Starting phenix.real_space_refine on Fri Feb 23 02:52:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xx2_33498/02_2024/7xx2_33498_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xx2_33498/02_2024/7xx2_33498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xx2_33498/02_2024/7xx2_33498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xx2_33498/02_2024/7xx2_33498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xx2_33498/02_2024/7xx2_33498_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xx2_33498/02_2024/7xx2_33498_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 194 5.16 5 C 23337 2.51 5 N 6133 2.21 5 O 6757 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A ASP 492": "OD1" <-> "OD2" Residue "A GLU 669": "OE1" <-> "OE2" Residue "A PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 528": "OE1" <-> "OE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ASP 176": "OD1" <-> "OD2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "E GLU 470": "OE1" <-> "OE2" Residue "E GLU 533": "OE1" <-> "OE2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 635": "OE1" <-> "OE2" Residue "E PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 234": "OE1" <-> "OE2" Residue "G ASP 266": "OD1" <-> "OD2" Residue "G TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 324": "OD1" <-> "OD2" Residue "G TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 516": "OE1" <-> "OE2" Residue "G ASP 523": "OD1" <-> "OD2" Residue "G TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 234": "OE1" <-> "OE2" Residue "I GLU 261": "OE1" <-> "OE2" Residue "I ASP 503": "OD1" <-> "OD2" Residue "I GLU 554": "OE1" <-> "OE2" Residue "I TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36436 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6617 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 32, 'TRANS': 794} Chain breaks: 2 Chain: "B" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3196 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 380} 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: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6617 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 32, 'TRANS': 794} Chain breaks: 2 Chain: "E" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6617 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 32, 'TRANS': 794} Chain breaks: 2 Chain: "G" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6617 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 32, 'TRANS': 794} Chain breaks: 2 Chain: "I" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6617 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 32, 'TRANS': 794} Chain breaks: 2 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: 18.70, per 1000 atoms: 0.51 Number of scatterers: 36436 At special positions: 0 Unit cell: (184.21, 168.95, 183.12, 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 194 16.00 P 15 15.00 O 6757 8.00 N 6133 7.00 C 23337 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: 13.78 Conformation dependent library (CDL) restraints added in 7.1 seconds 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8582 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 157 helices and 36 sheets defined 37.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.87 Creating SS restraints... Processing helix chain 'A' and resid 25 through 52 removed outlier: 3.824A pdb=" N VAL A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.507A 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: 3.725A pdb=" N GLU A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 137 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) 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 171 through 180 Processing helix chain 'A' and resid 206 through 216 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: 3.640A pdb=" N GLU A 291 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.066A 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 334 through 344 Processing helix chain 'A' and resid 357 through 367 Processing helix chain 'A' and resid 371 through 381 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 411 through 423 removed outlier: 3.659A pdb=" N LYS A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 416 " --> pdb=" O GLN A 412 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 437 removed outlier: 4.090A pdb=" N LEU A 435 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 503 through 515 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: 4.403A pdb=" N GLY A 619 " --> pdb=" O MET A 616 " (cutoff:3.500A) 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: 3.668A pdb=" N LEU A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY A 688 " --> pdb=" O VAL A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 717 removed outlier: 3.891A pdb=" N SER A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN A 717 " --> pdb=" O GLU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 793 removed outlier: 4.043A pdb=" N GLN A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 809 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: 4.573A pdb=" N TYR B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 removed outlier: 3.959A pdb=" N ASN B 189 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LYS B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 200 removed outlier: 3.601A 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 Processing helix chain 'B' and resid 230 through 241 removed outlier: 4.708A pdb=" N GLU B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 275 removed outlier: 3.527A pdb=" N SER B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 291 through 316 removed outlier: 3.638A pdb=" N LYS B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE B 310 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASP B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 312 " --> pdb=" O LYS B 308 " (cutoff:3.500A) removed outlier: 3.709A 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: 3.890A pdb=" N LEU B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 364 Processing helix chain 'B' and resid 380 through 390 Processing helix chain 'B' and resid 404 through 418 Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 450 through 454 Processing helix chain 'B' and resid 456 through 482 removed outlier: 3.669A pdb=" N GLU B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 482 " --> pdb=" O ARG B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 Processing helix chain 'B' and resid 534 through 537 No H-bonds generated for 'chain 'B' and resid 534 through 537' Processing helix chain 'B' and resid 541 through 551 Processing helix chain 'C' and resid 25 through 52 removed outlier: 4.032A pdb=" N VAL C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N SER C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 3.646A 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 171 through 182 Processing helix chain 'C' and resid 206 through 216 removed outlier: 3.502A pdb=" N LYS C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 263 through 271 Processing helix chain 'C' and resid 290 through 296 removed outlier: 4.103A pdb=" N CYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA C 296 " --> pdb=" O LEU C 292 " (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 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 334 through 345 removed outlier: 3.501A pdb=" N ILE C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 367 removed outlier: 3.506A pdb=" N LYS C 366 " --> pdb=" O GLU C 362 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS C 367 " --> pdb=" O ILE C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 381 Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 411 through 423 removed outlier: 4.485A pdb=" N ILE C 416 " --> pdb=" O GLN C 412 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TYR C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 437 removed outlier: 3.887A pdb=" N LEU C 435 " --> pdb=" O CYS C 431 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE C 437 " --> pdb=" O LEU C 433 " (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 515 Processing helix chain 'C' and resid 594 through 596 No H-bonds generated for 'chain 'C' and resid 594 through 596' Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.952A pdb=" N GLY C 619 " --> pdb=" O MET C 616 " (cutoff:3.500A) 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: 3.938A pdb=" N LEU C 687 " --> pdb=" O PHE C 683 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLY C 688 " --> pdb=" O VAL C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 717 removed outlier: 4.312A pdb=" N SER C 716 " --> pdb=" O GLU C 712 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN C 717 " --> pdb=" O GLU