193 " pdb=" CD1 LEU H 193 " pdb=" CD2 LEU H 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLN C 44 " pdb=" N GLN C 44 " pdb=" C GLN C 44 " pdb=" CB GLN C 44 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 7747 not shown) Planarity restraints: 8585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 305 " 1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG G 305 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 305 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 305 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG G 305 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 305 " 1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 305 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 305 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 305 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 305 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 311 " 0.273 9.50e-02 1.11e+02 1.23e-01 9.20e+00 pdb=" NE ARG C 311 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 311 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 311 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 311 " 0.010 2.00e-02 2.50e+03 ... (remaining 8582 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 5201 2.74 - 3.28: 54153 3.28 - 3.82: 81542 3.82 - 4.36: 97204 4.36 - 4.90: 156823 Nonbonded interactions: 394923 Sorted by model distance: nonbonded pdb=" NH2 ARG I 448 " pdb=" OD2 ASP I 583 " model vdw 2.201 2.520 nonbonded pdb=" OE2 GLU G 809 " pdb=" OH TYR H 387 " model vdw 2.202 2.440 nonbonded pdb=" NH2 ARG C 448 " pdb=" OD2 ASP C 583 " model vdw 2.206 2.520 nonbonded pdb=" NH2 ARG A 448 " pdb=" OD2 ASP A 583 " model vdw 2.210 2.520 nonbonded pdb=" OG SER A 467 " pdb=" OE1 GLU A 470 " model vdw 2.214 2.440 ... (remaining 394918 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' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 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: 0.010 Normalize map: mean=0, sd=1: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 16.860 Check model and map are aligned: 0.690 Set scattering table: 0.420 Process input model: 128.220 Find NCS groups from input model: 3.700 Set up NCS constraints: 0.440 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.004 0.051 50680 Z= 0.256 Angle : 0.680 10.142 68435 Z= 0.363 Chirality : 0.045 0.224 7750 Planarity : 0.009 0.492 8585 Dihedral : 13.369 89.002 19280 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.37 % Favored : 91.61 % Rotamer: Outliers : 0.41 % Allowed : 0.57 % Favored : 99.01 % 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: -1.40 (0.11), residues: 6090 helix: 0.05 (0.10), residues: 2650 sheet: -2.01 (0.24), residues: 430 loop : -1.66 (0.12), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 285 HIS 0.011 0.001 HIS G 386 PHE 0.024 0.001 PHE D 431 TYR 0.025 0.002 TYR D 429 ARG 0.007 0.001 ARG G 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 578 time to evaluate : 6.149 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: A 40 LEU cc_start: 0.9582 (mm) cc_final: 0.9298 (mm) REVERT: A 126 GLU cc_start: 0.8435 (pp20) cc_final: 0.8169 (pp20) REVERT: A 130 GLN cc_start: 0.8379 (mp10) cc_final: 0.8155 (mp10) REVERT: B 327 MET cc_start: 0.6844 (mmm) cc_final: 0.5824 (tmm) REVERT: B 356 TRP cc_start: 0.8797 (t60) cc_final: 0.8583 (t60) REVERT: C 136 GLU cc_start: 0.8481 (mp0) cc_final: 0.8237 (mp0) REVERT: C 263 TYR cc_start: 0.8120 (m-80) cc_final: 0.7305 (m-80) REVERT: C 311 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8221 (mtt180) REVERT: C 694 ARG cc_start: 0.8593 (mpp80) cc_final: 0.8322 (mpp80) REVERT: E 40 LEU cc_start: 0.9604 (mm) cc_final: 0.9156 (mm) REVERT: E 68 ASN cc_start: 0.8862 (m110) cc_final: 0.8564 (m110) REVERT: G 40 LEU cc_start: 0.9586 (mm) cc_final: 0.9201 (mm) REVERT: G 81 ASP cc_start: 0.8440 (t0) cc_final: 0.8037 (t0) REVERT: G 84 MET cc_start: 0.8708 (tmm) cc_final: 0.8501 (tmm) REVERT: G 470 GLU cc_start: 0.8042 (pp20) cc_final: 0.7829 (pp20) REVERT: G 594 TYR cc_start: 0.7474 (p90) cc_final: 0.6958 (p90) REVERT: I 40 LEU cc_start: 0.9521 (mt) cc_final: 0.9154 (mm) REVERT: I 413 MET cc_start: 0.8177 (ppp) cc_final: 0.7806 (ppp) REVERT: I 873 MET cc_start: 0.5125 (ppp) cc_final: 0.4861 (ppp) REVERT: D 327 MET cc_start: 0.5993 (mmm) cc_final: 0.5557 (tmm) REVERT: D 375 MET cc_start: 0.7775 (mtm) cc_final: 0.7560 (mtm) REVERT: D 460 MET cc_start: 0.8619 (ppp) cc_final: 0.8174 (tpp) REVERT: D 518 TYR cc_start: 0.7282 (t80) cc_final: 0.7073 (t80) REVERT: F 329 LEU cc_start: 0.8450 (mp) cc_final: 0.8124 (tt) REVERT: H 350 ASP cc_start: 0.9040 (m-30) cc_final: 0.8761 (m-30) REVERT: H 372 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7093 (tm-30) REVERT: H 373 ARG cc_start: 0.5603 (mmt180) cc_final: 0.5396 (mtt180) REVERT: H 433 GLU cc_start: 0.9562 (pm20) cc_final: 0.9358 (pm20) REVERT: J 326 MET cc_start: 0.8672 (mmt) cc_final: 0.8376 (mmp) REVERT: J 337 LYS cc_start: 0.9320 (mptt) cc_final: 0.8917 (mmtm) REVERT: J 356 TRP cc_start: 0.8789 (t60) cc_final: 0.8580 (t60) REVERT: J 361 TYR cc_start: 0.9492 (m-80) cc_final: 0.8686 (m-80) REVERT: J 364 LYS cc_start: 0.9106 (pttt) cc_final: 0.8857 (ptmm) outliers start: 23 outliers final: 4 residues processed: 601 average time/residue: 0.5987 time to fit residues: 600.3147 Evaluate side-chains 466 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 461 time to evaluate : 6.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 311 ARG Chi-restraints excluded: chain E residue 311 ARG Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain F residue 253 LYS Chi-restraints excluded: chain H residue 253 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 9.9990 chunk 462 optimal weight: 5.9990 chunk 256 optimal weight: 0.0050 chunk 157 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 478 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 290 optimal weight: 0.5980 chunk 355 optimal weight: 5.9990 chunk 553 optimal weight: 6.9990 overall best weight: 2.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 517 ASN C 664 ASN E 220 GLN E 517 ASN ** E 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 ASN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 610 HIS D 141 ASN D 378 GLN F 182 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 ASN H 182 GLN ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN J 158 GLN J 182 GLN ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 50680 Z= 0.238 Angle : 0.624 9.158 68435 Z= 0.317 Chirality : 0.043 0.156 7750 Planarity : 0.004 0.059 8585 Dihedral : 7.757 87.288 6830 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.56 % Favored : 91.38 % Rotamer: Outliers : 0.93 % Allowed : 9.00 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.11), residues: 6090 helix: 0.03 (0.10), residues: 2625 sheet: -2.12 (0.24), residues: 440 loop : -1.64 (0.12), residues: 3025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 210 HIS 0.007 0.001 HIS J 359 PHE 0.022 0.001 PHE D 431 TYR 0.019 0.001 TYR G 277 ARG 0.007 0.000 ARG D 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 517 time to evaluate : 6.471 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: A 40 LEU cc_start: 0.9619 (mm) cc_final: 0.9226 (mm) REVERT: A 556 MET cc_start: 0.8322 (tpp) cc_final: 0.8111 (tpp) REVERT: A 707 MET cc_start: 0.4690 (mmm) cc_final: 0.4432 (mmm) REVERT: B 326 MET cc_start: 0.8895 (mmm) cc_final: 0.8638 (mmp) REVERT: B 327 MET cc_start: 0.6583 (mmm) cc_final: 0.5719 (tmm) REVERT: B 353 TYR cc_start: 0.9085 (t80) cc_final: 0.8787 (t80) REVERT: B 356 TRP cc_start: 0.8928 (t60) cc_final: 0.8718 (t60) REVERT: B 453 LYS cc_start: 0.8945 (tmtt) cc_final: 0.8155 (pttt) REVERT: B 460 MET cc_start: 0.8516 (ptt) cc_final: 0.7469 (tpt) REVERT: C 44 GLN cc_start: 0.8558 (mp10) cc_final: 0.8293 (mp10) REVERT: C 136 GLU cc_start: 0.8368 (mp0) cc_final: 0.8075 (mp0) REVERT: C 158 MET cc_start: 