Starting phenix.real_space_refine (version: dev) on Thu Dec 22 15:22:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe0_33153/12_2022/7xe0_33153_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe0_33153/12_2022/7xe0_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_33153/12_2022/7xe0_33153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe0_33153/12_2022/7xe0_33153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe0_33153/12_2022/7xe0_33153_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xe0_33153/12_2022/7xe0_33153_updated.pdb" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 27.08, per 1000 atoms: 0.54 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: 21.02 Conformation dependent library (CDL) restraints added in 7.8 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: 5.82 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: 17.68 Time building geometry restraints manager: 22.60 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: 28346 17.80 - 35.60: 2119 35.60 - 53.40: 332 53.40 - 71.20: 52 71.20 - 89.00: 26 Dihedral angle restraints: 30875 sinusoidal: 12775 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 30872 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 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. 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: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 18.950 Check model and map are aligned: 0.710 Convert atoms to be neutral: 0.410 Process input model: 124.330 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 12.833 89.002 19125 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.37 % Favored : 91.61 % Rotamer Outliers : 0.41 % 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 *********************** 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 : 6.240 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 outliers start: 23 outliers final: 4 residues processed: 601 average time/residue: 0.5833 time to fit residues: 587.1818 Evaluate side-chains 458 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 454 time to evaluate : 6.063 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.8972 time to fit residues: 13.4079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 6.9990 chunk 462 optimal weight: 5.9990 chunk 256 optimal weight: 0.6980 chunk 157 optimal weight: 8.9990 chunk 311 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 478 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 290 optimal weight: 0.7980 chunk 355 optimal weight: 6.9990 chunk 553 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 50680 Z= 0.225 Angle : 0.625 9.559 68435 Z= 0.316 Chirality : 0.043 0.155 7750 Planarity : 0.004 0.060 8585 Dihedral : 4.738 29.948 6655 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.44 % Favored : 91.49 % Rotamer Outliers : 1.00 % 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: -1.44 (0.11), residues: 6090 helix: 0.01 (0.10), residues: 2625 sheet: -2.11 (0.24), residues: 440 loop : -1.64 (0.12), residues: 3025 *********************** 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 571 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 515 time to evaluate : 7.046 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 outliers start: 56 outliers final: 32 residues processed: 539 average time/residue: 0.6086 time to fit residues: 554.5746 Evaluate side-chains 484 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 452 time to evaluate : 5.932 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4351 time to fit residues: 34.3286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 461 optimal weight: 9.9990 chunk 377 optimal weight: 0.0570 chunk 152 optimal weight: 0.8980 chunk 554 optimal weight: 10.0000 chunk 599 optimal weight: 9.9990 chunk 494 optimal weight: 0.0370 chunk 550 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 445 optimal weight: 9.9990 overall best weight: 2.3980 ------------------------------------------------------------------------------- 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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 HIS E 273 ASN ** E 739 HIS ** 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 D 378 GLN ** D 394 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 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 50680 Z= 0.221 Angle : 0.603 10.528 68435 Z= 0.306 Chirality : 0.042 0.169 7750 Planarity : 0.003 0.060 8585 Dihedral : 4.734 29.384 6655 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.77 % Favored : 91.18 % Rotamer Outliers : 1.51 % 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: -1.37 (0.11), residues: 6090 helix: 0.08 (0.10), residues: 2625 sheet: -2.22 (0.24), residues: 450 loop : -1.59 (0.12), residues: 3015 *********************** 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 590 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 506 time to evaluate : 6.189 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 outliers start: 84 outliers final: 44 residues processed: 561 average time/residue: 0.5854 time to fit residues: 557.5536 Evaluate side-chains 516 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 472 time to evaluate : 6.243 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.4970 time to fit residues: 48.7381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 7.9990 chunk 417 optimal weight: 0.9990 chunk 288 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 264 optimal weight: 10.0000 chunk 372 optimal weight: 0.5980 chunk 556 optimal weight: 9.9990 chunk 589 optimal weight: 7.9990 chunk 290 optimal weight: 0.0570 chunk 527 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- 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 A 610 HIS ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 HIS E 68 ASN ** E 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** 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 182 GLN 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1395 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= 