C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 removed outlier: 4.223A pdb=" N GLN C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 809 Processing helix chain 'C' and resid 841 through 843 No H-bonds generated for 'chain 'C' and resid 841 through 843' 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: 3.870A pdb=" N VAL E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 34 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 86 Processing helix chain 'E' and resid 116 through 140 removed outlier: 3.592A pdb=" N GLU E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 162 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 171 through 183 removed outlier: 3.710A pdb=" N LEU E 182 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 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: 4.139A pdb=" N GLU E 291 " --> pdb=" O LYS E 288 " (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 Processing helix chain 'E' and resid 357 through 367 removed outlier: 3.638A pdb=" N LYS E 366 " --> pdb=" O GLU E 362 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS E 367 " --> pdb=" O ILE E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 381 removed outlier: 3.998A pdb=" N ALA E 378 " --> pdb=" O ILE E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 399 Processing helix chain 'E' and resid 411 through 423 removed outlier: 4.285A pdb=" N ILE E 416 " --> pdb=" O GLN E 412 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER E 420 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 437 removed outlier: 3.911A pdb=" N LEU E 435 " --> pdb=" O CYS E 431 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER E 436 " --> pdb=" O LEU E 432 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE E 437 " --> pdb=" O LEU E 433 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 456 Processing helix chain 'E' and resid 469 through 481 Processing helix chain 'E' and resid 503 through 514 Processing helix chain 'E' and resid 616 through 620 removed outlier: 4.248A pdb=" N GLY E 619 " --> pdb=" O MET E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 689 removed outlier: 3.763A pdb=" N LEU E 687 " --> pdb=" O PHE E 683 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY E 688 " --> pdb=" O VAL E 684 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG E 689 " --> pdb=" O LYS E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 717 removed outlier: 4.172A pdb=" N SER E 716 " --> pdb=" O GLU E 712 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN E 717 " --> pdb=" O GLU E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 793 removed outlier: 4.133A pdb=" N GLN E 789 " --> pdb=" O SER E 785 " (cutoff:3.500A) removed outlier: 3.763A 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 26 through 52 removed outlier: 3.522A pdb=" N SER G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 86 Processing helix chain 'G' and resid 116 through 139 Processing helix chain 'G' and resid 156 through 161 removed outlier: 3.996A pdb=" N MET G 159 " --> pdb=" O PRO G 156 " (cutoff:3.500A) 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 171 through 183 removed outlier: 3.616A pdb=" N LEU G 182 " --> pdb=" O LEU G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 removed outlier: 3.532A pdb=" N LYS G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 246 Processing helix chain 'G' and resid 261 through 272 Processing helix chain 'G' and resid 287 through 296 removed outlier: 3.800A pdb=" N GLU G 291 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS G 294 " --> pdb=" O GLU G 291 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS G 295 " --> pdb=" O LEU G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 317 No H-bonds generated for 'chain 'G' and resid 314 through 317' Processing helix chain 'G' and resid 334 through 345 removed outlier: 3.558A pdb=" N ILE G 345 " --> pdb=" O PHE G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 367 removed outlier: 3.595A pdb=" N LYS G 366 " --> pdb=" O GLU G 362 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS G 367 " --> pdb=" O ILE G 363 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 381 Processing helix chain 'G' and resid 392 through 399 Processing helix chain 'G' and resid 411 through 423 removed outlier: 4.697A pdb=" N ILE G 416 " --> pdb=" O GLN G 412 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 417 " --> pdb=" O MET G 413 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER G 420 " --> pdb=" O ILE G 416 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR G 421 " --> pdb=" O LEU G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 437 removed outlier: 4.100A pdb=" N LEU G 435 " --> pdb=" O CYS G 431 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER G 436 " --> pdb=" O LEU G 432 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE G 437 " --> pdb=" O LEU G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 456 Processing helix chain 'G' and resid 469 through 481 Processing helix chain 'G' and resid 503 through 515 Processing helix chain 'G' and resid 616 through 620 removed outlier: 4.165A pdb=" N GLY G 619 " --> pdb=" O MET G 616 " (cutoff:3.500A) 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 687 removed outlier: 3.515A pdb=" N LEU G 687 " --> pdb=" O PHE G 683 " (cutoff:3.500A) Processing helix chain 'G' and resid 706 through 716 removed outlier: 3.624A pdb=" N SER G 716 " --> pdb=" O GLU G 712 " (cutoff:3.500A) Processing helix chain 'G' and resid 787 through 792 Processing helix chain 'G' and resid 805 through 809 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: 3.820A pdb=" N VAL I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU I 34 " --> pdb=" O ARG I 30 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 3.609A 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: 3.822A pdb=" N GLU I 136 " --> pdb=" O LYS I 132 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU I 137 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG I 138 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN I 139 " --> pdb=" O ALA I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 158 No H-bonds generated for 'chain 'I' and resid 156 through 158' Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing helix chain 'I' and resid 171 through 182 removed outlier: 3.511A pdb=" N MET I 181 " --> pdb=" O LYS I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 235 through 246 Processing helix chain 'I' and resid 261 through 272 removed outlier: 3.677A pdb=" N ILE I 265 " --> pdb=" O GLU I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 296 removed outlier: 4.498A pdb=" N CYS I 295 " --> pdb=" O GLU I 291 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA I 296 " --> pdb=" O LEU I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 317 No H-bonds generated for 'chain 'I' and resid 314 through 317' Processing helix chain 'I' and resid 334 through 344 Processing helix chain 'I' and resid 357 through 367 removed outlier: 3.813A pdb=" N LYS I 366 " --> pdb=" O GLU I 362 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS I 367 " --> pdb=" O ILE I 363 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 381 Processing helix chain 'I' and resid 392 through 399 Processing helix chain 'I' and resid 411 through 423 removed outlier: 3.792A pdb=" N LYS I 415 " --> pdb=" O GLU I 411 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE I 416 " --> pdb=" O GLN I 412 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N SER I 420 " --> pdb=" O ILE I 416 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR I 421 " --> pdb=" O LEU I 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 437 removed outlier: 3.871A pdb=" N LEU I 435 " --> pdb=" O CYS I 431 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER I 436 " --> pdb=" O LEU I 432 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE I 437 " --> pdb=" O LEU I 433 " (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 617 through 620 removed outlier: 3.530A pdb=" N LYS I 620 " --> pdb=" O GLU I 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 617 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 689 removed outlier: 3.576A pdb=" N LEU I 687 " --> pdb=" O PHE I 683 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY I 688 " --> pdb=" O VAL I 684 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG I 689 " --> pdb=" O LYS I 685 " (cutoff:3.500A) Processing helix chain 'I' and resid 706 through 717 Processing helix chain 'I' and resid 785 through 791 removed outlier: 3.560A pdb=" N GLN I 789 " --> pdb=" O SER I 785 " (cutoff:3.500A) Processing helix chain 'I' and resid 805 through 809 Processing helix chain 'I' and resid 861 through 863 No H-bonds generated for 'chain 'I' and resid 861 through 863' Processing