0.8068 (tmm) cc_final: 0.7557 (tmm) REVERT: C 263 TYR cc_start: 0.8174 (m-80) cc_final: 0.7700 (m-80) REVERT: E 68 ASN cc_start: 0.8845 (m110) cc_final: 0.8567 (m-40) REVERT: G 81 ASP cc_start: 0.8461 (t0) cc_final: 0.7956 (t0) REVERT: G 136 GLU cc_start: 0.8627 (pm20) cc_final: 0.8075 (pm20) REVERT: G 158 MET cc_start: 0.8262 (tmm) cc_final: 0.7779 (tmm) REVERT: G 470 GLU cc_start: 0.8085 (pp20) cc_final: 0.7831 (pp20) REVERT: G 594 TYR cc_start: 0.7489 (p90) cc_final: 0.6929 (p90) REVERT: I 126 GLU cc_start: 0.8583 (pp20) cc_final: 0.8360 (pp20) REVERT: I 594 TYR cc_start: 0.7671 (p90) cc_final: 0.7459 (p90) REVERT: I 873 MET cc_start: 0.5246 (ppp) cc_final: 0.5008 (ppp) REVERT: D 295 LYS cc_start: 0.7584 (mttm) cc_final: 0.7378 (ptpt) REVERT: D 326 MET cc_start: 0.8835 (mpp) cc_final: 0.8246 (mpp) REVERT: D 327 MET cc_start: 0.5956 (mmm) cc_final: 0.5527 (tmm) REVERT: D 375 MET cc_start: 0.7762 (mtm) cc_final: 0.7514 (mtm) REVERT: F 329 LEU cc_start: 0.8449 (mp) cc_final: 0.8133 (tt) REVERT: F 460 MET cc_start: 0.8720 (ptt) cc_final: 0.7539 (tpp) REVERT: F 518 TYR cc_start: 0.7585 (t80) cc_final: 0.7300 (t80) REVERT: H 350 ASP cc_start: 0.9042 (m-30) cc_final: 0.8746 (m-30) REVERT: J 326 MET cc_start: 0.8661 (mmt) cc_final: 0.8305 (mmp) REVERT: J 327 MET cc_start: 0.6332 (mmm) cc_final: 0.6107 (mmm) REVERT: J 361 TYR cc_start: 0.9523 (m-80) cc_final: 0.8713 (m-80) REVERT: J 460 MET cc_start: 0.8449 (ptt) cc_final: 0.7644 (mmp) outliers start: 52 outliers final: 33 residues processed: 543 average time/residue: 0.6426 time to fit residues: 586.2970 Evaluate side-chains 491 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 458 time to evaluate : 6.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 320 CYS Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 320 CYS Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 726 VAL Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain I residue 715 ILE Chi-restraints excluded: chain I residue 749 LEU Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain H residue 431 PHE Chi-restraints excluded: chain J residue 258 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 307 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 461 optimal weight: 8.9990 chunk 377 optimal weight: 0.0050 chunk 152 optimal weight: 0.4980 chunk 554 optimal weight: 10.0000 chunk 599 optimal weight: 7.9990 chunk 494 optimal weight: 0.0370 chunk 550 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 445 optimal weight: 9.9990 overall best weight: 1.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN ** E 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 273 ASN F 182 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 GLN ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 50680 Z= 0.170 Angle : 0.579 10.735 68435 Z= 0.291 Chirality : 0.042 0.166 7750 Planarity : 0.003 0.060 8585 Dihedral : 7.315 89.452 6814 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.29 % Favored : 91.66 % Rotamer: Outliers : 1.56 % Allowed : 11.93 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.11), residues: 6090 helix: 0.15 (0.11), residues: 2625 sheet: -2.18 (0.24), residues: 450 loop : -1.56 (0.12), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J 356 HIS 0.006 0.001 HIS I 386 PHE 0.023 0.001 PHE D 431 TYR 0.018 0.001 TYR D 365 ARG 0.004 0.000 ARG F 427 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 518 time to evaluate : 6.310 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 63 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8700 (mttt) REVERT: A 413 MET cc_start: 0.8430 (tmm) cc_final: 0.8000 (tmm) REVERT: A 556 MET cc_start: 0.8312 (tpp) cc_final: 0.8026 (tpp) REVERT: B 326 MET cc_start: 0.8887 (mmm) cc_final: 0.8637 (mmm) REVERT: B 327 MET cc_start: 0.7037 (mmm) cc_final: 0.6172 (tmm) REVERT: B 353 TYR cc_start: 0.9086 (t80) cc_final: 0.8628 (t80) REVERT: B 356 TRP cc_start: 0.9064 (t60) cc_final: 0.8694 (t60) REVERT: B 453 LYS cc_start: 0.8933 (tmtt) cc_final: 0.8144 (pttm) REVERT: B 460 MET cc_start: 0.8443 (ptt) cc_final: 0.7468 (tpt) REVERT: C 126 GLU cc_start: 0.8366 (pp20) cc_final: 0.8034 (pp20) REVERT: C 158 MET cc_start: 0.8014 (tmm) cc_final: 0.7591 (tmm) REVERT: C 263 TYR cc_start: 0.8170 (m-80) cc_final: 0.7878 (m-80) REVERT: C 264 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8984 (pp) REVERT: C 413 MET cc_start: 0.8441 (ppp) cc_final: 0.8113 (ppp) REVERT: E 68 ASN cc_start: 0.8780 (m110) cc_final: 0.8498 (m-40) REVERT: E 126 GLU cc_start: 0.8364 (pp20) cc_final: 0.8108 (pp20) REVERT: E 264 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8660 (pp) REVERT: E 470 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7351 (pp20) REVERT: E 690 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8620 (pp) REVERT: G 136 GLU cc_start: 0.8619 (pm20) cc_final: 0.8101 (pm20) REVERT: G 158 MET cc_start: 0.8344 (tmm) cc_final: 0.7908 (tmm) REVERT: G 264 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8928 (pp) REVERT: G 329 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6100 (tpp) REVERT: G 594 TYR cc_start: 0.7479 (p90) cc_final: 0.6938 (p90) REVERT: G 690 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8850 (pp) REVERT: I 136 GLU cc_start: 0.8751 (pm20) cc_final: 0.8446 (pm20) REVERT: I 329 MET cc_start: 0.6972 (tpt) cc_final: 0.6686 (tpt) REVERT: I 413 MET cc_start: 0.8337 (ppp) cc_final: 0.7696 (tmm) REVERT: I 548 VAL cc_start: 0.6707 (OUTLIER) cc_final: 0.6244 (t) REVERT: I 553 MET cc_start: 0.9187 (mtm) cc_final: 0.8360 (mpp) REVERT: I 594 TYR cc_start: 0.7697 (p90) cc_final: 0.7452 (p90) REVERT: I 873 MET cc_start: 0.5132 (ppp) cc_final: 0.4875 (ppp) REVERT: D 271 HIS cc_start: 0.7189 (t-90) cc_final: 0.6448 (p-80) REVERT: D 326 MET cc_start: 0.8895 (mpp) cc_final: 0.8452 (mmp) REVERT: D 327 MET cc_start: 0.5991 (mmm) cc_final: 0.5575 (tmm) REVERT: D 375 MET cc_start: 0.7722 (mtm) cc_final: 0.7231 (mpp) REVERT: D 460 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7766 (ptt) REVERT: F 295 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7516 (mttm) REVERT: F 326 MET cc_start: 0.8665 (mpp) cc_final: 0.8437 (mpp) REVERT: F 329 LEU cc_start: 0.8463 (mp) cc_final: 0.8138 (tt) REVERT: F 453 LYS cc_start: 0.8907 (pptt) cc_final: 0.8194 (pttt) REVERT: F 460 MET cc_start: 0.8678 (ptt) cc_final: 0.7510 (tpt) REVERT: F 518 TYR cc_start: 0.7523 (t80) cc_final: 0.7244 (t80) REVERT: H 327 MET cc_start: 0.5938 (mmm) cc_final: 0.5436 (mmm) REVERT: H 350 ASP cc_start: 0.9055 (m-30) cc_final: 0.8757 (m-30) REVERT: H 365 TYR cc_start: 0.7645 (m-80) cc_final: 0.7353 (m-80) REVERT: J 361 TYR cc_start: 0.9542 (m-80) cc_final: 0.8736 (m-80) REVERT: J 460 MET cc_start: 0.8424 (ptt) cc_final: 0.7558 (tpp) outliers start: 87 outliers final: 55 residues processed: 576 average time/residue: 0.5966 time to fit residues: 576.9336 Evaluate side-chains 550 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 485 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 320 CYS Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 320 CYS Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 726 VAL Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 320 CYS Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 609 THR Chi-restraints excluded: chain I residue 715 ILE Chi-restraints excluded: chain I residue 749 LEU Chi-restraints excluded: chain I residue 770 LEU Chi-restraints excluded: chain I residue 876 LEU Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 457 ARG Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain H residue 431 PHE Chi-restraints excluded: chain J residue 295 LYS Chi-restraints excluded: chain J residue 421 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 9.9990 chunk 417 optimal weight: 0.3980 chunk 288 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 264 optimal weight: 10.0000 chunk 372 optimal weight: 0.7980 chunk 556 optimal