0.152 Angle : 0.581 11.021 68435 Z= 0.289 Chirality : 0.042 0.168 7750 Planarity : 0.003 0.059 8585 Dihedral : 4.578 28.288 6655 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.36 % Favored : 91.59 % Rotamer Outliers : 1.38 % 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: 0.17 (0.11), residues: 2640 sheet: -2.12 (0.24), residues: 450 loop : -1.59 (0.12), residues: 3000 *********************** 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 613 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 536 time to evaluate : 6.759 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 outliers start: 77 outliers final: 38 residues processed: 590 average time/residue: 0.5833 time to fit residues: 583.9544 Evaluate side-chains 525 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 487 time to evaluate : 5.798 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4083 time to fit residues: 37.2111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 491 optimal weight: 20.0000 chunk 334 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 439 optimal weight: 7.9990 chunk 243 optimal weight: 0.6980 chunk 503 optimal weight: 20.0000 chunk 407 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 301 optimal weight: 4.9990 chunk 529 optimal weight: 4.9990 chunk 148 optimal weight: 0.0980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 HIS ** E 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** F 471 GLN ** F 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 271 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 50680 Z= 0.196 Angle : 0.597 12.132 68435 Z= 0.299 Chirality : 0.042 0.172 7750 Planarity : 0.003 0.055 8585 Dihedral : 4.580 28.061 6655 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.37 % Favored : 91.58 % Rotamer Outliers : 1.11 % 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: 0.20 (0.11), residues: 2635 sheet: -2.09 (0.24), residues: 450 loop : -1.56 (0.12), residues: 3005 *********************** 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 571 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 509 time to evaluate : 6.626 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 outliers start: 62 outliers final: 29 residues processed: 548 average time/residue: 0.5852 time to fit residues: 544.5298 Evaluate side-chains 510 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 481 time to evaluate : 5.823 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4797 time to fit residues: 33.4487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 198 optimal weight: 4.9990 chunk 530 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 chunk 346 optimal weight: 8.9990 chunk 145 optimal weight: 4.9990 chunk 590 optimal weight: 10.0000 chunk 489 optimal weight: 4.9990 chunk 273 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 ASN C 610 HIS E 44 GLN ** E 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 GLN ** 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** ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 50680 Z= 0.273 Angle : 0.635 12.561 68435 Z= 0.320 Chirality : 0.043 0.193 7750 Planarity : 0.004 0.080 8585 Dihedral : 4.711 28.844 6655 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.10 % Favored : 90.84 % Rotamer Outliers : 1.49 % 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: -1.24 (0.11), residues: 6090 helix: 0.22 (0.11), residues: 2640 sheet: -1.97 (0.24), residues: 440 loop : -1.59 (0.12), residues: 3010 *********************** 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 570 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 487 time to evaluate : 6.386 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 outliers start: 83 outliers final: 45 residues processed: 531 average time/residue: 0.5976 time to fit residues: 538.1050 Evaluate side-chains 508 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 463 time to evaluate : 6.468 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.4593 time to fit residues: 47.6315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 569 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 336 optimal weight: 0.9980 chunk 431 optimal weight: 0.0770 chunk 333 optimal weight: 4.9990 chunk 496 optimal weight: 20.0000 chunk 329 optimal weight: 0.5980 chunk 587 optimal weight: 9.9990 chunk 367 optimal weight: 8.9990 chunk 358 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 overall best weight: 1.7342 ------------------------------------------------------------------------------- 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 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 HIS ** E 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.108 50680 Z= 0.191 Angle : 0.622 19.514 68435 Z= 0.308 Chirality : 0.042 0.200 7750 Planarity : 0.003 0.067 8585 Dihedral : 4.629 28.623 6655 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.62 % Favored : 91.35 % Rotamer Outliers : 1.08 % 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: -1.17 (0.11), residues: 6090 helix: 0.27 (0.11), residues: 2635 sheet: -1.91 (0.24), residues: 440 loop : -1.55 (0.12), residues: 3015 *********************** 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 566 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 506 time to evaluate : 6.453 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 outliers start: 60 outliers final: 27 residues processed: 551 average time/residue: 0.5948 time to fit residues: 554.9568 Evaluate side-chains 503 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 476 time to evaluate : 6.349 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.5667 time to fit residues: 35.1004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 363 optimal weight: 9.9990 chunk 234 optimal weight: 0.9980 chunk 351 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 373 optimal weight: 0.7980 chunk 400 optimal weight: 3.9990 chunk 290 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 462 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 HIS E 739 HIS ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 435 ASN ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN J 271 HIS ** J 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.074 50680 Z= 0.156 Angle : 0.627 13.396 68435 Z= 0.307 Chirality : 0.042 0.210 7750 Planarity : 0.003 0.079 8585 Dihedral : 4.525 30.686 6655 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.14 % Favored : 91.82 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.10 (0.11), residues: 6090 helix: 0.32 (0.11), residues: 2630 sheet: -1.69 (0.25), residues: 430 loop : -1.53 (0.12), residues: 3030 *********************** 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 553 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 513 time to evaluate : 7.010 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 outliers start: 40 outliers final: 24 residues processed: 538 average time/residue: 0.5740 time to fit residues: 525.1467 Evaluate side-chains 507 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 483 time to evaluate : 5.948 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4372 time to fit residues: 27.5638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 534 optimal weight: 20.0000 chunk 563 optimal weight: 9.9990 chunk 513 optimal weight: 1.9990 chunk 547 optimal weight: 9.9990 chunk 329 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 430 optimal weight: 6.9990 chunk 168 optimal weight: 0.0170 chunk 495 optimal weight: 5.9990 chunk 518 optimal weight: 6.9990 chunk 545 optimal weight: 0.0870 overall best weight: 2.8202 ------------------------------------------------------------------------------- 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 517 ASN A 555 HIS A 610 HIS B 340 ASN ** B 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 610 HIS ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 610 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 440 HIS ** H 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN ** J 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 50680 Z= 0.257 Angle : 0.672 13.830 68435 Z= 0.334 Chirality : 0.043 0.225 7750 Planarity : 0.004 0.087 8585 Dihedral : 4.683 34.884 6655 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.78 % Favored : 91.13 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.18 (0.11), residues: 6090 helix: 0.22 (0.11), residues: 2675 sheet: -1.87 (0.24), residues: 440 loop : -1.53 (0.12), residues: 2975 *********************** 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 521 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 488 time to evaluate : 6.233 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 outliers start: 33 outliers final: 23 residues processed: 506 average time/residue: 0.5962 time to fit residues: 512.2224 Evaluate side-chains 492 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 469 time to evaluate : 6.079 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4671 time to fit residues: 28.0590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 359 optimal weight: 8.9990 chunk 579 optimal weight: 0.5980 chunk 353 optimal weight: 6.9990 chunk 274 optimal weight: 1.9990 chunk 402 optimal weight: 5.9990 chunk 607 optimal weight: 50.0000 chunk 559 optimal weight: 9.9990 chunk 483 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 373 optimal weight: 0.7980 chunk 296 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 610 HIS ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 517 ASN ** D 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN ** F 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 50680 Z= 0.173 Angle : 0.658 14.222 68435 Z= 0.319 Chirality : 0.043 0.228 7750 Planarity : 0.003 0.055 8585 Dihedral : 4.576 31.823 6655 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.36 % Favored : 91.61 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.11 (0.11), residues: 6090 helix: 0.32 (0.11), residues: 2630 sheet: -1.61 (0.25), residues: 425 loop : -1.56 (0.12), residues: 3035 ********************** 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 520 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 499 time to evaluate : 6.555 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 outliers start: 21 outliers final: 14 residues processed: 510 average time/residue: 0.5984 time to fit residues: 518.6063 Evaluate side-chains 499 residues out of total 5620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 485 time to evaluate : 6.401 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.6286 time to fit residues: 23.0258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 384 optimal weight: 0.6980 chunk 515 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 446 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 134 optimal weight: 0.8980 chunk 484 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 497 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** 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 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4148 r_free = 0.4148 target = 0.106831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.081187 restraints weight = 241107.323| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 6.23 r_work: 0.3344 rms_B_bonded: 6.03 restraints_weight: 2.0000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4148 r_free = 0.4148 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4146 r_free = 0.4146 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 50680 Z= 0.181 Angle : 0.656 13.996 68435 Z= 0.319 Chirality : 0.043 0.224 7750 Planarity : 0.004 0.103 8585 Dihedral : 4.573 32.639 6655 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.11 % Favored : 91.86 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.08 (0.11), residues: 6090 helix: 0.35 (0.11), residues: 2630 sheet: -1.58 (0.25), residues: 425 loop : -1.56 (0.12), residues: 3035 =============================================================================== Job complete usr+sys time: 11829.11 seconds wall clock time: 213 minutes 35.56 seconds (12815.56 seconds total)