sheet with id= A, first strand: chain 'A' and resid 326 through 328 removed outlier: 7.868A pdb=" N TYR A 327 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER A 197 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE A 279 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N THR A 309 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE A 281 " --> pdb=" O THR A 309 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 486 through 488 removed outlier: 3.511A pdb=" N ALA A 498 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.773A pdb=" N SER A 558 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ILE A 541 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR A 560 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 581 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N VAL A 561 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP A 583 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TYR A 603 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR A 626 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N CYS A 649 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL A 670 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 674 through 676 removed outlier: 6.567A pdb=" N SER A 723 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N LEU A 698 " --> pdb=" O SER A 723 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP A 725 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N PHE A 700 " --> pdb=" O ASP A 725 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE A 727 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 778 through 780 removed outlier: 6.406A pdb=" N GLU A 831 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ILE A 802 " --> pdb=" O GLU A 831 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 833 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N ASN A 804 " --> pdb=" O ARG A 833 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE A 835 " --> pdb=" O ASN A 804 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 858 through 860 removed outlier: 6.689A pdb=" N ASP A 885 " --> pdb=" O PHE A 859 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 194 through 199 removed outlier: 6.864A pdb=" N ILE C 279 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N THR C 309 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ILE C 281 " --> pdb=" O THR C 309 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA C 225 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASP C 282 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL C 227 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 486 through 488 Processing sheet with id= I, first strand: chain 'C' and resid 520 through 522 removed outlier: 3.796A pdb=" N LEU C 522 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER C 558 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE C 541 " --> pdb=" O SER C 558 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR C 560 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 6.562A 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: 7.405A pdb=" N ASP C 583 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR C 603 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 626 through 628 removed outlier: 6.888A pdb=" N CYS C 649 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C 670 " --> pdb=" O LEU C 650 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 674 through 676 removed outlier: 3.569A pdb=" N ASP C 699 " --> pdb=" O LEU C 674 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 778 through 780 removed outlier: 6.384A pdb=" N GLU C 831 " --> pdb=" O LEU C 800 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE C 802 " --> pdb=" O GLU C 831 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG C 833 " --> pdb=" O ILE C 802 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ASN C 804 " --> pdb=" O ARG C 833 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE C 835 " --> pdb=" O ASN C 804 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG C 854 " --> pdb=" O CYS C 832 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N PHE C 834 " --> pdb=" O ARG C 854 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N TRP C 856 " --> pdb=" O PHE C 834 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 858 through 860 removed outlier: 6.405A pdb=" N ASP C 885 " --> pdb=" O PHE C 859 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 326 through 328 removed outlier: 7.830A pdb=" N TYR E 327 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER E 197 " --> pdb=" O TYR E 327 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE E 279 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N THR E 309 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE E 281 " --> pdb=" O THR E 309 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA E 225 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP E 282 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL E 227 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 486 through 488 Processing sheet with id= P, first strand: chain 'E' and resid 520 through 522 removed outlier: 3.522A pdb=" N LEU E 522 " --> pdb=" O SER E 540 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 558 through 560 removed outlier: 6.680A pdb=" N VAL E 581 " --> pdb=" O VAL E 559 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR E 603 " --> pdb=" O LEU E 582 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 626 through 628 removed outlier: 6.743A pdb=" N CYS E 649 " --> pdb=" O LEU E 627 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL E 670 " --> pdb=" O LEU E 650 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 674 through 676 removed outlier: 6.822A pdb=" N SER E 723 " --> pdb=" O LEU E 696 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N LEU E 698 " --> pdb=" O SER E 723 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP E 725 " --> pdb=" O LEU E 698 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N PHE E 700 " --> pdb=" O ASP E 725 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE E 727 " --> pdb=" O PHE E 700 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 778 through 780 removed outlier: 6.636A pdb=" N GLU E 831 " --> pdb=" O LEU E 800 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ILE E 802 " --> pdb=" O GLU E 831 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG E 833 " --> pdb=" O ILE E 802 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASN E 804 " --> pdb=" O ARG E 833 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE E 835 " --> pdb=" O ASN E 804 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG E 854 " --> pdb=" O CYS E 832 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N PHE E 834 " --> pdb=" O ARG E 854 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP E 856 " --> pdb=" O PHE E 834 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 858 through 860 removed outlier: 6.343A pdb=" N ASP E 885 " --> pdb=" O PHE E 859 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'G' and resid 326 through 328 removed outlier: 7.888A pdb=" N TYR G 327 " --> pdb=" O THR G 195 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER G 197 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE G 279 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N THR G 309 " --> pdb=" O ILE G 279 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ILE G 281 " --> pdb=" O THR G 309 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA G 225 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ASP G 282 " --> pdb=" O ALA G 225 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL G 227 " --> pdb=" O ASP G 282 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 486 through 488 Processing sheet with id= X, first strand: chain 'G' and resid 520 through 522 removed outlier: 6.344A pdb=" N SER G 558 " --> pdb=" O LEU G 539 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N ILE G 541 " --> pdb=" O SER G 558 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR G 560 " --> pdb=" O ILE G 541 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL G 581 " --> pdb=" O VAL G 559 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR G 603 " --> pdb=" O LEU G 582 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 626 through 628 removed outlier: 7.236A pdb=" N CYS G 649 " --> pdb=" O LEU G 627 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL G 670 " --> pdb=" O LEU G 650 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'G' and resid 674 through 676 removed outlier: 6.194A pdb=" N SER G 723 " --> pdb=" O LEU G 696 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU G 698 " --> pdb=" O SER G 723 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ASP G 725 " --> pdb=" O LEU G 698 