weight: 10.0000 chunk 589 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 527 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN C 610 HIS E 739 HIS ** G 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 GLN ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 182 GLN ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 50680 Z= 0.147 Angle : 0.566 12.170 68435 Z= 0.283 Chirality : 0.041 0.177 7750 Planarity : 0.003 0.059 8585 Dihedral : 6.958 89.892 6814 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.06 % Favored : 91.89 % Rotamer: Outliers : 2.35 % Allowed : 13.40 % Favored : 84.25 % 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: -1.22 (0.11), residues: 6090 helix: 0.25 (0.11), residues: 2645 sheet: -2.06 (0.24), residues: 460 loop : -1.57 (0.12), residues: 2985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP J 356 HIS 0.005 0.001 HIS H 271 PHE 0.023 0.001 PHE D 431 TYR 0.012 0.001 TYR A 775 ARG 0.028 0.000 ARG I 851 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 527 time to evaluate : 6.974 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: A 63 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8690 (mttt) REVERT: A 413 MET cc_start: 0.8334 (tmm) cc_final: 0.7891 (tmm) REVERT: A 556 MET cc_start: 0.8327 (tpp) cc_final: 0.7989 (tpp) REVERT: B 326 MET cc_start: 0.8897 (mmm) cc_final: 0.8679 (mmm) REVERT: B 327 MET cc_start: 0.7032 (mmm) cc_final: 0.6197 (tmm) REVERT: B 353 TYR cc_start: 0.9102 (t80) cc_final: 0.8822 (t80) REVERT: B 359 HIS cc_start: 0.8505 (t70) cc_final: 0.8144 (t-170) REVERT: B 361 TYR cc_start: 0.9320 (m-80) cc_final: 0.8329 (m-80) REVERT: B 385 GLU cc_start: 0.8803 (mp0) cc_final: 0.8596 (mp0) REVERT: B 453 LYS cc_start: 0.8912 (tmtt) cc_final: 0.8085 (pttm) REVERT: B 460 MET cc_start: 0.8425 (ptt) cc_final: 0.7532 (tpt) REVERT: C 158 MET cc_start: 0.8046 (tmm) cc_final: 0.7655 (tmm) REVERT: C 413 MET cc_start: 0.8293 (ppp) cc_final: 0.7984 (ppp) REVERT: C 556 MET cc_start: 0.8444 (tpp) cc_final: 0.8131 (tpp) REVERT: E 68 ASN cc_start: 0.8804 (m110) cc_final: 0.8538 (m110) REVERT: E 130 GLN cc_start: 0.8163 (mp10) cc_final: 0.7949 (mp10) REVERT: E 158 MET cc_start: 0.8134 (tmm) cc_final: 0.7621 (tmm) REVERT: E 264 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8937 (pp) REVERT: E 470 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7228 (pp20) REVERT: E 690 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8598 (pp) REVERT: G 136 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: G 158 MET cc_start: 0.8302 (tmm) cc_final: 0.7885 (tmm) REVERT: G 264 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9006 (pp) REVERT: G 329 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.6103 (tpp) REVERT: G 553 MET cc_start: 0.8850 (mtm) cc_final: 0.8209 (mpp) REVERT: G 594 TYR cc_start: 0.7599 (p90) cc_final: 0.7034 (p90) REVERT: G 690 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8848 (pp) REVERT: I 136 GLU cc_start: 0.8680 (pm20) cc_final: 0.8200 (pm20) REVERT: I 264 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8972 (pp) REVERT: I 413 MET cc_start: 0.8362 (ppp) cc_final: 0.7717 (tmm) REVERT: I 548 VAL cc_start: 0.6630 (OUTLIER) cc_final: 0.6159 (t) REVERT: I 594 TYR cc_start: 0.7693 (p90) cc_final: 0.7404 (p90) REVERT: I 694 ARG cc_start: 0.8890 (mmm-85) cc_final: 0.8304 (mmm160) REVERT: D 253 LYS cc_start: 0.6339 (OUTLIER) cc_final: 0.4928 (ptmt) REVERT: D 271 HIS cc_start: 0.7151 (t-90) cc_final: 0.6230 (p-80) REVERT: D 326 MET cc_start: 0.8920 (mpp) cc_final: 0.8532 (mmp) REVERT: D 327 MET cc_start: 0.5974 (mmm) cc_final: 0.5609 (tmm) REVERT: D 375 MET cc_start: 0.7705 (mtm) cc_final: 0.7227 (mpp) REVERT: D 460 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7658 (ptt) REVERT: F 292 GLU cc_start: 0.9310 (mm-30) cc_final: 0.9048 (mp0) REVERT: F 295 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7254 (mttm) REVERT: F 327 MET cc_start: 0.6144 (mmm) cc_final: 0.5735 (mmm) REVERT: F 329 LEU cc_start: 0.8533 (mp) cc_final: 0.8180 (tt) REVERT: F 361 TYR cc_start: 0.9202 (m-80) cc_final: 0.8267 (m-80) REVERT: F 432 HIS cc_start: 0.9189 (m90) cc_final: 0.8979 (m90) REVERT: F 453 LYS cc_start: 0.8939 (pptt) cc_final: 0.8238 (pttt) REVERT: F 460 MET cc_start: 0.8571 (ptt) cc_final: 0.7473 (tpt) REVERT: F 518 TYR cc_start: 0.7519 (t80) cc_final: 0.7261 (t80) REVERT: H 271 HIS cc_start: 0.7169 (t-90) cc_final: 0.6401 (p-80) REVERT: H 327 MET cc_start: 0.5963 (mmm) cc_final: 0.5371 (mmm) REVERT: H 350 ASP cc_start: 0.9054 (m-30) cc_final: 0.8737 (m-30) REVERT: H 365 TYR cc_start: 0.7595 (m-80) cc_final: 0.7319 (m-80) REVERT: H 432 HIS cc_start: 0.9137 (m90) cc_final: 0.8765 (m90) REVERT: J 359 HIS cc_start: 0.8827 (t70) cc_final: 0.8529 (t70) REVERT: J 361 TYR cc_start: 0.9515 (m-80) cc_final: 0.8904 (m-80) REVERT: J 460 MET cc_start: 0.8456 (ptt) cc_final: 0.7634 (tpp) outliers start: 131 outliers final: 74 residues processed: 616 average time/residue: 0.5755 time to fit residues: 599.9008 Evaluate side-chains 569 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 483 time to evaluate : 6.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 320 CYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 504 MET Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 680 ASP Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 876 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 320 CYS Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 609 THR Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 726 VAL Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 876 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 320 CYS Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 680 ASP Chi-restraints excluded: chain I residue 749 LEU Chi-restraints excluded: chain I residue 770 LEU Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 457 ARG Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 431 PHE Chi-restraints excluded: chain J residue 295 LYS Chi-restraints excluded: chain J residue 416 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 491 optimal weight: 7.9990 chunk 334 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 439 optimal weight: 8.9990 chunk 243 optimal weight: 0.7980 chunk 503 optimal weight: 3.9990 chunk 407 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 301 optimal weight: 0.0030 chunk 529 optimal weight: 20.0000 chunk 148 optimal weight: 0.1980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 HIS E 44 GLN ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 GLN ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 50680 Z= 0.133 Angle : 0.563 12.295 68435 Z= 0.280 Chirality : 0.041 0.168 7750 Planarity : 0.003 0.056 8585 Dihedral : 6.564 88.960 6814 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.95 % Favored : 92.02 % Rotamer: Outliers : 2.26 % Allowed : 15.23 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.11), residues: 6090 helix: 0.41 (0.11), residues: 2615 sheet: -1.94 (0.24), residues: 460 loop : -1.51 (0.12), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 356 HIS 0.005 0.001 HIS E 739 PHE 0.023 0.001 PHE D 431 TYR 0.016 0.001 TYR D 365 ARG 0.004 0.000 ARG H 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 539 time to evaluate : 6.176 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: A 413 MET cc_start: 0.8286 (tmm) cc_final: 0.7903 (tmm) REVERT: A 468 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7983 (tt) REVERT: A 556 MET cc_start: 0.8412 (tpp) cc_final: 0.8117 (tpp) REVERT: B 326 MET cc_start: 0.8890 (mmm) cc_final: 0.8677 (mmm) REVERT: B 327 MET cc_start: 0.7010 (mmm) cc_final: 0.6232 (tmm) REVERT: B 353 TYR cc_start: 0.9138 (t80) cc_final: 0.8855 (t80) REVERT: B 359 HIS cc_start: 0.8556 (t70) cc_final: 0.8352 (t-170) REVERT: B 361 TYR cc_start: 0.9297 (m-80) cc_final: 0.8307 (m-80) REVERT: B 385 GLU cc_start: 0.8821 (mp0) cc_final: 0.8613 (mp0) REVERT: B 453 LYS cc_start: 0.8914 (tmtt) cc_final: 0.8106 (pttm) REVERT: B 460 MET cc_start: 0.8456 (ptt) cc_final: 0.7482 (tpt) REVERT: C 158 MET cc_start: 0.7946 (tmm) cc_final: 0.7607 (tmm) REVERT: C 556 MET cc_start: 0.8465 (tpp) cc_final: 0.8111 (tpp) REVERT: E 68 ASN cc_start: 0.8763 (m110) cc_final: 0.8542 (m110) REVERT: E 126 GLU cc_start: 0.8295 (pp20) cc_final: 0.7866 (pp20) REVERT: E 158 MET cc_start: 0.8115 (tmm) cc_final: 0.7678 (tmm) REVERT: E 264 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8983 (pp) REVERT: E 470 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7197 (pp20) REVERT: E 690 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8593 (pp) REVERT: G 136 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7911 (pm20) REVERT: G 158 MET cc_start: 0.8241 (tmm) cc_final: 0.7875 (tmm) REVERT: G 264 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8942 (pp) REVERT: G 329 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.5976 (tpp) REVERT: G 548 VAL cc_start: 0.7046 (OUTLIER) cc_final: 0.6529 (t) REVERT: G 594 TYR cc_start: 0.7590 (p90) cc_final: 0.7083 (p90) REVERT: G 690 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8843 (pp) REVERT: I 126 GLU cc_start: 0.8416 (pp20) cc_final: 0.8203 (pp20) REVERT: I 136 GLU cc_start: 0.8650 (pm20) cc_final: 0.8219 (pm20) REVERT: I 264 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8994 (pp) REVERT: I 413 MET cc_start: 0.8371 (ppp) cc_final: 0.7742 (tmm) REVERT: I 548 VAL cc_start: 0.6614 (OUTLIER) cc_final: 0.6133 (t) REVERT: I 553 MET cc_start: 0.9165 (mtm) cc_final: 0.8163 (mpp) REVERT: I 594 TYR cc_start: 0.7739 (p90) cc_final: 0.7436 (p90) REVERT: I 694 ARG cc_start: 0.8886 (mmm-85) cc_final: 0.8527 (mmm-85) REVERT: I 873 MET cc_start: 0.4963 (ppp) cc_final: 0.4668 (ppp) REVERT: D 271 HIS cc_start: 0.7125 (t-90) cc_final: 0.6180 (p-80) REVERT: D 326 MET cc_start: 0.8925 (mpp) cc_final: 0.8507 (mmp) REVERT: D 327 MET cc_start: 0.5995 (mmm) cc_final: 0.5738 (tmm) REVERT: D 375 MET cc_start: 0.7678 (mtm) cc_final: 0.7221 (mpp) REVERT: F 292 GLU cc_start: 0.9319 (mm-30) cc_final: 0.9060 (mp0) REVERT: F 295 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7205 (mttm) REVERT: F 327 MET cc_start: 0.6264 (mmm) cc_final: 0.5810 (mmm) REVERT: F 329 LEU cc_start: 0.8542 (mp) cc_final: 0.8189 (tt) REVERT: F 361 TYR cc_start: 0.9242 (m-80) cc_final: 0.8278 (m-80) REVERT: F 453 LYS cc_start: 0.8921 (pptt) cc_final: 0.8240 (pttt) REVERT: F 460 MET cc_start: 0.8573 (ptt) cc_final: 0.7465 (tpt) REVERT: H 271 HIS cc_start: 0.7193 (t-90) cc_final: 0.6471 (p-80) REVERT: H 327 MET cc_start: 0.5894 (mmm) cc_final: 0.5247 (mmm) REVERT: H 350 ASP cc_start: 0.9049 (m-30) cc_final: 0.8760 (m-30) REVERT: H 365 TYR cc_start: 0.7671 (m-80) cc_final: 0.7339 (m-80) REVERT: H 432 HIS cc_start: 0.9220 (m90) cc_final: 0.8757 (m90) REVERT: J 359 HIS cc_start: 0.8720 (t70) cc_final: 0.8454 (t70) REVERT: J 361 TYR cc_start: 0.9327 (m-80) cc_final: 0.8526 (m-80) REVERT: J 460 MET cc_start: 0.8422 (ptt) cc_final: 0.7598 (tpp) outliers start: 126 outliers final: 71 residues processed: 629 average time/residue: 0.5765 time to fit residues: 616.2747 Evaluate side-chains 583 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 500 time to evaluate : 5.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 713 GLU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 320 CYS Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 680 ASP Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 713 GLU Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 320 CYS Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 470 GLU Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 609 THR Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 726 VAL Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 320 CYS Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 609 THR Chi-restraints excluded: chain I residue 749 LEU Chi-restraints excluded: chain I residue 770 LEU Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 457 ARG Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 431 PHE Chi-restraints excluded: chain J residue 295 LYS Chi-restraints excluded: chain J residue 416 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 198 optimal weight: 5.9990 chunk 530 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 346 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 590 optimal weight: 9.9990 chunk 489 optimal weight: 7.9990 chunk 273 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 195 optimal weight: 7.9990 chunk 309 optimal weight: 1.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN A 610 HIS C 610 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 50680 Z= 0.203 Angle : 0.587 12.255 68435 Z= 0.296 Chirality : 0.042 0.195 7750 Planarity : 0.003 0.056 8585 Dihedral : 6.678 89.871 6810 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.37 % Favored : 91.56 % Rotamer: Outliers : 2.53 % Allowed : 16.63 % Favored : 80.84 % 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: -1.04 (0.11), residues: 6090 helix: 0.46 (0.11), residues: 2595 sheet: -1.97 (0.24), residues: 460 loop : -1.52 (0.12), residues: 3035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP H 356 HIS 0.004 0.001 HIS E 739 PHE 0.021 0.001 PHE J 448 TYR 0.019 0.001 TYR H 383 ARG 0.003 0.000 ARG G 851 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 507 time to evaluate : 6.144 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: A 126 GLU cc_start: 0.8179 (pp20) cc_final: 0.7922 (pp20) REVERT: A 413 MET cc_start: 0.8349 (tmm) cc_final: 0.7989 (tmm) REVERT: A 468 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7983 (tt) REVERT: A 556 MET cc_start: 0.8489 (tpp) cc_final: 0.8151 (tpp) REVERT: B 326 MET cc_start: 0.8898 (mmm) cc_final: 0.8687 (mmm) REVERT: B 327 MET cc_start: 0.6969 (mmm) cc_final: 0.6265 (tmm) REVERT: B 353 TYR cc_start: 0.9151 (t80) cc_final: 0.8856 (t80) REVERT: B 361 TYR cc_start: 0.9354 (m-80) cc_final: 0.8400 (m-80) REVERT: B 385 GLU cc_start: 0.8834 (mp0) cc_final: 0.8606 (mp0) REVERT: B 460 MET cc_start: 0.8463 (ptt) cc_final: 0.7498 (tpt) REVERT: C 44 GLN cc_start: 0.8532 (mp10) cc_final: 0.8317 (mp10) REVERT: C 158 MET cc_start: 0.7987 (tmm) cc_final: 0.7597 (tmm) REVERT: C 413 MET cc_start: 0.8323 (ppp) cc_final: 0.7721 (ppp) REVERT: C 556 MET cc_start: 0.8437 (tpp) cc_final: 0.8065 (tpp) REVERT: E 68 ASN cc_start: 0.8845 (m110) cc_final: 0.8574 (m110) REVERT: E 158 MET cc_start: 0.8119 (tmm) cc_final: 0.7708 (tmm) REVERT: E 264 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8938 (pp) REVERT: E 694 ARG cc_start: 0.8148 (mpp-170) cc_final: 0.7926 (mpp80) REVERT: G 136 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7985 (pm20) REVERT: G 158 MET cc_start: 0.8302 (tmm) cc_final: 0.7936 (tmm) REVERT: G 264 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8952 (pp) REVERT: G 329 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6019 (tpp) REVERT: G 548 VAL cc_start: 0.7185 (OUTLIER) cc_final: 0.6688 (t) REVERT: G 553 MET cc_start: 0.8970 (mtm) cc_final: 0.8543 (mpp) REVERT: G 594 TYR cc_start: 0.7683 (p90) cc_final: 0.7107 (p90) REVERT: G 690 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8910 (pp) REVERT: I 136 GLU cc_start: 0.8642 (pm20) cc_final: 0.8260 (pm20) REVERT: I 264 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8923 (pp) REVERT: I 388 LYS cc_start: 0.3416 (OUTLIER) cc_final: 0.3072 (pptt) REVERT: I 413 MET cc_start: 0.8460 (ppp) cc_final: 0.7856 (tmm) REVERT: I 548 VAL cc_start: 0.6775 (OUTLIER) cc_final: 0.6314 (t) REVERT: I 553 MET cc_start: 0.9251 (mtm) cc_final: 0.8129 (mpp) REVERT: I 594 TYR cc_start: 0.7766 (p90) cc_final: 0.7399 (p90) REVERT: I 694 ARG cc_start: 0.8900 (mmm-85) cc_final: 0.8551 (mmm160) REVERT: I 873 MET cc_start: 0.5014 (ppp) cc_final: 0.4759 (ppp) REVERT: D 271 HIS cc_start: 0.7213 (t-90) cc_final: 0.6313 (p90) REVERT: