Starting phenix.real_space_refine on Wed Nov 22 02:53:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xx2_33498/11_2023/7xx2_33498_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xx2_33498/11_2023/7xx2_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_33498/11_2023/7xx2_33498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xx2_33498/11_2023/7xx2_33498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xx2_33498/11_2023/7xx2_33498_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xx2_33498/11_2023/7xx2_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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 19.38, per 1000 atoms: 0.53 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: 14.69 Conformation dependent library (CDL) restraints added in 6.5 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: 8.64 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: 12.80 Time building geometry restraints manager: 15.72 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 - 17.84: 20275 17.84 - 35.69: 1955 35.69 - 53.53: 299 53.53 - 71.37: 52 71.37 - 89.22: 18 Dihedral angle restraints: 22599 sinusoidal: 9364 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 22596 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: 2.210 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: 0.040 Extract box with map and model: 11.660 Check model and map are aligned: 0.630 Set scattering table: 0.380 Process input model: 95.600 Find NCS groups from input model: 2.530 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.270 ------------------------------------------------------------------------------- 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 : 13.959 89.218 14017 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 *********************** 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 : 4.329 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 outliers start: 52 outliers final: 28 residues processed: 513 average time/residue: 0.5299 time to fit residues: 427.7022 Evaluate side-chains 351 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 323 time to evaluate : 4.539 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.4176 time to fit residues: 26.2043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 261 optimal weight: 0.9980 chunk 407 optimal weight: 0.0070 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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: 0.8096 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37140 Z= 0.178 Angle : 0.633 11.767 50201 Z= 0.313 Chirality : 0.044 0.162 5728 Planarity : 0.004 0.055 6278 Dihedral : 5.436 88.757 4916 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.24 % Favored : 91.73 % Rotamer: Outliers : 1.30 % Allowed : 9.18 % Favored : 89.52 % 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: -1.06 (0.13), residues: 4488 helix: 0.56 (0.13), residues: 1704 sheet: -1.30 (0.25), residues: 450 loop : -1.56 (0.13), residues: 2334 *********************** 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 462 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 409 time to evaluate : 4.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 27 residues processed: 441 average time/residue: 0.5352 time to fit residues: 372.5652 Evaluate side-chains 366 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 339 time to evaluate : 4.320 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3278 time to fit residues: 22.5442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 226 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 339 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 408 optimal weight: 2.9990 chunk 441 optimal weight: 10.0000 chunk 363 optimal weight: 0.3980 chunk 405 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 327 optimal weight: 0.0980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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: 0.8094 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 37140 Z= 0.157 Angle : 0.582 11.844 50201 Z= 0.287 Chirality : 0.043 0.146 5728 Planarity : 0.004 0.055 6278 Dihedral : 5.166 89.016 4916 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.81 % Allowed : 12.66 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 4488 helix: 0.76 (0.13), residues: 1705 sheet: -1.21 (0.25), residues: 450 loop : -1.54 (0.13), residues: 2333 *********************** 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 475 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 401 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 21 residues processed: 456 average time/residue: 0.5412 time to fit residues: 393.6686 Evaluate side-chains 365 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 344 time to evaluate : 4.256 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3634 time to fit residues: 21.0185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 449 random chunks: chunk 403 optimal weight: 0.9980 chunk 307 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 274 optimal weight: 0.9980 chunk 409 optimal weight: 0.9980 chunk 434 optimal weight: 10.0000 chunk 214 optimal weight: 0.8980 chunk 388 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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: 0.8111 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37140 Z= 0.185 Angle : 0.593 16.243 50201 Z= 0.291 Chirality : 0.043 0.188 5728 Planarity : 0.004 0.055 6278 Dihedral : 5.077 88.247 4916 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.30 % Allowed : 15.38 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4488 helix: 0.95 (0.13), residues: 1675 sheet: -1.16 (0.25), residues: 450 loop : -1.40 (0.13), residues: 2363 *********************** 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 427 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 374 time to evaluate : 4.264 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 outliers start: 53 outliers final: 26 residues processed: 409 average time/residue: 0.5480 time to fit residues: 355.1047 Evaluate side-chains 373 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 347 time to evaluate : 4.399 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3446 time to fit residues: 22.3500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6245 > 50: distance: 35 - 56: 7.042 distance: 43 - 64: 7.754 distance: 48 - 72: 7.138 distance: 52 - 56: 7.149 distance: 53 - 80: 29.891 distance: 56 - 57: 6.855 distance: 57 - 58: 7.296 distance: 57 - 60: 6.147 distance: 58 - 59: 14.990 distance: 58 - 64: 7.337 distance: 59 - 92: 12.583 distance: 60 - 61: 7.185 distance: 61 - 62: 14.542 distance: 61 - 63: 17.714 distance: 64 - 65: 4.160 distance: 65 - 66: 10.354 distance: 65 - 68: 9.654 distance: 66 - 72: 14.875 distance: 67 - 96: 19.595 distance: 68 - 69: 7.573 distance: 68 - 70: 6.841 distance: 69 - 71: 12.387 distance: 72 - 73: 17.578 distance: 73 - 74: 23.941 distance: 73 - 76: 43.704 distance: 74 - 75: 9.932 distance: 74 - 80: 21.564 distance: 76 - 77: 10.027 distance: 77 - 78: 15.616 distance: 77 - 79: 11.154 distance: 80 - 81: 10.439 distance: 81 - 82: 12.401 distance: 81 - 84: 38.254 distance: 82 - 83: 4.258 distance: 82 - 92: 9.840 distance: 84 - 85: 12.842 distance: 85 - 86: 14.447 distance: 85 - 87: 20.384 distance: 87 - 89: 3.491 distance: 88 - 90: 14.592 distance: 89 - 90: 20.919 distance: 90 - 91: 7.176 distance: 92 - 93: 6.730 distance: 93 - 94: 21.517 distance: 94 - 95: 18.742 distance: 94 - 96: 12.436 distance: 96 - 97: 6.520 distance: 97 - 98: 3.294 distance: 97 - 100: 15.940 distance: 98 - 99: 12.137 distance: 98 - 104: 7.057 distance: 100 - 101: 10.213 distance: 101 - 102: 4.845 distance: 101 - 103: 6.968 distance: 104 - 105: 3.403 distance: 105 - 108: 5.434 distance: 106 - 107: 22.312 distance: 106 - 112: 6.371 distance: 108 - 109: 10.667 distance: 109 - 110: 3.267 distance: 109 - 111: 18.952 distance: 112 - 113: 10.184 distance: 113 - 114: 5.303 distance: 113 - 116: 13.074 distance: 114 - 115: 18.864 distance: 114 - 121: 18.154 distance: 116 - 117: 13.279 distance: 117 - 118: 12.552 distance: 118 - 119: 23.356 distance: 119 - 120: 4.940 distance: 121 - 122: 7.624 distance: 122 - 123: 15.510 distance: 122 - 125: 32.778 distance: 123 - 124: 6.435 distance: 123 - 128: 5.491 distance: 125 - 126: 11.122 distance: 125 - 127: 17.045 distance: 129 - 130: 3.843 distance: 129 - 132: 7.824 distance: 130 - 131: 8.589 distance: 130 - 137: 28.990 distance: 133 - 134: 11.821 distance: 134 - 135: 13.030 distance: 135 - 136: 23.011