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N PHE G 700 " --> pdb=" O ASP G 725 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE G 727 " --> pdb=" O PHE G 700 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 778 through 780 removed outlier: 6.506A pdb=" N GLU G 831 " --> pdb=" O LEU G 800 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ILE G 802 " --> pdb=" O GLU G 831 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG G 833 " --> pdb=" O ILE G 802 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN G 804 " --> pdb=" O ARG G 833 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE G 835 " --> pdb=" O ASN G 804 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG G 854 " --> pdb=" O CYS G 832 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE G 834 " --> pdb=" O ARG G 854 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TRP G 856 " --> pdb=" O PHE G 834 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 858 through 860 removed outlier: 6.456A pdb=" N ASP G 885 " --> pdb=" O PHE G 859 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'I' and resid 326 through 328 removed outlier: 7.590A pdb=" N TYR I 327 " --> pdb=" O THR I 195 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N SER I 197 " --> pdb=" O TYR I 327 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE I 279 " --> pdb=" O ILE I 307 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N THR I 309 " --> pdb=" O ILE I 279 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE I 281 " --> pdb=" O THR I 309 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA I 225 " --> pdb=" O VAL I 280 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASP I 282 " --> pdb=" O ALA I 225 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL I 227 " --> pdb=" O ASP I 282 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 486 through 488 Processing sheet with id= AE, first strand: chain 'I' and resid 519 through 522 removed outlier: 6.905A pdb=" N ARG I 538 " --> pdb=" O THR I 520 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N LEU I 522 " --> pdb=" O ARG I 538 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER I 540 " --> pdb=" O LEU I 522 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER I 558 " --> pdb=" O LEU I 539 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE I 541 " --> pdb=" O SER I 558 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR I 560 " --> pdb=" O ILE I 541 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'I' and resid 581 through 583 removed outlier: 6.127A pdb=" N TYR I 603 " --> pdb=" O LEU I 582 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'I' and resid 626 through 628 removed outlier: 7.097A pdb=" N CYS I 649 " --> pdb=" O LEU I 627 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL I 670 " --> pdb=" O LEU I 650 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'I' and resid 674 through 676 removed outlier: 3.637A pdb=" N ASP I 699 " --> pdb=" O LEU I 674 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 778 through 780 removed outlier: 3.555A pdb=" N LEU I 780 " --> pdb=" O TRP I 803 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLU I 831 " --> pdb=" O LEU I 800 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ILE I 802 " --> pdb=" O GLU I 831 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG I 833 " --> pdb=" O ILE I 802 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN I 804 " --> pdb=" O ARG I 833 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE I 835 " --> pdb=" O ASN I 804 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG I 854 " --> pdb=" O CYS I 832 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N PHE I 834 " --> pdb=" O ARG I 854 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TRP I 856 " --> pdb=" O PHE I 834 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 858 through 860 removed outlier: 6.158A pdb=" N ASP I 885 " --> pdb=" O PHE I 859 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ 1040 hydrogen bonds defined for protein. 2991 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: 13.21 Time building geometry restraints manager: 14.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6053 1.32 - 1.44: 9259 1.44 - 1.57: 21497 1.57 - 1.69: 25 1.69 - 1.81: 306 Bond restraints: 37140 Sorted by residual: bond pdb=" C4 ATP G1001 " pdb=" C5 ATP G1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.00e+01 bond pdb=" C ALA E 212 " pdb=" O ALA E 212 " ideal model delta sigma weight residual 1.236 1.315 -0.079 1.15e-02 7.56e+03 4.70e+01 bond pdb=" C4 ATP I1001 " pdb=" C5 ATP I1001 " ideal model delta sigma weight residual 1.388 1.451 -0.063 1.00e-02 1.00e+04 4.00e+01 bond pdb=" C4 ATP C1001 " pdb=" C5 ATP C1001 " ideal model delta sigma weight residual 1.388 1.451 -0.063 1.00e-02 1.00e+04 3.94e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.449 -0.061 1.00e-02 1.00e+04 3.71e+01 ... (remaining 37135 not shown) Histogram of bond angle deviations from ideal: 96.66 - 104.66: 599 104.66 - 112.66: 20025 112.66 - 120.65: 17205 120.65 - 128.65: 12111 128.65 - 136.65: 261 Bond angle restraints: 50201 Sorted by residual: angle pdb=" PB ATP G1001 " pdb=" O3B ATP G1001 " pdb=" PG ATP G1001 " ideal model delta sigma weight residual 139.87 113.24 26.63 1.00e+00 1.00e+00 7.09e+02 angle pdb=" PA ATP E1001 " pdb=" O3A ATP E1001 " pdb=" PB ATP E1001 " ideal model delta sigma weight residual 136.83 111.45 25.38 1.00e+00 1.00e+00 6.44e+02 angle pdb=" PB ATP I1001 " pdb=" O3B ATP I1001 " pdb=" PG ATP I1001 " ideal model delta sigma weight residual 139.87 115.60 24.27 1.00e+00 1.00e+00 5.89e+02 angle pdb=" PA ATP C1001 " pdb=" O3A ATP C1001 " pdb=" PB ATP C1001 " ideal model delta sigma weight residual 136.83 114.55 22.28 1.00e+00 1.00e+00 4.96e+02 angle pdb=" PB ATP E1001 " pdb=" O3B ATP E1001 " pdb=" PG ATP E1001 " ideal model delta sigma weight residual 139.87 120.32 19.55 1.00e+00 1.00e+00 3.82e+02 ... (remaining 50196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 20329 17.96 - 35.91: 1987 35.91 - 53.87: 340 53.87 - 71.82: 77 71.82 - 89.78: 21 Dihedral angle restraints: 22754 sinusoidal: 9519 harmonic: 13235 Sorted by residual: dihedral pdb=" C THR A 174 " pdb=" N THR A 174 " pdb=" CA THR A 174 " pdb=" CB THR A 174 " ideal model delta harmonic sigma weight residual -122.00 -137.01 15.01 0 2.50e+00 1.60e-01 3.61e+01 dihedral pdb=" C LEU C 204 " pdb=" N LEU C 204 " pdb=" CA LEU C 204 " pdb=" CB LEU C 204 " ideal model delta harmonic sigma weight residual -122.60 -109.86 -12.74 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C ASP A 507 " pdb=" N ASP A 507 " pdb=" CA ASP A 507 " pdb=" CB ASP A 507 " ideal model delta harmonic sigma weight residual -122.60 -134.87 12.27 0 2.50e+00 1.60e-01 2.41e+01 ... (remaining 22751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 5292 0.098 - 0.197: 399 0.197 - 0.295: 32 0.295 - 0.393: 3 0.393 - 0.491: 2 Chirality restraints: 5728 Sorted by residual: chirality pdb=" CA LEU C 204 " pdb=" N LEU C 204 " pdb=" C LEU C 204 " pdb=" CB LEU C 204 " both_signs ideal model delta sigma weight residual False 2.51 3.00 -0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CA THR A 174 " pdb=" N THR A 174 " pdb=" C THR A 174 " pdb=" CB THR A 174 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASP A 507 " pdb=" N ASP A 507 " pdb=" C ASP A 507 " pdb=" CB ASP A 507 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 5725 not shown) Planarity restraints: 6278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 171 " 0.021 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C ILE E 171 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE E 171 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU E 172 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 173 " 0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C GLU A 173 " -0.063 2.00e-02 2.50e+03 pdb=" O GLU A 173 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 174 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 173 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C GLU E 173 " -0.062 2.00e-02 2.50e+03 pdb=" O GLU E 173 " 0.023 2.00e-02 2.50e+03 pdb=" N THR E 174 " 0.021 2.00e-02 2.50e+03 ... (remaining 6275 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 512 2.61 - 3.18: 33931 3.18 - 3.75: 56032 3.75 - 4.33: 76823 4.33 - 4.90: 122005 Nonbonded interactions: 289303 Sorted by model distance: nonbonded pdb=" O LEU I 770 " pdb=" CD1 LEU I 770 " model vdw 2.033 3.460 nonbonded pdb=" O SER A 640 " pdb=" OG SER A 640 " model vdw 2.143 2.440 nonbonded pdb=" N GLU A 172 " pdb=" OE1 GLU A 172 " model vdw 2.161 2.520 nonbonded pdb=" O GLY E 351 " pdb=" NE2 GLN E 354 " model vdw 2.198 2.520 nonbonded pdb=" O SER C 189 " pdb=" OG SER C 189 " model vdw 2.200 2.440 ... (remaining 289298 