D 326 MET cc_start: 0.8932 (mpp) cc_final: 0.8506 (mmp) REVERT: D 327 MET cc_start: 0.6031 (mmm) cc_final: 0.5785 (tmm) REVERT: D 375 MET cc_start: 0.7761 (mtm) cc_final: 0.7220 (mpp) REVERT: F 292 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9080 (mp0) REVERT: F 295 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7166 (mttm) REVERT: F 327 MET cc_start: 0.6256 (mmm) cc_final: 0.5763 (mmm) REVERT: F 329 LEU cc_start: 0.8573 (mp) cc_final: 0.8212 (tt) REVERT: F 361 TYR cc_start: 0.9295 (m-80) cc_final: 0.8330 (m-80) REVERT: F 453 LYS cc_start: 0.8878 (pptt) cc_final: 0.8318 (pttt) REVERT: F 460 MET cc_start: 0.8624 (ptt) cc_final: 0.7514 (tpt) REVERT: H 327 MET cc_start: 0.6049 (mmm) cc_final: 0.5321 (mmm) REVERT: H 350 ASP cc_start: 0.9069 (m-30) cc_final: 0.8771 (m-30) REVERT: H 365 TYR cc_start: 0.7845 (m-80) cc_final: 0.7475 (m-80) REVERT: H 432 HIS cc_start: 0.9263 (m90) cc_final: 0.8776 (m90) REVERT: H 435 ASN cc_start: 0.8454 (m-40) cc_final: 0.8226 (m110) REVERT: J 359 HIS cc_start: 0.8826 (t70) cc_final: 0.8503 (t70) REVERT: J 361 TYR cc_start: 0.9221 (m-80) cc_final: 0.8340 (m-80) REVERT: J 460 MET cc_start: 0.8380 (ptt) cc_final: 0.7577 (tpp) outliers start: 141 outliers final: 100 residues processed: 600 average time/residue: 0.5702 time to fit residues: 582.7261 Evaluate side-chains 585 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 474 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 320 CYS Chi-restraints excluded: chain E residue 329 MET Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 680 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain E residue 876 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 320 CYS Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 444 ILE Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 470 GLU Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 581 VAL Chi-restraints excluded: chain G residue 609 THR Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 726 VAL Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 876 LEU Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 320 CYS Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 609 THR Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 680 ASP Chi-restraints excluded: chain I residue 749 LEU Chi-restraints excluded: chain I residue 770 LEU Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 457 ARG Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 431 PHE Chi-restraints excluded: chain J residue 182 GLN Chi-restraints excluded: chain J residue 295 LYS Chi-restraints excluded: chain J residue 416 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 569 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 336 optimal weight: 2.9990 chunk 431 optimal weight: 8.9990 chunk 333 optimal weight: 1.9990 chunk 496 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 587 optimal weight: 8.9990 chunk 367 optimal weight: 6.9990 chunk 358 optimal weight: 8.9990 chunk 271 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN A 517 ASN A 555 HIS C 273 ASN ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 610 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 50680 Z= 0.345 Angle : 0.684 12.983 68435 Z= 0.351 Chirality : 0.044 0.267 7750 Planarity : 0.004 0.086 8585 Dihedral : 7.434 89.456 6810 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.44 % Favored : 90.48 % Rotamer: Outliers : 2.82 % Allowed : 17.27 % Favored : 79.91 % 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: -1.48 (0.11), residues: 6090 helix: -0.02 (0.10), residues: 2750 sheet: -2.21 (0.23), residues: 470 loop : -1.69 (0.12), residues: 2870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 285 HIS 0.014 0.001 HIS F 432 PHE 0.021 0.002 PHE J 448 TYR 0.029 0.002 TYR G 277 ARG 0.011 0.001 ARG I 851 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 483 time to evaluate : 6.686 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 139 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8314 (mm-40) REVERT: A 388 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7977 (mtmt) REVERT: A 413 MET cc_start: 0.8447 (tmm) cc_final: 0.8054 (tmm) REVERT: A 556 MET cc_start: 0.8394 (tpp) cc_final: 0.8173 (tpp) REVERT: B 327 MET cc_start: 0.6960 (mmm) cc_final: 0.6481 (tmm) REVERT: B 353 TYR cc_start: 0.9129 (t80) cc_final: 0.8850 (t80) REVERT: B 361 TYR cc_start: 0.9394 (m-80) cc_final: 0.8458 (m-80) REVERT: B 385 GLU cc_start: 0.8843 (mp0) cc_final: 0.8563 (mp0) REVERT: B 460 MET cc_start: 0.8440 (ptt) cc_final: 0.7387 (tpt) REVERT: C 158 MET cc_start: 0.8135 (tmm) cc_final: 0.7698 (tmm) REVERT: C 413 MET cc_start: 0.8368 (ppp) cc_final: 0.7686 (ppp) REVERT: E 68 ASN cc_start: 0.8911 (m110) cc_final: 0.8565 (m-40) REVERT: E 158 MET cc_start: 0.8281 (tmm) cc_final: 0.7800 (tmm) REVERT: E 264 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8768 (pp) REVERT: G 136 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8131 (pm20) REVERT: G 158 MET cc_start: 0.8258 (tmm) cc_final: 0.7975 (tmm) REVERT: G 264 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9002 (pp) REVERT: G 329 MET cc_start: 0.6666 (OUTLIER) cc_final: 0.5879 (tpp) REVERT: G 413 MET cc_start: 0.8402 (ppp) cc_final: 0.8005 (ppp) REVERT: G 553 MET cc_start: 0.9088 (mtm) cc_final: 0.8355 (mpp) REVERT: G 594 TYR cc_start: 0.7709 (p90) cc_final: 0.7113 (p90) REVERT: G 690 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8922 (pp) REVERT: I 136 GLU cc_start: 0.8764 (pm20) cc_final: 0.8297 (pm20) REVERT: I 264 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8939 (pp) REVERT: I 284 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8819 (mp) REVERT: I 285 TRP cc_start: 0.7852 (OUTLIER) cc_final: 0.6770 (m-10) REVERT: I 388 LYS cc_start: 0.5018 (OUTLIER) cc_final: 0.4781 (pptt) REVERT: I 553 MET cc_start: 0.9207 (mtm) cc_final: 0.8281 (mpp) REVERT: I 594 TYR cc_start: 0.7818 (p90) cc_final: 0.7349 (p90) REVERT: I 694 ARG cc_start: 0.8985 (mmm-85) cc_final: 0.8626 (mmm160) REVERT: I 873 MET cc_start: 0.5224 (ppp) cc_final: 0.4949 (ppp) REVERT: D 326 MET cc_start: 0.8938 (mpp) cc_final: 0.8529 (mmp) REVERT: D 327 MET cc_start: 0.6149 (mmm) cc_final: 0.5947 (tmm) REVERT: D 375 MET cc_start: 0.7737 (mtm) cc_final: 0.7182 (mpp) REVERT: F 292 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9094 (mp0) REVERT: F 361 TYR cc_start: 0.9386 (m-80) cc_final: 0.8499 (m-80) REVERT: F 453 LYS cc_start: 0.8766 (pptt) cc_final: 0.8219 (pttt) REVERT: F 460 MET cc_start: 0.8567 (ptt) cc_final: 0.7443 (tpt) REVERT: H 327 MET cc_start: 0.6217 (mmm) cc_final: 0.5450 (mmm) REVERT: H 350 ASP cc_start: 0.9074 (m-30) cc_final: 0.8736 (m-30) REVERT: H 365 TYR cc_start: 0.8036 (m-80) cc_final: 0.7617 (m-80) REVERT: H 432 HIS cc_start: 0.9301 (m90) cc_final: 0.8715 (m90) REVERT: H 435 ASN cc_start: 0.8431 (m-40) cc_final: 0.8214 (m110) REVERT: H 457 ARG cc_start: 0.8688 (ptp90) cc_final: 0.8177 (ptp90) REVERT: J 359 HIS cc_start: 0.8850 (t70) cc_final: 0.8492 (t70) REVERT: J 361 TYR cc_start: 0.9251 (m-80) cc_final: 0.8378 (m-80) REVERT: J 460 MET cc_start: 0.8409 (ptt) cc_final: 0.7484 (tpp) outliers start: 157 outliers final: 120 residues processed: 586 average time/residue: 0.5915 time to fit residues: 591.8941 Evaluate side-chains 585 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 455 time to evaluate : 6.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 195 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 285 TRP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 285 TRP Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 320 CYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 470 GLU Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 680 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 876 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 285 TRP Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 320 CYS Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 444 ILE Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 470 GLU Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 581 VAL Chi-restraints excluded: chain G residue 609 THR Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 726 VAL Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 876 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 268 ILE Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 285 TRP Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 320 CYS Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 609 THR Chi-restraints excluded: chain I residue 662 ILE Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 680 ASP Chi-restraints excluded: chain I residue 715 ILE Chi-restraints excluded: chain I residue 749 LEU Chi-restraints excluded: chain I residue 770 LEU Chi-restraints excluded: chain I residue 876 LEU Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 457 ARG Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain H residue 397 ILE Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 431 PHE Chi-restraints excluded: chain J residue 295 LYS Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 421 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 363 optimal weight: 3.9990 chunk 234 optimal weight: 0.9980 chunk 351 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 115 optimal weight: 40.0000 chunk 113 optimal weight: 1.9990 chunk 373 optimal weight: 3.9990 chunk 400 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 54 optimal weight: 0.0270 chunk 462 optimal weight: 4.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 610 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS ** D 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 HIS ** F 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50680 Z= 0.182 Angle : 0.624 13.110 68435 Z= 0.309 Chirality : 0.042 0.204 7750 Planarity : 0.003 0.075 8585 Dihedral : 6.879 89.488 6810 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.62 % Favored : 91.35 % Rotamer: Outliers : 2.51 % Allowed : 18.17 % Favored : 79.32 % 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: -1.25 (0.11), residues: 6090 helix: 0.24 (0.10), residues: 2680 sheet: -1.77 (0.24), residues: 440 loop : -1.70 (0.12), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 356 HIS 0.026 0.001 HIS F 432 PHE 0.023 0.001 PHE J 448 TYR 0.016 0.001 TYR A 141 ARG 0.015 0.000 ARG I 851 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 501 time to evaluate : 6.686 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: A 388 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8012 (mtmt) REVERT: A 413 MET cc_start: 0.8385 (tmm) cc_final: 0.7941 (tmm) REVERT: A 556 MET cc_start: 0.8497 (tpp) cc_final: 0.8167 (tpp) REVERT: B 293 MET cc_start: 0.7194 (ptt) cc_final: 0.6957 (pmm) REVERT: B 326 MET cc_start: 0.8817 (mmm) cc_final: 0.8545 (mmp) REVERT: B 327 MET cc_start: 0.7079 (mmm) cc_final: 0.6678 (tmm) REVERT: B 353 TYR cc_start: 0.9133 (t80) cc_final: 0.8867 (t80) REVERT: B 385 GLU cc_start: 0.8870 (mp0) cc_final: 0.8489 (mp0) REVERT: B 460 MET cc_start: 0.8387 (ptt) cc_final: 0.7381 (tpt) REVERT: C 158 MET cc_start: 0.7963 (tmm) cc_final: 0.7544 (tmm) REVERT: C 413 MET cc_start: 0.8293 (ppp) cc_final: 0.7524 (ppp) REVERT: E 68 ASN cc_start: 0.8830 (m110) cc_final: 0.8537 (m110) REVERT: E 158 MET cc_start: 0.8140 (tmm) cc_final: 0.7432 (tmm) REVERT: E 264 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8940 (pp) REVERT: G 136 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: G 158 MET cc_start: 0.8202 (tmm) cc_final: 0.7929 (tmm) REVERT: G 264 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8921 (pp) REVERT: G 284 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8563 (mp) REVERT: G 329 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6016 (tpp) REVERT: G 553 MET cc_start: 0.9009 (mtm) cc_final: 0.8454 (mpp) REVERT: G 556 MET cc_start: 0.8731 (tpp) cc_final: 0.8467 (tpp) REVERT: G 594 TYR cc_start: 0.7723 (p90) cc_final: 0.7111 (p90) REVERT: G 690 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8818 (pp) REVERT: G 718 MET cc_start: 0.6492 (mmm) cc_final: 0.6223 (mmm) REVERT: I 136 GLU cc_start: 0.8632 (pm20) cc_final: 0.8249 (pm20) REVERT: I 264 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8980 (pp) REVERT: I 284 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8778 (mp) REVERT: I 285 TRP cc_start: 0.7578 (OUTLIER) cc_final: 0.6932 (m-10) REVERT: I 388 LYS cc_start: 0.4343 (OUTLIER) cc_final: 0.4002 (pptt) REVERT: I 413 MET cc_start: 0.8435 (tmm) cc_final: 0.8032 (tmm) REVERT: I 548 VAL cc_start: 0.6632 (OUTLIER) cc_final: 0.6145 (t) REVERT: I 553 MET cc_start: 0.9197 (mtm) cc_final: 0.8658 (mpp) REVERT: I 594 TYR cc_start: 0.7744 (p90) cc_final: 0.7278 (p90) REVERT: I 694 ARG cc_start: 0.8978 (mmm-85) cc_final: 0.8257 (mmm-85) REVERT: I 873 MET cc_start: 0.5027 (ppp) cc_final: 0.4742 (ppp) REVERT: D 326 MET cc_start: 0.8942 (mpp) cc_final: 0.8536 (mmp) REVERT: D 375 MET cc_start: 0.7666 (mtm) cc_final: 0.7141 (mpp) REVERT: F 292 GLU cc_start: 0.9358 (mm-30) cc_final: 0.9060 (mp0) REVERT: F 327 MET cc_start: 0.6075 (mmm) cc_final: 0.5643 (mmm) REVERT: F 329 LEU cc_start: 0.8522 (mp) cc_final: 0.8165 (tt) REVERT: F 361 TYR cc_start: 0.9343 (m-80) cc_final: 0.8389 (m-80) REVERT: F 453 LYS cc_start: 0.8791 (pptt) cc_final: 0.8239 (pttt) REVERT: F 460 MET cc_start: 0.8511 (ptt) cc_final: 0.7405 (tpt) REVERT: H 327 MET cc_start: 0.6246 (mmm) cc_final: 0.5403 (mmm) REVERT: H 350 ASP cc_start: 0.9054 (m-30) cc_final: 0.8732 (m-30) REVERT: H 365 TYR cc_start: 0.7991 (m-80) cc_final: 0.7557 (m-80) REVERT: H 432 HIS cc_start: 0.9319 (m90) cc_final: 0.8717 (m90) REVERT: H 435 ASN cc_start: 0.8371 (m-40) cc_final: 0.8140 (m110) REVERT: J 359 HIS cc_start: 0.8766 (t70) cc_final: 0.8485 (t70) REVERT: J 361 TYR cc_start: 0.9183 (m-80) cc_final: 0.8314 (m-80) REVERT: J 460 MET cc_start: 0.8351 (ptt) cc_final: 0.7402 (tpp) outliers start: 140 outliers final: 96 residues processed: 600 average time/residue: 0.5975 time to fit residues: 608.7508 Evaluate side-chains 591 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 483 time to evaluate : 6.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 320 CYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 680 ASP Chi-restraints excluded: chain E residue 713 GLU Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 797 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 320 CYS Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 470 GLU Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 609 THR Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 726 VAL Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 797 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 285 TRP Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 320 CYS Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 609 THR Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 680 ASP Chi-restraints excluded: chain I residue 749 LEU Chi-restraints excluded: chain I residue 770 LEU Chi-restraints excluded: chain I residue 876 LEU Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 457 ARG Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain F residue 325 GLU Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 431 PHE Chi-restraints excluded: chain J residue 295 LYS Chi-restraints excluded: chain J residue 416 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 534 optimal weight: 5.9990 chunk 563 optimal weight: 9.9990 chunk 513 optimal weight: 7.9990 chunk 547 optimal weight: 0.0670 chunk 329 optimal weight: 0.4980 chunk 238 optimal weight: 8.9990 chunk 430 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 495 optimal weight: 9.9990 chunk 518 optimal weight: 6.9990 chunk 545 optimal weight: 3.9990 overall best weight: 3.