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.140 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: 11.530 Check model and map are aligned: 0.610 Set scattering table: 0.350 Process input model: 93.500 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.006 0.079 37140 Z= 0.412 Angle : 0.955 26.630 50201 Z= 0.615 Chirality : 0.055 0.491 5728 Planarity : 0.006 0.094 6278 Dihedral : 14.509 89.776 14172 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.94 % Favored : 90.02 % Rotamer: Outliers : 1.27 % Allowed : 1.45 % Favored : 97.28 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4488 helix: 0.27 (0.13), residues: 1683 sheet: -1.32 (0.25), residues: 450 loop : -1.61 (0.13), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 285 HIS 0.007 0.001 HIS A 600 PHE 0.025 0.002 PHE G 201 TYR 0.025 0.002 TYR E 74 ARG 0.017 0.001 ARG G 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 467 time to evaluate : 4.840 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: A 260 ASP cc_start: 0.7703 (p0) cc_final: 0.7239 (p0) REVERT: A 263 TYR cc_start: 0.8429 (m-80) cc_final: 0.7666 (m-80) REVERT: A 346 PHE cc_start: 0.4808 (m-10) cc_final: 0.4551 (m-10) REVERT: A 843 MET cc_start: 0.5683 (tpp) cc_final: 0.5418 (tpp) REVERT: B 245 LYS cc_start: 0.6899 (mmpt) cc_final: 0.6518 (mmtt) REVERT: C 413 MET cc_start: 0.9060 (ppp) cc_final: 0.8821 (tmm) REVERT: C 614 LEU cc_start: 0.8880 (tt) cc_final: 0.8637 (mm) REVERT: C 843 MET cc_start: 0.7247 (mmm) cc_final: 0.7036 (mmm) REVERT: E 173 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7668 (tp30) REVERT: E 854 ARG cc_start: 0.6418 (mmp80) cc_final: 0.6200 (mmp80) REVERT: G 34 GLU cc_start: 0.7769 (mp0) cc_final: 0.7553 (mp0) REVERT: G 529 MET cc_start: 0.8058 (mmm) cc_final: 0.6360 (tpp) REVERT: G 687 LEU cc_start: 0.9104 (mm) cc_final: 0.8631 (tt) REVERT: I 31 LYS cc_start: 0.8523 (ptpp) cc_final: 0.8323 (ptpp) REVERT: I 158 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7665 (ttp) REVERT: I 416 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8634 (mm) REVERT: I 637 LEU cc_start: 0.8945 (mm) cc_final: 0.8707 (mt) REVERT: I 645 ARG cc_start: 0.7577 (ttp-110) cc_final: 0.7366 (ttp-110) outliers start: 52 outliers final: 28 residues processed: 513 average time/residue: 0.5263 time to fit residues: 421.7089 Evaluate side-chains 358 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 327 time to evaluate : 4.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 277 TYR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 173 GLU Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 175 ARG Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 375 ILE Chi-restraints excluded: chain I residue 416 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 379 optimal weight: 0.7980 chunk 340 optimal weight: 0.0370 chunk 188 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 351 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 213 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 407 optimal weight: 0.0070 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 ASN B 263 GLN B 549 ASN C 44 GLN E 477 ASN E 610 HIS G 354 GLN G 610 HIS I 232 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37140 Z= 0.175 Angle : 0.629 11.769 50201 Z= 0.312 Chirality : 0.044 0.160 5728 Planarity : 0.004 0.055 6278 Dihedral : 8.489 86.593 5136 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.29 % Favored : 91.69 % Rotamer: Outliers : 1.67 % Allowed : 9.23 % Favored : 89.10 % 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: -0.95 (0.13), residues: 4488 helix: 0.65 (0.13), residues: 1674 sheet: -1.29 (0.25), residues: 450 loop : -1.46 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 188 HIS 0.008 0.001 HIS G 555 PHE 0.017 0.001 PHE A 781 TYR 0.029 0.001 TYR E 654 ARG 0.009 0.001 ARG E 851 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 410 time to evaluate : 4.524 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: A 260 ASP cc_start: 0.7449 (p0) cc_final: 0.7087 (p0) REVERT: A 263 TYR cc_start: 0.8371 (m-80) cc_final: 0.7841 (m-80) REVERT: A 507 ASP cc_start: 0.8220 (p0) cc_final: 0.7963 (p0) REVERT: A 873 MET cc_start: 0.3288 (ppp) cc_final: 0.3010 (ppp) REVERT: B 245 LYS cc_start: 0.6859 (mmpt) cc_final: 0.6528 (mmtt) REVERT: E 81 ASP cc_start: 0.8840 (t0) cc_final: 0.8495 (t0) REVERT: G 529 MET cc_start: 0.7725 (mmm) cc_final: 0.6624 (tpp) REVERT: G 687 LEU cc_start: 0.9195 (mm) cc_final: 0.8653 (tt) REVERT: G 873 MET cc_start: 0.4006 (tmm) cc_final: 0.3775 (tmm) REVERT: I 28 LYS cc_start: 0.8620 (pttt) cc_final: 0.8340 (pptt) REVERT: I 31 LYS cc_start: 0.8426 (ptpp) cc_final: 0.7853 (ptpp) REVERT: I 188 TRP cc_start: 0.5135 (m-90) cc_final: 0.4048 (m-90) REVERT: I 548 VAL cc_start: 0.6568 (t) cc_final: 0.6289 (t) REVERT: I 746 LEU cc_start: 0.7408 (mt) cc_final: 0.6681 (pp) outliers start: 68 outliers final: 38 residues processed: 454 average time/residue: 0.5153 time to fit residues: 368.8138 Evaluate side-chains 380 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 342 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 735 CYS Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 715 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 226 optimal weight: 0.4980 chunk 126 optimal weight: 0.8980 chunk 339 optimal weight: 0.9990 chunk 277 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 408 optimal weight: 2.9990 chunk 441 optimal weight: 10.0000 chunk 363 optimal weight: 6.9990 chunk 405 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 GLN E 610 HIS G 354 GLN I 597 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37140 Z= 0.194 Angle : 0.585 10.236 50201 Z= 0.292 Chirality : 0.043 0.143 5728 Planarity : 0.004 0.056 6278 Dihedral : 7.894 86.600 5096 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.50 % Allowed : 12.83 % Favored : 84.67 % 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: -0.91 (0.13), residues: 4488 helix: 0.75 (0.13), residues: 1710 sheet: -1.23 (0.25), residues: 450 loop : -1.54 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 188 HIS 0.006 0.001 HIS B 271 PHE 0.015 0.001 PHE E 683 TYR 0.025 0.001 TYR E 654 ARG 0.007 0.000 ARG G 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 386 time to evaluate : 4.015 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: A 136 GLU cc_start: 0.7467 (pm20) cc_final: 0.7208 (pm20) REVERT: A 260 ASP cc_start: 0.7620 (p0) cc_final: 0.7307 (p0) REVERT: A 263 TYR cc_start: 0.8322 (m-80) cc_final: 0.7882 (m-80) REVERT: A 770 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8891 (pp) REVERT: B 245 LYS cc_start: 0.6887 (mmpt) cc_final: 0.6591 (mmtt) REVERT: B 327 MET cc_start: 0.5376 (tpt) cc_final: 0.5143 (tpt) REVERT: C 37 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9052 (tp) REVERT: C 770 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8748 (pp) REVERT: E 648 MET cc_start: 0.8530 (mmm) cc_final: 0.8284 (mtt) REVERT: E 690 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8271 (pp) REVERT: E 843 MET cc_start: 0.6997 (tpp) cc_final: 0.6065 (mpp) REVERT: G 27 LYS cc_start: 0.8845 (mmtm) cc_final: 0.8284 (mmtm) REVERT: G 556 MET cc_start: 0.8505 (tpp) cc_final: 0.8195 (tpp) REVERT: I 27 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8200 (mmmt) REVERT: I 28 LYS cc_start: 0.8686 (pttt) cc_final: 0.8401 (pptt) REVERT: I 31 LYS cc_start: 0.8450 (ptpp) cc_final: 0.7976 (ptpp) REVERT: I 44 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8048 (mp10) REVERT: I 188 TRP cc_start: 0.5104 (m-90) cc_final: 0.4105 (m-90) REVERT: I 548 VAL cc_start: 0.6676 (t) cc_final: 0.6409 (t) REVERT: I 680 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7961 (p0) REVERT: I 712 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.7033 (tp30) outliers start: 102 outliers final: 53 residues processed: 461 average time/residue: 0.5048 time to fit residues: 368.9968 Evaluate side-chains 407 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 347 time to evaluate : 4.