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 610 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN J 271 HIS ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 50680 Z= 0.274 Angle : 0.662 12.148 68435 Z= 0.331 Chirality : 0.043 0.224 7750 Planarity : 0.004 0.109 8585 Dihedral : 7.104 89.727 6810 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.06 % Favored : 90.85 % Rotamer: Outliers : 2.39 % Allowed : 18.39 % Favored : 79.23 % 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: -1.31 (0.11), residues: 6090 helix: 0.16 (0.10), residues: 2715 sheet: -1.93 (0.24), residues: 435 loop : -1.69 (0.12), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 285 HIS 0.005 0.001 HIS B 359 PHE 0.024 0.001 PHE J 448 TYR 0.025 0.001 TYR A 141 ARG 0.019 0.001 ARG C 851 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 487 time to evaluate : 7.446 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: A 388 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8134 (mtmt) REVERT: A 413 MET cc_start: 0.8410 (tmm) cc_final: 0.8012 (tmm) REVERT: B 326 MET cc_start: 0.8841 (mmm) cc_final: 0.8588 (mmp) REVERT: B 327 MET cc_start: 0.6982 (mmm) cc_final: 0.6558 (tmm) REVERT: B 353 TYR cc_start: 0.9116 (t80) cc_final: 0.8817 (t80) REVERT: B 361 TYR cc_start: 0.9429 (m-80) cc_final: 0.8479 (m-80) REVERT: B 460 MET cc_start: 0.8406 (ptt) cc_final: 0.7388 (tpt) REVERT: C 158 MET cc_start: 0.8068 (tmm) cc_final: 0.7576 (tmm) REVERT: C 413 MET cc_start: 0.8305 (ppp) cc_final: 0.7528 (ppp) REVERT: C 548 VAL cc_start: 0.6956 (OUTLIER) cc_final: 0.6490 (t) REVERT: C 553 MET cc_start: 0.8796 (mpp) cc_final: 0.8522 (mpp) REVERT: E 68 ASN cc_start: 0.8854 (m110) cc_final: 0.8554 (m110) REVERT: E 158 MET cc_start: 0.8086 (tmm) cc_final: 0.7791 (tmm) REVERT: E 264 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8936 (pp) REVERT: E 648 MET cc_start: 0.7352 (mtm) cc_final: 0.7140 (mtm) REVERT: G 136 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: G 158 MET cc_start: 0.8305 (tmm) cc_final: 0.8023 (tmm) REVERT: G 264 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8990 (pp) REVERT: G 284 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8548 (mp) REVERT: G 329 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.5966 (tpp) REVERT: G 413 MET cc_start: 0.8364 (ppp) cc_final: 0.7947 (ppp) REVERT: G 553 MET cc_start: 0.9086 (mtm) cc_final: 0.8652 (mpp) REVERT: G 594 TYR cc_start: 0.7810 (p90) cc_final: 0.7177 (p90) REVERT: G 690 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8928 (pp) REVERT: I 60 GLU cc_start: 0.7918 (pm20) cc_final: 0.7673 (pm20) REVERT: I 136 GLU cc_start: 0.8680 (pm20) cc_final: 0.8289 (pm20) REVERT: I 264 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8957 (pp) REVERT: I 284 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8815 (mp) REVERT: I 285 TRP cc_start: 0.7777 (OUTLIER) cc_final: 0.6982 (m-10) REVERT: I 388 LYS cc_start: 0.5092 (OUTLIER) cc_final: 0.4802 (pptt) REVERT: I 413 MET cc_start: 0.8490 (tmm) cc_final: 0.8114 (tmm) REVERT: I 548 VAL cc_start: 0.6742 (OUTLIER) cc_final: 0.6260 (t) REVERT: I 553 MET cc_start: 0.9232 (mtm) cc_final: 0.8359 (mpp) REVERT: I 594 TYR cc_start: 0.7791 (p90) cc_final: 0.7306 (p90) REVERT: I 694 ARG cc_start: 0.8958 (mmm-85) cc_final: 0.8397 (mmm160) REVERT: I 873 MET cc_start: 0.5143 (ppp) cc_final: 0.4872 (ppp) REVERT: D 327 MET cc_start: 0.5945 (tmm) cc_final: 0.5591 (tmm) REVERT: F 292 GLU cc_start: 0.9364 (mm-30) cc_final: 0.9064 (mp0) REVERT: F 327 MET cc_start: 0.6093 (mmm) cc_final: 0.5640 (mmm) REVERT: F 329 LEU cc_start: 0.8509 (mp) cc_final: 0.8135 (tt) REVERT: F 361 TYR cc_start: 0.9359 (m-80) cc_final: 0.8480 (m-80) REVERT: F 453 LYS cc_start: 0.8785 (pptt) cc_final: 0.8208 (pttt) REVERT: F 460 MET cc_start: 0.8530 (ptt) cc_final: 0.7343 (tpt) REVERT: H 327 MET cc_start: 0.6176 (mmm) cc_final: 0.5307 (mmm) REVERT: H 350 ASP cc_start: 0.9067 (m-30) cc_final: 0.8750 (m-30) REVERT: H 365 TYR cc_start: 0.8004 (m-80) cc_final: 0.7573 (m-80) REVERT: H 432 HIS cc_start: 0.9331 (m90) cc_final: 0.8743 (m90) REVERT: H 435 ASN cc_start: 0.8393 (m-40) cc_final: 0.8168 (m110) REVERT: H 457 ARG cc_start: 0.8667 (ptp90) cc_final: 0.8152 (ptp90) REVERT: J 359 HIS cc_start: 0.8815 (t70) cc_final: 0.8492 (t70) REVERT: J 361 TYR cc_start: 0.9225 (m-80) cc_final: 0.8361 (m-80) REVERT: J 460 MET cc_start: 0.8329 (ptt) cc_final: 0.7427 (tpp) outliers start: 133 outliers final: 108 residues processed: 578 average time/residue: 0.5976 time to fit residues: 587.1838 Evaluate side-chains 598 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 477 time to evaluate : 6.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 285 TRP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 306 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 320 CYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 680 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 741 VAL Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 320 CYS Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 444 ILE Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 470 GLU Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 609 THR Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 726 VAL Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 876 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 285 TRP Chi-restraints excluded: chain I residue 297 PHE Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 320 CYS Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 529 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 609 THR Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 680 ASP Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain I residue 749 LEU Chi-restraints excluded: chain I residue 770 LEU Chi-restraints excluded: chain I residue 876 LEU Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 457 ARG Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain H residue 397 ILE Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 431 PHE Chi-restraints excluded: chain J residue 295 LYS Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 421 ASN Chi-restraints excluded: chain J residue 431 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 359 optimal weight: 0.0020 chunk 579 optimal weight: 0.0270 chunk 353 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 chunk 402 optimal weight: 4.9990 chunk 607 optimal weight: 20.0000 chunk 559 optimal weight: 7.9990 chunk 483 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 373 optimal weight: 8.9990 chunk 296 optimal weight: 0.4980 overall best weight: 2.3050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 610 HIS I 133 GLN ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN F 271 HIS ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 50680 Z= 0.224 Angle : 0.656 13.000 68435 Z= 0.325 Chirality : 0.043 0.226 7750 Planarity : 0.004 0.101 8585 Dihedral : 6.996 89.858 6810 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.03 % Favored : 90.92 % Rotamer: Outliers : 2.46 % Allowed : 18.60 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.29 (0.11), residues: 6090 helix: 0.18 (0.10), residues: 2715 sheet: -1.92 (0.24), residues: 435 loop : -1.68 (0.12), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 356 HIS 0.006 0.001 HIS H 271 PHE 0.026 0.001 PHE J 448 TYR 0.018 0.001 TYR G 277 ARG 0.021 0.000 ARG C 851 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12180 Ramachandran restraints generated. 