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 639 TRP Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 484 MET Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 680 ASP Chi-restraints excluded: chain I residue 712 GLU Chi-restraints excluded: chain I residue 715 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 403 optimal weight: 0.0070 chunk 307 optimal weight: 0.0670 chunk 211 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 194 optimal weight: 0.0170 chunk 274 optimal weight: 3.9990 chunk 409 optimal weight: 0.8980 chunk 434 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS E 610 HIS G 354 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 37140 Z= 0.153 Angle : 0.569 12.863 50201 Z= 0.281 Chirality : 0.042 0.173 5728 Planarity : 0.004 0.055 6278 Dihedral : 7.324 88.117 5092 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.20 % Allowed : 15.06 % Favored : 82.73 % 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: -0.81 (0.13), residues: 4488 helix: 0.85 (0.13), residues: 1710 sheet: -1.17 (0.25), residues: 450 loop : -1.50 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 188 HIS 0.004 0.001 HIS B 271 PHE 0.020 0.001 PHE A 781 TYR 0.025 0.001 TYR E 654 ARG 0.006 0.000 ARG G 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 387 time to evaluate : 4.396 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: A 226 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8667 (m-80) REVERT: A 260 ASP cc_start: 0.7644 (p0) cc_final: 0.7250 (p0) REVERT: A 263 TYR cc_start: 0.8303 (m-80) cc_final: 0.7898 (m-80) REVERT: A 680 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7687 (p0) REVERT: A 770 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8873 (pp) REVERT: B 245 LYS cc_start: 0.6913 (mmpt) cc_final: 0.6548 (mmtt) REVERT: C 37 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9030 (tp) REVERT: C 770 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8773 (pp) REVERT: E 177 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8856 (tmmm) REVERT: E 690 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8301 (pp) REVERT: E 843 MET cc_start: 0.6888 (tpp) cc_final: 0.6456 (tpp) REVERT: G 27 LYS cc_start: 0.8706 (mmtm) cc_final: 0.8505 (mmtm) REVERT: G 39 GLU cc_start: 0.8217 (tt0) cc_final: 0.8015 (tp30) REVERT: G 133 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7916 (mp10) REVERT: G 158 MET cc_start: 0.8440 (tpp) cc_final: 0.7879 (ttt) REVERT: G 556 MET cc_start: 0.8526 (tpp) cc_final: 0.8238 (tpp) REVERT: G 687 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8590 (tt) REVERT: I 27 LYS cc_start: 0.8439 (mmmt) cc_final: 0.8181 (mmmt) REVERT: I 31 LYS cc_start: 0.8443 (ptpp) cc_final: 0.8156 (ptpp) REVERT: I 132 LYS cc_start: 0.8708 (mptt) cc_final: 0.8503 (mmmt) REVERT: I 188 TRP cc_start: 0.4877 (m-90) cc_final: 0.3915 (m-90) REVERT: I 548 VAL cc_start: 0.6534 (t) cc_final: 0.6220 (t) REVERT: I 712 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7159 (tp30) outliers start: 90 outliers final: 54 residues processed: 454 average time/residue: 0.4987 time to fit residues: 363.4792 Evaluate side-chains 406 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 342 time to evaluate : 4.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 551 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 484 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 712 GLU Chi-restraints excluded: chain I residue 715 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 361 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 323 optimal weight: 0.5980 chunk 179 optimal weight: 4.9990 chunk 370 optimal weight: 2.9990 chunk 300 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 389 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 610 HIS G 354 GLN I 789 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37140 Z= 0.221 Angle : 0.583 12.108 50201 Z= 0.290 Chirality : 0.043 0.205 5728 Planarity : 0.004 0.055 6278 Dihedral : 7.099 87.727 5085 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.76 % Favored : 91.22 % Rotamer: Outliers : 2.62 % Allowed : 16.43 % Favored : 80.95 % 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: -0.68 (0.13), residues: 4488 helix: 0.94 (0.13), residues: 1710 sheet: -1.28 (0.25), residues: 460 loop : -1.37 (0.14), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 188 HIS 0.004 0.001 HIS A 600 PHE 0.013 0.001 PHE A 438 TYR 0.026 0.001 TYR E 654 ARG 0.008 0.000 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 372 time to evaluate : 4.348 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: A 260 ASP cc_start: 0.7724 (p0) cc_final: 0.7377 (p0) REVERT: A 263 TYR cc_start: 0.8377 (m-80) cc_final: 0.8034 (m-80) REVERT: A 335 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7229 (p0) REVERT: A 680 ASP cc_start: 0.8161 (OUTLIER) cc_final: 0.7590 (p0) REVERT: A 770 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8876 (pp) REVERT: B 245 LYS cc_start: 0.6934 (mmpt) cc_final: 0.6564 (mmtt) REVERT: B 327 MET cc_start: 0.5176 (tpt) cc_final: 0.4905 (tpt) REVERT: C 37 ILE cc_start: 0.9444 (OUTLIER) cc_final: 0.9067 (tp) REVERT: C 770 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8822 (pp) REVERT: E 30 ARG cc_start: 0.8157 (mmt90) cc_final: 0.7948 (mtt90) REVERT: E 177 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8824 (tmmm) REVERT: E 690 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8431 (pp) REVERT: G 39 GLU cc_start: 0.8265 (tt0) cc_final: 0.8043 (tp30) REVERT: G 133 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: G 158 MET cc_start: 0.8401 (tpp) cc_final: 0.7903 (ttt) REVERT: G 556 MET cc_start: 0.8577 (tpp) cc_final: 0.8321 (tpp) REVERT: G 687 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8619 (tt) REVERT: I 27 LYS cc_start: 0.8489 (mmmt) cc_final: 0.8249 (mmmt) REVERT: I 31 LYS cc_start: 0.8511 (ptpp) cc_final: 0.8217 (ptpp) REVERT: I 44 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: I 132 LYS cc_start: 0.8822 (mptt) cc_final: 0.8580 (mmmt) REVERT: I 548 VAL cc_start: 0.6712 (OUTLIER) cc_final: 0.6392 (t) REVERT: I 553 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7237 (ptm) outliers start: 107 outliers final: 74 residues processed: 450 average time/residue: 0.5061 time to fit residues: 364.3990 Evaluate side-chains 434 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 348 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 639 TRP Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 133 GLN Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 581 VAL Chi-restraints excluded: chain G residue 639 TRP Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 363 ILE Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 484 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 715 ILE Chi-restraints excluded: chain I residue 773 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 146 optimal weight: 0.7980 chunk 390 optimal weight: 0.1980 chunk 85 optimal weight: 0.6980 chunk 254 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 434 optimal weight: 0.4980 chunk 360 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 143 optimal weight: 0.6980 chunk 228 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 130 GLN G 354 GLN I 531 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 37140 Z= 0.145 Angle : 0.571 11.651 50201 Z= 0.279 Chirality : 0.042 0.213 5728 Planarity : 0.004 0.057 6278 Dihedral : 6.730 89.232 5085 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.62 % Allowed : 17.19 % Favored : 80.19 % 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: -0.61 (0.13), residues: 4488 helix: 1.12 (0.13), residues: 1690 sheet: -1.28 (0.26), residues: 460 loop : -1.40 (0.13), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 188 HIS 0.004 0.000 HIS B 271 PHE 0.022 0.001 PHE A 781 TYR 0.029 0.001 TYR A 603 ARG 0.010 0.000 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 380 time to evaluate : 4.665 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: A 157 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8086 (ptt180) REVERT: A 260 ASP cc_start: 0.7658 (p0) cc_final: 0.7255 (p0) REVERT: A 680 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7791 (p0) REVERT: B 245 LYS cc_start: 0.6856 (mmpt) cc_final: 0.6585 (mmtt) REVERT: B 327 MET cc_start: 0.5388 (tpt) cc_final: 0.5180 (tpt) REVERT: C 770 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8821 (pp) REVERT: E 30 ARG cc_start: 0.8141 (mmt90) cc_final: 0.7798 (mtt90) REVERT: E 177 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8830 (tmmm) REVERT: E 690 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8319 (pp) REVERT: G 39 GLU cc_start: 0.8237 (tt0) cc_final: 0.8020 (tp30) REVERT: G 158 MET cc_start: 0.8380 (tpp) cc_final: 0.7845 (ttt) REVERT: G 183 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8155 (t) REVERT: G 556 MET cc_start: 0.8531 (tpp) cc_final: 0.8250 (tpp) REVERT: G 687 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8603 (tt) REVERT: I 27 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8194 (mmmt) REVERT: I 31 LYS cc_start: 0.8451 (ptpp) cc_final: 0.8195 (ptpp) REVERT: I 44 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: I 132 LYS cc_start: 0.8756 (mptt) cc_final: 0.8532 (mmmt) REVERT: I 188 TRP cc_start: 0.4928 (m-90) cc_final: 0.4013 (m-90) REVERT: I 548 VAL cc_start: 0.6707 (OUTLIER) cc_final: 0.6387 (t) outliers start: 107 outliers final: 67 residues processed: 465 average time/residue: 0.5070 time to fit residues: 375.9819 Evaluate side-chains 431 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 355 time to evaluate : 4.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 523 ASP Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 44 GLN Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 363 ILE Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 707 MET Chi-restraints excluded: chain I residue 773 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 418 optimal weight: 0.3980 chunk 48 optimal weight: 0.0870 chunk 247 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 245 optimal weight: 0.8980 chunk 365 optimal weight: 0.8980 chunk 242 optimal weight: 0.9980 chunk 432 optimal weight: 3.9990 chunk 270 optimal weight: 10.0000 chunk 263 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 502 HIS G 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 37140 Z= 0.160 Angle : 0.578 15.513 50201 Z= 0.282 Chirality : 0.042 0.185 5728 Planarity : 0.004 0.058 6278 Dihedral : 6.639 89.810 5084 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.50 % Allowed : 17.68 % Favored : 79.82 % 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: -0.57 (0.13), residues: 4488 helix: 1.14 (0.13), residues: 1697 sheet: -1.26 (0.26), residues: 460 loop : -1.38 (0.13), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 188 HIS 0.005 0.000 HIS B 271 PHE 0.025 0.001 PHE E 341 TYR 0.026 0.001 TYR E 654 ARG 0.012 0.000 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 366 time to evaluate : 4.346 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: A 157 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8073 (ptt180) REVERT: A 263 TYR cc_start: 0.8451 (m-80) cc_final: 0.7948 (m-80) REVERT: A 335 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7531 (p0) REVERT: A 680 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7772 (p0) REVERT: B 245 LYS cc_start: 0.6836 (mmpt) cc_final: 0.6567 (mmtt) REVERT: B 327 MET cc_start: 0.5419 (tpt) cc_final: 0.5188 (tpt) REVERT: B 409 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8575 (mtmt) REVERT: C 31 LYS cc_start: 0.8593 (ptmm) cc_final: 0.8266 (pttp) REVERT: C 37 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9047 (tp) REVERT: C 648 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7132 (mpp) REVERT: C 770 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8844 (pp) REVERT: E 30 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7873 (mtt90) REVERT: E 177 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8856 (tmmm) REVERT: E 690 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8325 (pp) REVERT: G 158 MET cc_start: 0.8400 (tpp) cc_final: 0.7905 (ttt) REVERT: G 183 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8183 (t) REVERT: G 529 MET cc_start: 0.8145 (mmm) cc_final: 0.6044 (tpp) REVERT: G 556 MET cc_start: 0.8547 (tpp) cc_final: 0.8306 (tpp) REVERT: G 687 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8578 (tt) REVERT: I 27 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8169 (mmmt) REVERT: I 31 LYS cc_start: 0.8382 (ptpp) cc_final: 0.8140 (ptpp) REVERT: I 132 LYS cc_start: 0.8782 (mptt) cc_final: 0.8551 (mmmt) REVERT: I 188 TRP cc_start: 0.4945 (m-90) cc_final: 0.4051 (m-90) REVERT: I 388 LYS cc_start: 0.3414 (OUTLIER) cc_final: 0.2275 (pptt) REVERT: I 548 VAL cc_start: 0.6713 (OUTLIER) cc_final: 0.6419 (t) REVERT: I 553 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6689 (ptp) outliers start: 102 outliers final: 71 residues processed: 442 average time/residue: 0.5185 time to fit residues: 367.8805 Evaluate side-chains 438 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 354 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 316 MET Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 363 ILE Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 484 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 670 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 267 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 130 optimal weight: 0.0570 chunk 85 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 275 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 213 optimal weight: 0.1980 chunk 40 optimal weight: 0.0170 chunk 340 optimal weight: 2.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 130 GLN I 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 37140 Z= 0.147 Angle : 0.585 15.502 50201 Z= 0.283 Chirality : 0.042 0.176 5728 Planarity : 0.004 0.060 6278 Dihedral : 6.507 88.184 5083 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.57 % Allowed : 17.95 % Favored : 79.48 % 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: -0.46 (0.13), residues: 4488 helix: 1.29 (0.13), residues: 1660 sheet: -1.13 (0.25), residues: 500 loop : -1.34 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 188 HIS 0.004 0.000 HIS B 271 PHE 0.022 0.001 PHE E 341 TYR 0.026 0.001 TYR E 654 ARG 0.011 0.000 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 376 time to evaluate : 4.447 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: A 157 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8033 (ptt180) REVERT: A 263 TYR cc_start: 0.8274 (m-80) cc_final: 0.7980 (m-80) REVERT: A 591 ASP cc_start: 0.7525 (p0) cc_final: 0.7178 (p0) REVERT: A 680 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7760 (p0) REVERT: B 245 LYS cc_start: 0.6835 (mmpt) cc_final: 0.6568 (mmtt) REVERT: B 327 MET cc_start: 0.5432 (tpt) cc_final: 0.5211 (tpt) REVERT: B 409 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8558 (mtmt) REVERT: B 457 ARG cc_start: 0.7345 (mmm-85) cc_final: 0.7087 (mmm-85) REVERT: C 31 LYS cc_start: 0.8594 (ptmm) cc_final: 0.7986 (pttp) REVERT: C 648 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7180 (mpp) REVERT: C 770 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8851 (pp) REVERT: E 30 ARG cc_start: 0.8165 (mmt90) cc_final: 0.7937 (mtt90) REVERT: E 177 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8857 (tmmm) REVERT: E 648 MET cc_start: 0.8280 (mtt) cc_final: 0.7854 (mtt) REVERT: E 690 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8256 (pp) REVERT: E 843 MET cc_start: 0.7170 (tpp) cc_final: 0.6271 (mpp) REVERT: G 39 GLU cc_start: 0.8227 (tt0) cc_final: 0.8003 (tp30) REVERT: G 158 MET cc_start: 0.8399 (tpp) cc_final: 0.7897 (ttt) REVERT: G 183 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8161 (t) REVERT: G 529 MET cc_start: 0.7997 (mmm) cc_final: 0.6016 (tpp) REVERT: G 556 MET cc_start: 0.8540 (tpp) cc_final: 0.8296 (tpp) REVERT: G 687 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8586 (tt) REVERT: I 27 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8127 (mmmt) REVERT: I 132 LYS cc_start: 0.8714 (mptt) cc_final: 0.8466 (mmmt) REVERT: I 188 TRP cc_start: 0.4880 (m-90) cc_final: 0.4002 (m-90) REVERT: I 388 LYS cc_start: 0.3394 (OUTLIER) cc_final: 0.2312 (pptt) REVERT: I 527 ARG cc_start: 0.4447 (tpm170) cc_final: 0.4104 (tpp-160) REVERT: I 548 VAL cc_start: 0.6664 (OUTLIER) cc_final: 0.6364 (t) REVERT: I 553 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7174 (ptm) outliers start: 105 outliers final: 78 residues processed: 454 average time/residue: 0.5042 time to fit residues: 369.5368 Evaluate side-chains 438 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 349 time to evaluate : 3.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 181 MET Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 484 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 707 MET Chi-restraints excluded: chain I residue 773 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 393 optimal weight: 0.6980 chunk 414 optimal weight: 3.9990 chunk 378 optimal weight: 0.9990 chunk 403 optimal weight: 0.7980 chunk 242 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 316 optimal weight: 2.9990 chunk 123 optimal weight: 0.4980 chunk 364 optimal weight: 6.9990 chunk 381 optimal weight: 1.9990 chunk 401 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN I 133 GLN I 517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37140 Z= 0.187 Angle : 0.594 14.482 50201 Z= 0.290 Chirality : 0.042 0.185 5728 Planarity : 0.004 0.072 6278 Dihedral : 6.574 88.376 5083 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 2.67 % Allowed : 18.25 % Favored : 79.08 % 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: -0.46 (0.13), residues: 4488 helix: 1.28 (0.13), residues: 1666 sheet: -1.13 (0.25), residues: 500 loop : -1.33 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 188 HIS 0.003 0.001 HIS B 271 PHE 0.021 0.001 PHE E 341 TYR 0.025 0.001 TYR E 654 ARG 0.018 0.000 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 366 time to evaluate : 4.391 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: A 136 GLU cc_start: 0.7409 (pm20) cc_final: 0.6876 (pm20) REVERT: A 157 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8108 (ptt180) REVERT: A 591 ASP cc_start: 