6090 Oldfield, 0 Emsley, 6090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 491 time to evaluate : 6.658 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 388 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8138 (mtmt) REVERT: A 413 MET cc_start: 0.8379 (tmm) cc_final: 0.7981 (tmm) REVERT: A 556 MET cc_start: 0.8168 (tpp) cc_final: 0.7867 (tpp) REVERT: B 326 MET cc_start: 0.8839 (mmm) cc_final: 0.8586 (mmp) REVERT: B 327 MET cc_start: 0.7048 (mmm) cc_final: 0.6723 (tmm) REVERT: B 353 TYR cc_start: 0.9121 (t80) cc_final: 0.8834 (t80) REVERT: B 359 HIS cc_start: 0.8463 (t70) cc_final: 0.8225 (t70) REVERT: B 361 TYR cc_start: 0.9412 (m-80) cc_final: 0.8493 (m-80) REVERT: B 460 MET cc_start: 0.8341 (ptt) cc_final: 0.7317 (tpt) REVERT: C 60 GLU cc_start: 0.7702 (pm20) cc_final: 0.7475 (pm20) REVERT: C 158 MET cc_start: 0.8073 (tmm) cc_final: 0.7560 (tmm) REVERT: C 413 MET cc_start: 0.8269 (ppp) cc_final: 0.7721 (tmm) REVERT: C 548 VAL cc_start: 0.6981 (OUTLIER) cc_final: 0.6500 (t) REVERT: C 553 MET cc_start: 0.8809 (mpp) cc_final: 0.8533 (mpp) REVERT: E 68 ASN cc_start: 0.8858 (m110) cc_final: 0.8595 (m110) REVERT: E 158 MET cc_start: 0.8081 (tmm) cc_final: 0.7712 (tmm) REVERT: E 264 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8969 (pp) REVERT: G 60 GLU cc_start: 0.7672 (pm20) cc_final: 0.7431 (pm20) REVERT: G 136 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: G 158 MET cc_start: 0.8228 (tmm) cc_final: 0.7957 (tmm) REVERT: G 264 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8969 (pp) REVERT: G 284 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8513 (mp) REVERT: G 329 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.5983 (tpp) REVERT: G 553 MET cc_start: 0.9066 (mtm) cc_final: 0.8638 (mpp) REVERT: G 556 MET cc_start: 0.8664 (tpp) cc_final: 0.8242 (tpp) REVERT: G 594 TYR cc_start: 0.7824 (p90) cc_final: 0.7083 (p90) REVERT: G 690 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8878 (pp) REVERT: I 136 GLU cc_start: 0.8668 (pm20) cc_final: 0.8293 (pm20) REVERT: I 264 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8952 (pp) REVERT: I 284 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8784 (mp) REVERT: I 285 TRP cc_start: 0.7675 (OUTLIER) cc_final: 0.6951 (m-10) REVERT: I 388 LYS cc_start: 0.4954 (OUTLIER) cc_final: 0.4636 (pptt) REVERT: I 413 MET cc_start: 0.8486 (tmm) cc_final: 0.8172 (tmm) REVERT: I 548 VAL cc_start: 0.6728 (OUTLIER) cc_final: 0.6242 (t) REVERT: I 553 MET cc_start: 0.9271 (mtm) cc_final: 0.8742 (mpp) REVERT: I 594 TYR cc_start: 0.7750 (p90) cc_final: 0.7260 (p90) REVERT: I 694 ARG cc_start: 0.8939 (mmm-85) cc_final: 0.8343 (mmm160) REVERT: I 873 MET cc_start: 0.5058 (ppp) cc_final: 0.4759 (ppp) REVERT: D 327 MET cc_start: 0.6038 (tmm) cc_final: 0.5681 (tmm) REVERT: F 292 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9048 (mp0) REVERT: F 327 MET cc_start: 0.6080 (mmm) cc_final: 0.5615 (mmm) REVERT: F 329 LEU cc_start: 0.8489 (mp) cc_final: 0.8127 (tt) REVERT: F 361 TYR cc_start: 0.9349 (m-80) cc_final: 0.8463 (m-80) REVERT: F 453 LYS cc_start: 0.8789 (pptt) cc_final: 0.8205 (pttt) REVERT: F 460 MET cc_start: 0.8479 (ptt) cc_final: 0.7300 (tpt) REVERT: H 327 MET cc_start: 0.6311 (mmm) cc_final: 0.5415 (mmm) REVERT: H 350 ASP cc_start: 0.9061 (m-30) cc_final: 0.8753 (m-30) REVERT: H 365 TYR cc_start: 0.7986 (m-80) cc_final: 0.7526 (m-80) REVERT: H 432 HIS cc_start: 0.9338 (m90) cc_final: 0.8748 (m90) REVERT: H 435 ASN cc_start: 0.8366 (m-40) cc_final: 0.8144 (m110) REVERT: H 457 ARG cc_start: 0.8647 (ptp90) cc_final: 0.8124 (ptp90) REVERT: J 359 HIS cc_start: 0.8770 (t70) cc_final: 0.8455 (t70) REVERT: J 361 TYR cc_start: 0.9211 (m-80) cc_final: 0.8421 (m-80) REVERT: J 365 TYR cc_start: 0.8455 (m-10) cc_final: 0.8124 (m-10) REVERT: J 460 MET cc_start: 0.8300 (ptt) cc_final: 0.7344 (tpp) outliers start: 137 outliers final: 113 residues processed: 585 average time/residue: 0.5810 time to fit residues: 577.9330 Evaluate side-chains 608 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 482 time to evaluate : 5.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 329 MET Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 LYS Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 329 MET Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 488 ILE Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 680 ASP Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 707 MET Chi-restraints excluded: chain C residue 725 ASP Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 264 LEU Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 320 CYS Chi-restraints excluded: chain E residue 361 GLU Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain E residue 400 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 555 HIS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 680 ASP Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 741 VAL Chi-restraints excluded: chain E residue 749 LEU Chi-restraints excluded: chain E residue 770 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 310 THR Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 320 CYS Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain G residue 359 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 418 LEU Chi-restraints excluded: chain G residue 444 ILE Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 470 GLU Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 609 THR Chi-restraints excluded: chain G residue 644 LEU Chi-restraints excluded: chain G residue 680 ASP Chi-restraints excluded: chain G residue 690 LEU Chi-restraints excluded: chain G residue 726 VAL Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain G residue 876 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 264 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 284 ILE Chi-restraints excluded: chain I residue 285 TRP Chi-restraints excluded: chain I residue 297 PHE Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain I residue 320 CYS Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 540 SER Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 581 VAL Chi-restraints excluded: chain I residue 609 THR Chi-restraints excluded: chain I residue 662 ILE Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 680 ASP Chi-restraints excluded: chain I residue 741 VAL Chi-restraints excluded: chain I residue 749 LEU Chi-restraints excluded: chain I residue 770 LEU Chi-restraints excluded: chain I residue 876 LEU Chi-restraints excluded: chain D residue 255 TYR Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 457 ARG Chi-restraints excluded: chain F residue 295 LYS Chi-restraints excluded: chain F residue 325 GLU Chi-restraints excluded: chain F residue 416 ILE Chi-restraints excluded: chain H residue 397 ILE Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 431 PHE Chi-restraints excluded: chain J residue 295 LYS Chi-restraints excluded: chain J residue 416 ILE Chi-restraints excluded: chain J residue 431 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 384 optimal weight: 0.0570 chunk 515 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 446 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 484 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 497 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 HIS ** B 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 610 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.105746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.081070 restraints weight = 241938.560| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 5.85 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50680 Z= 0.208 Angle : 0.651 13.296 68435 Z= 0.321 Chirality : 0.043 0.221 7750 Planarity : 0.004 0.098 8585 Dihedral : 6.883 89.593 6810 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.83 % Favored : 91.12 % Rotamer: Outliers : 2.33 % Allowed : 18.87 % Favored : 78.80 % 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: -1.26 (0.11), residues: 6090 helix: 0.21 (0.10), residues: 2715 sheet: -1.91 (0.24), residues: 435 loop : -1.67 (0.12), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 356 HIS 0.006 0.001 HIS F 271 PHE 0.025 0.001 PHE J 448 TYR 0.019 0.001 TYR A 141 ARG 0.025 0.000 ARG G 851 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11824.39 seconds wall clock time: 219 minutes 25.47 seconds (13165.47 seconds total)