0.7561 (p0) cc_final: 0.7218 (p0) REVERT: B 245 LYS cc_start: 0.6868 (mmpt) cc_final: 0.6609 (mmtt) REVERT: B 513 GLU cc_start: 0.5667 (pt0) cc_final: 0.5133 (tm-30) REVERT: C 37 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9053 (tp) REVERT: C 648 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7177 (mpp) REVERT: C 770 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8870 (pp) REVERT: C 843 MET cc_start: 0.7126 (mmm) cc_final: 0.6897 (mmm) REVERT: E 30 ARG cc_start: 0.8228 (mmt90) cc_final: 0.8024 (mtt90) REVERT: E 177 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8787 (tmmm) REVERT: E 648 MET cc_start: 0.8341 (mtt) cc_final: 0.7926 (mtt) REVERT: E 690 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8343 (pp) REVERT: G 158 MET cc_start: 0.8407 (tpp) cc_final: 0.8006 (ttt) REVERT: G 183 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8280 (t) REVERT: G 529 MET cc_start: 0.8061 (mmm) cc_final: 0.6114 (tpp) REVERT: G 556 MET cc_start: 0.8550 (tpp) cc_final: 0.8326 (tpp) REVERT: G 687 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8616 (tt) REVERT: I 31 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8114 (ptpp) REVERT: I 132 LYS cc_start: 0.8698 (mptt) cc_final: 0.8432 (mmmt) REVERT: I 188 TRP cc_start: 0.5015 (m-90) cc_final: 0.3612 (m-90) REVERT: I 388 LYS cc_start: 0.3896 (OUTLIER) cc_final: 0.2794 (pptt) REVERT: I 548 VAL cc_start: 0.6725 (OUTLIER) cc_final: 0.6444 (t) REVERT: I 553 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.7168 (ptp) outliers start: 109 outliers final: 88 residues processed: 449 average time/residue: 0.5093 time to fit residues: 366.2176 Evaluate side-chains 449 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 350 time to evaluate : 4.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 285 TRP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain E residue 44 GLN Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain E residue 840 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 479 LEU Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 581 VAL Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 181 MET Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 484 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 773 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 264 optimal weight: 5.9990 chunk 426 optimal weight: 9.9990 chunk 260 optimal weight: 8.9990 chunk 202 optimal weight: 0.6980 chunk 296 optimal weight: 1.9990 chunk 447 optimal weight: 0.5980 chunk 411 optimal weight: 0.9980 chunk 356 optimal weight: 0.3980 chunk 36 optimal weight: 0.4980 chunk 275 optimal weight: 0.1980 chunk 218 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN I 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 37140 Z= 0.154 Angle : 0.602 13.979 50201 Z= 0.292 Chirality : 0.042 0.186 5728 Planarity : 0.004 0.099 6278 Dihedral : 6.471 87.855 5083 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.38 % Allowed : 18.88 % Favored : 78.74 % 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: -0.45 (0.13), residues: 4488 helix: 1.30 (0.13), residues: 1661 sheet: -1.13 (0.25), residues: 500 loop : -1.33 (0.13), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 188 HIS 0.004 0.000 HIS B 271 PHE 0.020 0.001 PHE E 341 TYR 0.026 0.001 TYR E 654 ARG 0.026 0.000 ARG C 552 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8976 Ramachandran restraints generated. 4488 Oldfield, 0 Emsley, 4488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 372 time to evaluate : 4.361 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: A 157 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8106 (ptt180) REVERT: A 263 TYR cc_start: 0.8324 (m-80) cc_final: 0.8113 (m-80) REVERT: A 591 ASP cc_start: 0.7510 (p0) cc_final: 0.7178 (p0) REVERT: A 680 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7798 (p0) REVERT: A 873 MET cc_start: 0.2122 (ppp) cc_final: 0.1910 (ppp) REVERT: B 245 LYS cc_start: 0.6835 (mmpt) cc_final: 0.6572 (mmtt) REVERT: B 513 GLU cc_start: 0.5668 (pt0) cc_final: 0.5157 (tm-30) REVERT: C 648 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7148 (mpp) REVERT: C 770 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8859 (pp) REVERT: E 30 ARG cc_start: 0.8198 (mmt90) cc_final: 0.7992 (mtt90) REVERT: E 177 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8763 (tmmm) REVERT: E 552 ARG cc_start: 0.7331 (mmm160) cc_final: 0.7104 (mmm160) REVERT: E 690 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8303 (pp) REVERT: E 843 MET cc_start: 0.7263 (tpp) cc_final: 0.6458 (mpp) REVERT: G 125 GLU cc_start: 0.7128 (pp20) cc_final: 0.6849 (pp20) REVERT: G 158 MET cc_start: 0.8389 (tpp) cc_final: 0.7986 (ttt) REVERT: G 183 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8190 (t) REVERT: G 529 MET cc_start: 0.8085 (mmm) cc_final: 0.6181 (tpp) REVERT: G 556 MET cc_start: 0.8544 (tpp) cc_final: 0.8312 (tpp) REVERT: G 687 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8580 (tt) REVERT: I 31 LYS cc_start: 0.8509 (ptpp) cc_final: 0.8029 (ptpp) REVERT: I 188 TRP cc_start: 0.4917 (m-90) cc_final: 0.4024 (m-90) REVERT: I 388 LYS cc_start: 0.3601 (OUTLIER) cc_final: 0.2536 (pptt) REVERT: I 548 VAL cc_start: 0.6646 (OUTLIER) cc_final: 0.6375 (t) REVERT: I 553 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7081 (ptp) outliers start: 97 outliers final: 78 residues processed: 445 average time/residue: 0.5068 time to fit residues: 362.3431 Evaluate side-chains 443 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 354 time to evaluate : 4.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 555 HIS Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain B residue 216 TYR Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 441 ASP Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 553 MET Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 678 ASP Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LEU Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain E residue 177 LYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 413 MET Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 577 LYS Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 597 ASN Chi-restraints excluded: chain E residue 609 THR Chi-restraints excluded: chain E residue 690 LEU Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 130 GLN Chi-restraints excluded: chain G residue 183 THR Chi-restraints excluded: chain G residue 201 PHE Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 270 GLU Chi-restraints excluded: chain G residue 386 HIS Chi-restraints excluded: chain G residue 432 LEU Chi-restraints excluded: chain G residue 466 ILE Chi-restraints excluded: chain G residue 555 HIS Chi-restraints excluded: chain G residue 581 VAL Chi-restraints excluded: chain G residue 649 CYS Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 770 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 181 MET Chi-restraints excluded: chain I residue 182 LEU Chi-restraints excluded: chain I residue 230 SER Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain I residue 388 LYS Chi-restraints excluded: chain I residue 418 LEU Chi-restraints excluded: chain I residue 484 MET Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 553 MET Chi-restraints excluded: chain I residue 571 LEU Chi-restraints excluded: chain I residue 632 THR Chi-restraints excluded: chain I residue 670 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 282 optimal weight: 3.9990 chunk 379 optimal weight: 0.4980 chunk 109 optimal weight: 8.9990 chunk 328 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 356 optimal weight: 0.0770 chunk 149 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 GLN I 133 GLN I 517 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.096477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.072343 restraints weight = 119001.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074190 restraints weight = 63166.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075374 restraints weight = 42719.998| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 37140 Z= 0.240 Angle : 0.631 12.710 50201 Z= 0.310 Chirality : 0.043 0.197 5728 Planarity : 0.004 0.095 6278 Dihedral : 6.730 89.009 5083 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 2.47 % Allowed : 19.01 % Favored : 78.52 % 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: -0.50 (0.13), residues: 4488 helix: 1.24 (0.13), residues: 1666 sheet: -1.15 (0.25), residues: 500 loop : -1.34 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 285 HIS 0.004 0.001 HIS A 555 PHE 0.021 0.001 PHE E 341 TYR 0.026 0.001 TYR E 654 ARG 0.022 0.001 ARG C 552 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7553.56 seconds wall clock time: 138 minutes 38.90 seconds (8318.90 seconds total)